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Laghouaouta H, Laplana M, Ros-Freixedes R, Fraile LJ, Pena RN. Sequence variants associated with resilient responses in growing pigs. J Anim Breed Genet 2024. [PMID: 38967062 DOI: 10.1111/jbg.12886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 05/23/2024] [Accepted: 06/18/2024] [Indexed: 07/06/2024]
Abstract
The current work aimed to identify genomic regions and candidate genes associated with resilience in pigs. In previous work, we proposed the body weight deviation from the expected growth curve (ΔBW) and the increase of the positive acute-phase protein haptoglobin (ΔHP) after a vaccine challenge as resilience indicators which may be improved through selective breeding in pigs. Individuals with steady growth rate and minor activation of haptoglobin (high ΔBW and low ΔHP values) were considered resilient. In contrast, pigs with perturbed growth rate and high activation of haptoglobin (low ΔBW and high ΔHP values) were considered susceptible. Both ∆BW and ∆HP were simultaneously considered to select the most resilient (N = 40) and susceptible (N = 40) pigs. A genome-wide association study was carried out for the pigs' response classification to the challenge test using whole-genome sequence data (7,760,720 variants). Eleven associated genomic regions were identified, harbouring relevant candidate genes related to the immune response (such as pro- and anti-inflammatory responses) and growth pathways. These associated genomic regions harboured 41 potential functional mutations (frameshift, splice donor, splice acceptor, start loss and stop loss/gain) in candidate genes. Overall, this study advances our knowledge about the genetic determinism of resilience, highlighting its polygenic nature and strong relationship with immunity and growth.
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Affiliation(s)
- Houda Laghouaouta
- Department of Animal Science, University of Lleida-Agrotecnio-CERCA Center, Lleida, Spain
| | - Marina Laplana
- Department of Animal Science, University of Lleida-Agrotecnio-CERCA Center, Lleida, Spain
| | - Roger Ros-Freixedes
- Department of Animal Science, University of Lleida-Agrotecnio-CERCA Center, Lleida, Spain
| | - Lorenzo J Fraile
- Department of Animal Science, University of Lleida-Agrotecnio-CERCA Center, Lleida, Spain
| | - Ramona N Pena
- Department of Animal Science, University of Lleida-Agrotecnio-CERCA Center, Lleida, Spain
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2
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Qiao Y, Zhu S, Yang N, Zou SS, Gao B, Wu J, Liu C, Li X, Liu YJ, Chen J. The RNA helicase DHX35 functions as a co-sensor for RIG-I-mediated innate immunity. PLoS Pathog 2024; 20:e1012379. [PMID: 39037956 PMCID: PMC11262647 DOI: 10.1371/journal.ppat.1012379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 06/27/2024] [Indexed: 07/24/2024] Open
Abstract
RNA helicases are involved in the innate immune response against pathogens, including bacteria and viruses; however, their mechanism in the human airway epithelial cells is still not fully understood. Here, we demonstrated that DEAH (Asp-Glu-Ala-His) box polypeptide 35 (DHX35), a member of the DExD/H (Asp-Glu-x-Asp/His)-box helicase family, boosts antiviral innate immunity in human airway epithelial cells. DHX35 knockdown attenuated the production of interferon-β (IFN-β), IL6, and CXCL10, whereas DHX35 overexpression increased their production. Upon stimulation, DHX35 was constitutively expressed, but it translocated from the nucleus into the cytosol, where it recognized cytosolic poly(I:C) and poly(dA:dT) via its HELICc domain. Mitochondrial antiviral signaling protein (MAVS) acted as an adaptor for DHX35 and interacted with the HELICc domain of DHX35 using amino acids 360-510. Interestingly, DHX35 interacted with retinoic acid-inducible gene 1 (RIG-I), enhanced the binding affinity of RIG-I with poly(I:C) and poly(dA:dT), and formed a signalsome with MAVS to activate interferon regulatory factor 3 (IRF3), NF-κB-p65, and MAPK signaling pathways. These results indicate that DHX35 not only acted as a cytosolic nucleic acid sensor but also synergized with RIG-I to enhance antiviral immunity in human airway epithelial cells. Our results demonstrate a novel molecular mechanism for DHX35 in RIG-I-mediated innate immunity and provide a novel candidate for drug and vaccine design to control viral infections in the human airway.
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Affiliation(s)
- Yuan Qiao
- Cancer Center, The First Hospital of Jilin University, Changchun, China
- Laboratory for Tumor Immunology, The First Hospital of Jilin University, Changchun, China
| | - Shan Zhu
- Cancer Center, The First Hospital of Jilin University, Changchun, China
- Laboratory for Tumor Immunology, The First Hospital of Jilin University, Changchun, China
| | - Ning Yang
- Laboratory for Tumor Immunology, The First Hospital of Jilin University, Changchun, China
| | - Shan-Shan Zou
- Laboratory for Tumor Immunology, The First Hospital of Jilin University, Changchun, China
| | - Bao Gao
- Laboratory for Tumor Immunology, The First Hospital of Jilin University, Changchun, China
| | - Jing Wu
- Laboratory for Tumor Immunology, The First Hospital of Jilin University, Changchun, China
| | - Chunyan Liu
- Laboratory for Tumor Immunology, The First Hospital of Jilin University, Changchun, China
| | - Xiaoping Li
- Laboratory for Tumor Immunology, The First Hospital of Jilin University, Changchun, China
| | - Yong-Jun Liu
- Laboratory for Tumor Immunology, The First Hospital of Jilin University, Changchun, China
| | - Jingtao Chen
- Cancer Center, The First Hospital of Jilin University, Changchun, China
- Laboratory for Tumor Immunology, The First Hospital of Jilin University, Changchun, China
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3
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Portolés I, Ribera J, Fernandez-Galán E, Lecue E, Casals G, Melgar-Lesmes P, Fernández-Varo G, Boix L, Sanduzzi M, Aishwarya V, Reig M, Jiménez W, Morales-Ruiz M. Identification of Dhx15 as a Major Regulator of Liver Development, Regeneration, and Tumor Growth in Zebrafish and Mice. Int J Mol Sci 2024; 25:3716. [PMID: 38612527 PMCID: PMC11011938 DOI: 10.3390/ijms25073716] [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: 02/26/2024] [Revised: 03/15/2024] [Accepted: 03/25/2024] [Indexed: 04/14/2024] Open
Abstract
RNA helicase DHX15 plays a significant role in vasculature development and lung metastasis in vertebrates. In addition, several studies have demonstrated the overexpression of DHX15 in the context of hepatocellular carcinoma. Therefore, we hypothesized that this helicase may play a significant role in liver regeneration, physiology, and pathology. Dhx15 gene deficiency was generated by CRISPR/Cas9 in zebrafish and by TALEN-RNA in mice. AUM Antisense-Oligonucleotides were used to silence Dhx15 in wild-type mice. The hepatocellular carcinoma tumor induction model was generated by subcutaneous injection of Hepa 1-6 cells. Homozygous Dhx15 gene deficiency was lethal in zebrafish and mouse embryos. Dhx15 gene deficiency impaired liver organogenesis in zebrafish embryos and liver regeneration after partial hepatectomy in mice. Also, heterozygous mice presented decreased number and size of liver metastasis after Hepa 1-6 cells injection compared to wild-type mice. Dhx15 gene silencing with AUM Antisense-Oligonucleotides in wild-type mice resulted in 80% reduced expression in the liver and a significant reduction in other major organs. In addition, Dhx15 gene silencing significantly hindered primary tumor growth in the hepatocellular carcinoma experimental model. Regarding the potential use of DHX15 as a diagnostic marker for liver disease, patients with hepatocellular carcinoma showed increased levels of DHX15 in blood samples compared with subjects without hepatic affectation. In conclusion, Dhx15 is a key regulator of liver physiology and organogenesis, is increased in the blood of cirrhotic and hepatocellular carcinoma patients, and plays a key role in controlling hepatocellular carcinoma tumor growth and expansion in experimental models.
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Affiliation(s)
- Irene Portolés
- Biochemistry and Molecular Genetics Department-CDB, Hospital Clínic of Barcelona, Fundació de Recerca Clínic Barcelona-Institut d’Investigacions Biomèdiques August Pi i Sunyer (FRCB-IDIBAPS), 170 Villarroel St. Barcelona, 08036 Barcelona, Spain; (I.P.); (J.R.); (E.F.-G.); (E.L.); (G.C.); (P.M.-L.); (G.F.-V.); (W.J.)
| | - Jordi Ribera
- Biochemistry and Molecular Genetics Department-CDB, Hospital Clínic of Barcelona, Fundació de Recerca Clínic Barcelona-Institut d’Investigacions Biomèdiques August Pi i Sunyer (FRCB-IDIBAPS), 170 Villarroel St. Barcelona, 08036 Barcelona, Spain; (I.P.); (J.R.); (E.F.-G.); (E.L.); (G.C.); (P.M.-L.); (G.F.-V.); (W.J.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28222 Madrid, Spain; (L.B.); (M.S.); (M.R.)
| | - Esther Fernandez-Galán
- Biochemistry and Molecular Genetics Department-CDB, Hospital Clínic of Barcelona, Fundació de Recerca Clínic Barcelona-Institut d’Investigacions Biomèdiques August Pi i Sunyer (FRCB-IDIBAPS), 170 Villarroel St. Barcelona, 08036 Barcelona, Spain; (I.P.); (J.R.); (E.F.-G.); (E.L.); (G.C.); (P.M.-L.); (G.F.-V.); (W.J.)
| | - Elena Lecue
- Biochemistry and Molecular Genetics Department-CDB, Hospital Clínic of Barcelona, Fundació de Recerca Clínic Barcelona-Institut d’Investigacions Biomèdiques August Pi i Sunyer (FRCB-IDIBAPS), 170 Villarroel St. Barcelona, 08036 Barcelona, Spain; (I.P.); (J.R.); (E.F.-G.); (E.L.); (G.C.); (P.M.-L.); (G.F.-V.); (W.J.)
| | - Gregori Casals
- Biochemistry and Molecular Genetics Department-CDB, Hospital Clínic of Barcelona, Fundació de Recerca Clínic Barcelona-Institut d’Investigacions Biomèdiques August Pi i Sunyer (FRCB-IDIBAPS), 170 Villarroel St. Barcelona, 08036 Barcelona, Spain; (I.P.); (J.R.); (E.F.-G.); (E.L.); (G.C.); (P.M.-L.); (G.F.-V.); (W.J.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28222 Madrid, Spain; (L.B.); (M.S.); (M.R.)
- Commission for the Biochemical Evaluation of the Hepatic Disease-SEQCML, 08036 Barcelona, Spain
| | - Pedro Melgar-Lesmes
- Biochemistry and Molecular Genetics Department-CDB, Hospital Clínic of Barcelona, Fundació de Recerca Clínic Barcelona-Institut d’Investigacions Biomèdiques August Pi i Sunyer (FRCB-IDIBAPS), 170 Villarroel St. Barcelona, 08036 Barcelona, Spain; (I.P.); (J.R.); (E.F.-G.); (E.L.); (G.C.); (P.M.-L.); (G.F.-V.); (W.J.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28222 Madrid, Spain; (L.B.); (M.S.); (M.R.)
- Biomedicine Department, Faculty of Medicine and Health Sciences, University of Barcelona, 08036 Barcelona, Spain
| | - Guillermo Fernández-Varo
- Biochemistry and Molecular Genetics Department-CDB, Hospital Clínic of Barcelona, Fundació de Recerca Clínic Barcelona-Institut d’Investigacions Biomèdiques August Pi i Sunyer (FRCB-IDIBAPS), 170 Villarroel St. Barcelona, 08036 Barcelona, Spain; (I.P.); (J.R.); (E.F.-G.); (E.L.); (G.C.); (P.M.-L.); (G.F.-V.); (W.J.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28222 Madrid, Spain; (L.B.); (M.S.); (M.R.)
| | - Loreto Boix
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28222 Madrid, Spain; (L.B.); (M.S.); (M.R.)
- Barcelona Clinic Liver Cancer Group, Liver Unit, Hospital Clinic, University of Barcelona, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain
| | - Marco Sanduzzi
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28222 Madrid, Spain; (L.B.); (M.S.); (M.R.)
- Barcelona Clinic Liver Cancer Group, Liver Unit, Hospital Clinic, University of Barcelona, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain
| | - Veenu Aishwarya
- AUM LifeTech, Inc., 3675 Market Street, Suite 200, Philadelphia, PA 19104, USA;
| | - Maria Reig
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28222 Madrid, Spain; (L.B.); (M.S.); (M.R.)
- Barcelona Clinic Liver Cancer Group, Liver Unit, Hospital Clinic, University of Barcelona, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain
| | - Wladimiro Jiménez
- Biochemistry and Molecular Genetics Department-CDB, Hospital Clínic of Barcelona, Fundació de Recerca Clínic Barcelona-Institut d’Investigacions Biomèdiques August Pi i Sunyer (FRCB-IDIBAPS), 170 Villarroel St. Barcelona, 08036 Barcelona, Spain; (I.P.); (J.R.); (E.F.-G.); (E.L.); (G.C.); (P.M.-L.); (G.F.-V.); (W.J.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28222 Madrid, Spain; (L.B.); (M.S.); (M.R.)
- Biomedicine Department, Faculty of Medicine and Health Sciences, University of Barcelona, 08036 Barcelona, Spain
| | - Manuel Morales-Ruiz
- Biochemistry and Molecular Genetics Department-CDB, Hospital Clínic of Barcelona, Fundació de Recerca Clínic Barcelona-Institut d’Investigacions Biomèdiques August Pi i Sunyer (FRCB-IDIBAPS), 170 Villarroel St. Barcelona, 08036 Barcelona, Spain; (I.P.); (J.R.); (E.F.-G.); (E.L.); (G.C.); (P.M.-L.); (G.F.-V.); (W.J.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28222 Madrid, Spain; (L.B.); (M.S.); (M.R.)
- Commission for the Biochemical Evaluation of the Hepatic Disease-SEQCML, 08036 Barcelona, Spain
- Biomedicine Department, Faculty of Medicine and Health Sciences, University of Barcelona, 08036 Barcelona, Spain
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4
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Hemann EA, Knoll ML, Wilkins CR, Subra C, Green R, García-Sastre A, Thomas PG, Trautmann L, Ireton RC, Loo YM, Gale M. A Small Molecule RIG-I Agonist Serves as an Adjuvant to Induce Broad Multifaceted Influenza Virus Vaccine Immunity. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 210:1247-1256. [PMID: 36939421 PMCID: PMC10149148 DOI: 10.4049/jimmunol.2300026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 02/10/2023] [Indexed: 03/21/2023]
Abstract
Retinoic acid-inducible gene I (RIG-I) is essential for activating host cell innate immunity to regulate the immune response against many RNA viruses. We previously identified that a small molecule compound, KIN1148, led to the activation of IFN regulatory factor 3 (IRF3) and served to enhance protection against influenza A virus (IAV) A/California/04/2009 infection. We have now determined direct binding of KIN1148 to RIG-I to drive expression of IFN regulatory factor 3 and NF-κB target genes, including specific immunomodulatory cytokines and chemokines. Intriguingly, KIN1148 does not lead to ATPase activity or compete with ATP for binding but activates RIG-I to induce antiviral gene expression programs distinct from type I IFN treatment. When administered in combination with a vaccine against IAV, KIN1148 induces both neutralizing Ab and IAV-specific T cell responses compared with vaccination alone, which induces comparatively poor responses. This robust KIN1148-adjuvanted immune response protects mice from lethal A/California/04/2009 and H5N1 IAV challenge. Importantly, KIN1148 also augments human CD8+ T cell activation. Thus, we have identified a small molecule RIG-I agonist that serves as an effective adjuvant in inducing noncanonical RIG-I activation for induction of innate immune programs that enhance adaptive immune protection of antiviral vaccination.
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Affiliation(s)
- Emily A. Hemann
- Department of Immunology, Center for Innate Immunity and Immune Disease, University of Washington, Seattle, Washington, USA
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, Ohio, USA
| | - Megan L. Knoll
- Department of Immunology, Center for Innate Immunity and Immune Disease, University of Washington, Seattle, Washington, USA
| | - Courtney R. Wilkins
- Department of Immunology, Center for Innate Immunity and Immune Disease, University of Washington, Seattle, Washington, USA
| | - Caroline Subra
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, and the U.S. Military HIV Research Program, Bethesda, Maryland, USA
| | - Richard Green
- Department of Immunology, Center for Innate Immunity and Immune Disease, University of Washington, Seattle, Washington, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Department of Medicine, Division of Infectious Diseases, Department of Pathology, Molecular and Cell-Based Medicine, The Tisch Cancer Institute, Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Paul G. Thomas
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Lydie Trautmann
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, and the U.S. Military HIV Research Program, Bethesda, Maryland, USA
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, USA
| | - Renee C. Ireton
- Department of Immunology, Center for Innate Immunity and Immune Disease, University of Washington, Seattle, Washington, USA
| | - Yueh-Ming Loo
- Department of Immunology, Center for Innate Immunity and Immune Disease, University of Washington, Seattle, Washington, USA
| | - Michael Gale
- Department of Immunology, Center for Innate Immunity and Immune Disease, University of Washington, Seattle, Washington, USA
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5
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Zhang L, Zhang Y, Wang R, Liu X, Zhao J, Tsuda M, Li Y. SARS-CoV-2 infection of intestinal epithelia cells sensed by RIG-I and DHX-15 evokes innate immune response and immune cross-talk. Front Cell Infect Microbiol 2023; 12:1035711. [PMID: 36825215 PMCID: PMC9941539 DOI: 10.3389/fcimb.2022.1035711] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 12/13/2022] [Indexed: 02/10/2023] Open
Abstract
SARS-CoV-2 causes a spectrum of clinical symptoms from respiratory damage to gastrointestinal disorders. Intestinal infection of SARS-CoV-2 triggers immune response. However, the cellular mechanism that how SARS-CoV-2 initiates and induces intestinal immunity is not understood. Here, we exploited SARS-CoV-2-GFP/ΔN trVLP pseudo-virus system and demonstrated that RIG-I and DHX15 are required for sensing SARS-CoV-2 and inducing cellular immune response through MAVS signaling in intestinal epithelial cells (IECs) upon SARS-CoV-2 infection. NLRP6 also engages in the regulation of SARS-CoV-2 immunity by producing IL-18. Furthermore, primary cellular immune response provoked by SARS-CoV-2 in IECs further cascades activation of MAIT cells and produces cytotoxic cytokines including IFN-γ, granzyme B via an IL-18 dependent mechanism. These findings taken together unveil molecular basis of immune recognition in IECs in response to SARS-CoV-2, and provide insights that intestinal immune cross-talk with other immune cells triggers amplified immunity and probably contributes to immunopathogenesis of COVID-19.
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Affiliation(s)
- Lijuan Zhang
- School of Medicine, Huanghe Science and Technology College, Zhengzhou, China
| | - Yize Zhang
- Precision Medicine Center, Gene Hospital of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ruiqin Wang
- School of Life Science and Technology, Tongji University, Shanghai, China
| | - Xiaoning Liu
- School of Medicine, Huanghe Science and Technology College, Zhengzhou, China
| | - Jinmeng Zhao
- School of Life Science, Zhengzhou University, Zhengzhou, China
| | - Masato Tsuda
- School of Medicine, Niigata University, Niigata, Japan
| | - You Li
- School of Medicine, Huanghe Science and Technology College, Zhengzhou, China,School of Life Science and Technology, Tongji University, Shanghai, China,*Correspondence: You Li,
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6
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Ren X, Wang D, Zhang G, Zhou T, Wei Z, Yang Y, Zheng Y, Lei X, Tao W, Wang A, Li M, Flavell RA, Zhu S. Nucleic DHX9 cooperates with STAT1 to transcribe interferon-stimulated genes. SCIENCE ADVANCES 2023; 9:eadd5005. [PMID: 36735791 PMCID: PMC9897671 DOI: 10.1126/sciadv.add5005] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 01/05/2023] [Indexed: 06/13/2023]
Abstract
RNA helicase DHX9 has been extensively characterized as a transcriptional regulator, which is consistent with its mostly nucleic localization. It is also involved in recognizing RNA viruses in the cytoplasm. However, there is no in vivo data to support the antiviral role of DHX9; meanwhile, as a nuclear protein, if and how nucleic DHX9 promotes antiviral immunity remains largely unknown. Here, we generated myeloid-specific and hepatocyte-specific DHX9 knockout mice and confirmed that DHX9 is crucial for host resistance to RNA virus infections in vivo. By additional knockout MAVS or STAT1 in DHX9-deficient mice, we demonstrated that nucleic DHX9 plays a positive role in regulating interferon-stimulated gene (ISG) expression downstream of type I interferon. Mechanistically, upon interferon stimulation, DHX9 is directly bound to STAT1 and recruits Pol II to the ISG promoter region to participate in STAT1-mediated transcription of ISGs. Collectively, these findings uncover an important role for nucleic DHX9 in antiviral immunity.
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Affiliation(s)
- Xingxing Ren
- Department of Digestive Disease, Division of Life Sciences and Medicine, The First Affiliated Hospital of University of Science and Technology of China, University of Science and Technology of China, 230001 Hefei, China
- Institute of Immunology and the CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
- Department of Gastroenterology, Third Affiliated Hospital of Guangzhou Medical University, 510145 Guangzhou, China
| | - Decai Wang
- Department of Digestive Disease, Division of Life Sciences and Medicine, The First Affiliated Hospital of University of Science and Technology of China, University of Science and Technology of China, 230001 Hefei, China
- Institute of Immunology and the CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Guorong Zhang
- Department of Digestive Disease, Division of Life Sciences and Medicine, The First Affiliated Hospital of University of Science and Technology of China, University of Science and Technology of China, 230001 Hefei, China
- Institute of Immunology and the CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Tingyue Zhou
- Department of Digestive Disease, Division of Life Sciences and Medicine, The First Affiliated Hospital of University of Science and Technology of China, University of Science and Technology of China, 230001 Hefei, China
- Institute of Immunology and the CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Zheng Wei
- Department of Immunobiology, Yale University School of Medicine, 300 Cedar Street, New Haven, CT 06510, USA
| | - Yi Yang
- Department of Immunobiology, Yale University School of Medicine, 300 Cedar Street, New Haven, CT 06510, USA
| | - Yunjiang Zheng
- Department of Immunobiology, Yale University School of Medicine, 300 Cedar Street, New Haven, CT 06510, USA
| | - Xuqiu Lei
- Department of Immunobiology, Yale University School of Medicine, 300 Cedar Street, New Haven, CT 06510, USA
| | - Wanyin Tao
- Department of Digestive Disease, Division of Life Sciences and Medicine, The First Affiliated Hospital of University of Science and Technology of China, University of Science and Technology of China, 230001 Hefei, China
- Institute of Immunology and the CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Anmin Wang
- Department of Digestive Disease, Division of Life Sciences and Medicine, The First Affiliated Hospital of University of Science and Technology of China, University of Science and Technology of China, 230001 Hefei, China
- Institute of Immunology and the CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Mingsong Li
- Department of Gastroenterology, Third Affiliated Hospital of Guangzhou Medical University, 510145 Guangzhou, China
| | - Richard A. Flavell
- Department of Immunobiology, Yale University School of Medicine, 300 Cedar Street, New Haven, CT 06510, USA
- Howard Hughes Medical Institute, Yale University School of Medicine, 300 Cedar Street, New Haven, CT 06510, USA
| | - Shu Zhu
- Department of Digestive Disease, Division of Life Sciences and Medicine, The First Affiliated Hospital of University of Science and Technology of China, University of Science and Technology of China, 230001 Hefei, China
- Institute of Immunology and the CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
- School of Data Science, University of Science and Technology of China, Hefei 230026, China
- Institute of Health and Medicine, Hefei Comprehensive National Science Center, Hefei, China
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7
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Hu X, Wu X, Ding Z, Chen Z, Wu H. Characterization and functional analysis of chicken dsRNA binding protein hnRNPU. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2023; 138:104521. [PMID: 36044969 DOI: 10.1016/j.dci.2022.104521] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 06/15/2023]
Abstract
In mammals, heterogeneous ribonucleoprotein U (hnRNPU), also named as nuclear matrix protein-nuclear scaffold attachment factor (SAFA), was originally identified as a DNA/RNA interactor protein. It has been reported that human hnRNPU facilitates IFN-β generation after vesicular stomatitis virus (VSV) infection. Nevertheless, the role of chicken hnRNPU (chhnRNPU) in IFN-β regulation as well as in infectious bursal diseases virus (IBDV) replication is still unclear. Here, we found that chhnRNPU inhibits IFN-β production via interacting with MDA5 and MAVS, and facilitates IBDV replication via associating with genomic dsRNA of IBDV. Firstly, chicken hnRNPU (chhnRNPU) was widely expressed in different tissues of chickens and was distributed in the nucleus of DF-1 cells. Overexpression of chhnRNPU significantly suppresses IFN-β promoter activities induced by MDA5 and MAVS. Additionally, immunoprecipitated by dsRNA antibodies, which followed LC-MS analysis demonstrate that chhnRNPU is a partner of viral genomic dsRNA. chhnRNPU is translocated from nucleus to cytosol to co-localize with replication complex of IBDV after IBDV infection. Over-expression of chhnRNPU significantly promotes IBDV replication, which was determined by western blotting, qRT-PCR and TCID50 assay. Furthermore, knock down chhnRNPU by siRNA remarkably facilitates IFN-β production, and inhibits IBDV proliferation. These data collectively reveal that chhnRNPU positively regulates IBDV replication via negatively regulating IFN-β response.
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Affiliation(s)
- Xifeng Hu
- Department of Veterinary Preventive Medicine, College of Animal Science and Technology, Jiangxi Agricultural University, Zhimin Street, Qingshan Lake, Nanchang, 330045, PR China; Jiangxi Provincial Key Laboratory for Animal Science and Technology, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, 330045, PR China
| | - Xiangdong Wu
- Department of Veterinary Preventive Medicine, College of Animal Science and Technology, Jiangxi Agricultural University, Zhimin Street, Qingshan Lake, Nanchang, 330045, PR China; Jiangxi Provincial Key Laboratory for Animal Science and Technology, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, 330045, PR China
| | - Zhen Ding
- Department of Veterinary Preventive Medicine, College of Animal Science and Technology, Jiangxi Agricultural University, Zhimin Street, Qingshan Lake, Nanchang, 330045, PR China; Jiangxi Provincial Key Laboratory for Animal Science and Technology, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, 330045, PR China
| | - Zheng Chen
- Department of Veterinary Preventive Medicine, College of Animal Science and Technology, Jiangxi Agricultural University, Zhimin Street, Qingshan Lake, Nanchang, 330045, PR China; Jiangxi Provincial Key Laboratory for Animal Science and Technology, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, 330045, PR China
| | - Huansheng Wu
- Department of Veterinary Preventive Medicine, College of Animal Science and Technology, Jiangxi Agricultural University, Zhimin Street, Qingshan Lake, Nanchang, 330045, PR China; Jiangxi Provincial Key Laboratory for Animal Science and Technology, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, 330045, PR China.
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8
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Rosendo Machado S, Qu J, Koopman WJH, Miesen P. The DEAD-box RNA helicase Dhx15 controls glycolysis and arbovirus replication in Aedes aegypti mosquito cells. PLoS Pathog 2022; 18:e1010694. [PMID: 36441781 PMCID: PMC9731432 DOI: 10.1371/journal.ppat.1010694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 12/08/2022] [Accepted: 11/11/2022] [Indexed: 11/30/2022] Open
Abstract
Aedes aegypti mosquitoes are responsible for the transmission of arthropod-borne (arbo)viruses including dengue and chikungunya virus (CHIKV) but in contrast to human hosts, arbovirus-infected mosquitoes are able to efficiently control virus replication to sub-pathological levels. Yet, our knowledge of the molecular interactions of arboviruses with their mosquito hosts is incomplete. Here, we aimed to identify and characterize novel host genes that control arbovirus replication in Aedes mosquitoes. RNA binding proteins (RBPs) are well-known to regulate immune signaling pathways in all kingdoms of life. We therefore performed a knockdown screen targeting 461 genes encoding predicted RBPs in Aedes aegypti Aag2 cells and identified 15 genes with antiviral activity against Sindbis virus. Amongst these, the three DEAD-box RNA helicases AAEL004419/Dhx15, AAEL008728, and AAEL004859 also acted as antiviral factors in dengue and CHIKV infections. Here, we explored the mechanism of Dhx15 in regulating an antiviral transcriptional response in mosquitoes by silencing Dhx15 in Aag2 cells followed by deep-sequencing of poly-A enriched RNAs. Dhx15 knockdown in uninfected and CHIKV-infected cells resulted in differential expression of 856 and 372 genes, respectively. Interestingly, amongst the consistently downregulated genes, glycolytic process was the most enriched gene ontology (GO) term as the expression of all core enzymes of the glycolytic pathway was reduced, suggesting that Dhx15 regulates glycolytic function. A decrease in lactate production indicated that Dhx15 silencing indeed functionally impaired glycolysis. Modified rates of glycolytic metabolism have been implicated in controlling the replication of several classes of viruses and strikingly, infection of Aag2 cells with CHIKV by itself also resulted in the decrease of several glycolytic genes. Our data suggests that Dhx15 regulates replication of CHIKV, and possibly other arboviruses, by controlling glycolysis in mosquito cells.
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Affiliation(s)
- Samara Rosendo Machado
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jieqiong Qu
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Werner J. H. Koopman
- Department of Pediatrics, Amalia Children’s Hospital, Radboud Institute for Molecular Life Sciences, Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Pascal Miesen
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
- * E-mail:
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9
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Li J, Zhang X, Ren P, Wu Y, Wang Y, Zhou W, Wang Z, Chao P. Landscape of RNA-binding proteins in diagnostic utility, immune cell infiltration and PANoptosis features of heart failure. Front Genet 2022; 13:1004163. [PMID: 36313471 PMCID: PMC9614340 DOI: 10.3389/fgene.2022.1004163] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 09/27/2022] [Indexed: 11/13/2022] Open
Abstract
Objective: Heart failure remains a global public health problem linked to rising morbidity and mortality. RNA-binding proteins (RBPs) are crucial regulators in post-transcriptionally determining gene expression. Our study aimed to comprehensively elucidate the diagnostic utility and biological roles of RBPs in heart failure. Methods: Genomic data of human failing and nonfailing left ventricular myocardium specimens were retrieved from the GEO datasets. Heart failure-specific RBPs were screened with differential expression analyses, and RBP-based subtypes were clustered with consensus clustering approach. GSEA was implemented for comparing KEGG pathways across subtypes. RBP-based subtype-related genes were screened with WGCNA. Afterwards, characteristic genes were selected through integrating LASSO and SVM-RFE approaches. A nomogram based on characteristic genes was established and verified through calibration curve, decision curve and clinical impact curve analyses. The abundance of immune cell types was estimated with CIBERSORT approach. Results: Heart failure-specific RBPs were determined, which were remarkably linked to RNA metabolism process. Three RBP-based subtypes (namely C1, C2, C3) were established, characterized by distinct pathway activities and PANoptosis gene levels. C2 subtype presented the highest abundance of immune cells, followed by C1 and C3. Afterwards, ten characteristic genes were selected, which enabled to reliably diagnose heart failure risk. The characteristic gene-based nomogram enabled to accurately predict risk of heart failure, with the excellent clinical utility. Additionally, characteristic genes correlated to immune cell infiltration and PANoptosis genes. Conclusion: Our findings comprehensively described the roles of RBPs in heart failure. Further research is required for verifying the effectiveness of RBP-based subtypes and characteristic genes in heart failure.
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Affiliation(s)
- Jie Li
- Department of Cardiology, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, China
| | - Xueqin Zhang
- Department of Nephrology, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, China
| | - Peng Ren
- Department of Cardiology, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, China
| | - Yu Wu
- Department of Medical Administration, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, China
| | - Yaoguo Wang
- Department of Information Center, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, China
| | - Wenzheng Zhou
- Department of Orthopaedics, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, China
- *Correspondence: Wenzheng Zhou, ; Zhao Wang, ; Peng Chao,
| | - Zhao Wang
- Department of Cardiology, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, China
- *Correspondence: Wenzheng Zhou, ; Zhao Wang, ; Peng Chao,
| | - Peng Chao
- Department of Cardiology, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, China
- *Correspondence: Wenzheng Zhou, ; Zhao Wang, ; Peng Chao,
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10
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Bohnsack KE, Kanwal N, Bohnsack MT. Prp43/DHX15 exemplify RNA helicase multifunctionality in the gene expression network. Nucleic Acids Res 2022; 50:9012-9022. [PMID: 35993807 PMCID: PMC9458436 DOI: 10.1093/nar/gkac687] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 07/10/2022] [Accepted: 08/01/2022] [Indexed: 12/24/2022] Open
Abstract
Dynamic regulation of RNA folding and structure is critical for the biogenesis and function of RNAs and ribonucleoprotein (RNP) complexes. Through their nucleotide triphosphate-dependent remodelling functions, RNA helicases are key modulators of RNA/RNP structure. While some RNA helicases are dedicated to a specific target RNA, others are multifunctional and engage numerous substrate RNAs in different aspects of RNA metabolism. The discovery of such multitasking RNA helicases raises the intriguing question of how these enzymes can act on diverse RNAs but also maintain specificity for their particular targets within the RNA-dense cellular environment. Furthermore, the identification of RNA helicases that sit at the nexus between different aspects of RNA metabolism raises the possibility that they mediate cross-regulation of different cellular processes. Prominent and extensively characterized multifunctional DEAH/RHA-box RNA helicases are DHX15 and its Saccharomyces cerevisiae (yeast) homologue Prp43. Due to their central roles in key cellular processes, these enzymes have also served as prototypes for mechanistic studies elucidating the mode of action of this type of enzyme. Here, we summarize the current knowledge on the structure, regulation and cellular functions of Prp43/DHX15, and discuss the general concept and implications of RNA helicase multifunctionality.
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Affiliation(s)
- Katherine E Bohnsack
- Correspondence may also be addressed to Katherine E. Bohnsack. Tel: +49 551 3969305; Fax: +49 551 395960;
| | - Nidhi Kanwal
- Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
| | - Markus T Bohnsack
- To whom correspondence should be addressed. Tel: +49 551 395968; Fax: +49 551 395960;
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11
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Bonaventure B, Goujon C. DExH/D-box helicases at the frontline of intrinsic and innate immunity against viral infections. J Gen Virol 2022; 103. [PMID: 36006669 DOI: 10.1099/jgv.0.001766] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022] Open
Abstract
DExH/D-box helicases are essential nucleic acid and ribonucleoprotein remodelers involved in all aspects of nucleic acid metabolism including replication, gene expression and post-transcriptional modifications. In parallel to their importance in basic cellular functions, DExH/D-box helicases play multiple roles in viral life cycles, with some of them highjacked by viruses or negatively regulating innate immune activation. However, other DExH/D-box helicases have recurrently been highlighted as direct antiviral effectors or as positive regulators of innate immune activation. Innate immunity relies on the ability of Pathogen Recognition Receptors to recognize viral signatures and trigger the production of interferons (IFNs) and pro-inflammatory cytokines. Secreted IFNs interact with their receptors to establish antiviral cellular reprogramming via expression regulation of the interferon-stimulated genes (ISGs). Several DExH/D-box helicases have been reported to act as viral sensors (DDX3, DDX41, DHX9, DDX1/DDX21/DHX36 complex), and others to play roles in innate immune activation (DDX60, DDX60L, DDX23). In contrast, the DDX39A, DDX46, DDX5 and DDX24 helicases act as negative regulators and impede IFN production upon viral infection. Beyond their role in viral sensing, the ISGs DDX60 and DDX60L act as viral inhibitors. Interestingly, the constitutively expressed DEAD-box helicases DDX56, DDX17, DDX42 intrinsically restrict viral replication. Hence, DExH/D-box helicases appear to form a multilayer network of primary and secondary factors involved in both intrinsic and innate antiviral immunity. In this review, we highlight recent findings on the extent of antiviral defences played by helicases and emphasize the need to better understand their immune functions as well as their complex interplay.
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Affiliation(s)
- Boris Bonaventure
- IRIM, CNRS, Montpellier University, France.,Present address: Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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12
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Pandit R, Singh I, Ansari A, Raval J, Patel Z, Dixit R, Shah P, Upadhyay K, Chauhan N, Desai K, Shah M, Modi B, Joshi M, Joshi C. First report on genome wide association study in western Indian population reveals host genetic factors for COVID-19 severity and outcome. Genomics 2022; 114:110399. [PMID: 35680011 PMCID: PMC9169419 DOI: 10.1016/j.ygeno.2022.110399] [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: 10/12/2021] [Revised: 05/18/2022] [Accepted: 06/01/2022] [Indexed: 02/07/2023]
Abstract
Different human races across the globe responded in a different way to the SARS-CoV-2 infection leading to different disease severity. Therefore, it is anticipated that host genetic factors have a straight association with the COVID-19. We identified a total 6, 7, and 6 genomic loci for deceased-recovered, asymptomatic-recovered, and deceased-asymptomatic group comparison, respectively. Unfavourable alleles of the markers nearby the genes which are associated with lung and heart diseases such as Tumor necrosis factor superfamily (TNFSF4&18), showed noteworthy association with the disease severity and outcome for the COVID-19 patients in the western Indian population. The markers found with significant association with disease prognosis or recovery are of value in determining the individual's response to SARS-CoV-2 infection and can be used for the risk prediction in COVID-19. Besides, GWAS study in other populations from India may help to strengthen the outcome of this study.
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Affiliation(s)
- Ramesh Pandit
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology (Government of Gujarat), Gandhinagar, Gujarat 382011, India
| | - Indra Singh
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology (Government of Gujarat), Gandhinagar, Gujarat 382011, India
| | - Afzal Ansari
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology (Government of Gujarat), Gandhinagar, Gujarat 382011, India
| | - Janvi Raval
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology (Government of Gujarat), Gandhinagar, Gujarat 382011, India
| | - Zarna Patel
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology (Government of Gujarat), Gandhinagar, Gujarat 382011, India
| | - Raghav Dixit
- Commissionerate of Health Medical Services and Medical Education Gandhinagar, Gujarat 382010, India
| | - Pranay Shah
- Department of Microbiology, B.J. Medical College and Civil hospital, Institute of Medical Post-Graduate Studies and Research, Ahmedabad, Gujarat 380016, India
| | - Kamlesh Upadhyay
- Department of Medicine, B.J. Medical College and Civil hospital, Institute of Medical Post-Graduate Studies and Research, Ahmedabad, Gujarat 380016, India
| | - Naresh Chauhan
- Department of Community Medicine, Government Medical College, Surat, Gujarat 395001, India
| | - Kairavi Desai
- Department of Microbiology, Government Medical College, Bhavnagar, Gujarat 364001, India
| | - Meenakshi Shah
- Department of General Medicine, GMERS Medical College & Hospital, Gotri, Vadodara, Gujarat 390021, India
| | - Bhavesh Modi
- Department of Community Medicine, GMERS Medical College, Gandhinagar, Gujarat 382012, India
| | - Madhvi Joshi
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology (Government of Gujarat), Gandhinagar, Gujarat 382011, India.
| | - Chaitanya Joshi
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology (Government of Gujarat), Gandhinagar, Gujarat 382011, India.
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13
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The RNA helicase DHX15 is a critical regulator of natural killer-cell homeostasis and functions. Cell Mol Immunol 2022; 19:687-701. [PMID: 35322175 DOI: 10.1038/s41423-022-00852-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 02/28/2022] [Indexed: 11/08/2022] Open
Abstract
The RNA helicase DHX15 is widely expressed in immune cells and traditionally thought to be an RNA splicing factor or a viral RNA sensor. However, the role of DHX15 in NK-cell activities has not been studied thus far. Here, we generated Dhx15-floxed mice and found that conditional deletion of Dhx15 in NK cells (Ncr1CreDhx15fl/fl mice) resulted in a marked reduction in NK cells in the periphery and that the remaining Dhx15-deleted NK cells failed to acquire a mature phenotype. As a result, Dhx15-deleted NK cells exhibited profound defects in their cytolytic functions. We also found that deletion of Dhx15 in NK cells abrogated their responsiveness to IL-15, which was associated with inhibition of IL-2/IL-15Rβ (CD122) expression and IL-15R signaling. The defects in Dhx15-deleted NK cells were rescued by ectopic expression of a constitutively active form of STAT5. Mechanistically, DHX15 did not affect CD122 mRNA splicing and stability in NK cells but instead facilitated the surface expression of CD122, likely through interaction with its 3'UTR, which was dependent on the ATPase domain of DHX15 rather than its splicing domain. Collectively, our data identify a key role for DHX15 in regulating NK-cell activities and provide novel mechanistic insights into how DHX15 regulates the IL-15 signaling pathway in NK cells.
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14
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Mechanisms involved in controlling RNA virus-induced intestinal inflammation. Cell Mol Life Sci 2022; 79:313. [PMID: 35604464 PMCID: PMC9125963 DOI: 10.1007/s00018-022-04332-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/10/2022] [Accepted: 04/27/2022] [Indexed: 12/24/2022]
Abstract
Gastroenteritis is inflammation of the lining of stomach and intestines and causes significant morbidity and mortality worldwide. Many viruses, especially RNA viruses are the most common cause of enteritis. Innate immunity is the first line of host defense against enteric RNA viruses and virus-induced intestinal inflammation. The first layer of defense against enteric RNA viruses in the intestinal tract is intestinal epithelial cells (IECs), dendritic cells and macrophages under the intestinal epithelium. These innate immune cells express pathogen-recognition receptors (PRRs) for recognizing enteric RNA viruses through sensing viral pathogen-associated molecular patterns (PAMPs). As a result of this recognition type I interferon (IFN), type III IFN and inflammasome activation occurs, which function cooperatively to clear infection and reduce viral-induced intestinal inflammation. In this review, we summarize recent findings about mechanisms involved in enteric RNA virus-induced intestinal inflammation. We will provide an overview of the enteric RNA viruses, their RNA sensing mechanisms by host PRRs, and signaling pathways triggered by host PRRs, which shape the intestinal immune response to maintain intestinal homeostasis.
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15
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Chan CP, Jin DY. Cytoplasmic RNA sensors and their interplay with RNA-binding partners in innate antiviral response: theme and variations. RNA (NEW YORK, N.Y.) 2022; 28:449-477. [PMID: 35031583 PMCID: PMC8925969 DOI: 10.1261/rna.079016.121] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Sensing of pathogen-associated molecular patterns including viral RNA by innate immunity represents the first line of defense against viral infection. In addition to RIG-I-like receptors and NOD-like receptors, several other RNA sensors are known to mediate innate antiviral response in the cytoplasm. Double-stranded RNA-binding protein PACT interacts with prototypic RNA sensor RIG-I to facilitate its recognition of viral RNA and induction of host interferon response, but variations of this theme are seen when the functions of RNA sensors are modulated by other RNA-binding proteins to impinge on antiviral defense, proinflammatory cytokine production and cell death programs. Their discrete and coordinated actions are crucial to protect the host from infection. In this review, we will focus on cytoplasmic RNA sensors with an emphasis on their interplay with RNA-binding partners. Classical sensors such as RIG-I will be briefly reviewed. More attention will be brought to new insights on how RNA-binding partners of RNA sensors modulate innate RNA sensing and how viruses perturb the functions of RNA-binding partners.
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Affiliation(s)
- Chi-Ping Chan
- School of Biomedical Sciences and State Key Laboratory of Liver Research, Faculty of Medicine Building, Pokfulam, Hong Kong
| | - Dong-Yan Jin
- School of Biomedical Sciences and State Key Laboratory of Liver Research, Faculty of Medicine Building, Pokfulam, Hong Kong
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16
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Hage A, Bharaj P, van Tol S, Giraldo MI, Gonzalez-Orozco M, Valerdi KM, Warren AN, Aguilera-Aguirre L, Xie X, Widen SG, Moulton HM, Lee B, Johnson JR, Krogan NJ, García-Sastre A, Shi PY, Freiberg AN, Rajsbaum R. The RNA helicase DHX16 recognizes specific viral RNA to trigger RIG-I-dependent innate antiviral immunity. Cell Rep 2022; 38:110434. [PMID: 35263596 PMCID: PMC8903195 DOI: 10.1016/j.celrep.2022.110434] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 11/02/2021] [Accepted: 02/02/2022] [Indexed: 12/13/2022] Open
Abstract
Type I interferons (IFN-I) are essential to establish antiviral innate immunity. Unanchored (or free) polyubiquitin (poly-Ub) has been shown to regulate IFN-I responses. However, few unanchored poly-Ub interactors are known. To identify factors regulated by unanchored poly-Ub in a physiological setting, we developed an approach to isolate unanchored poly-Ub from lung tissue. We identified the RNA helicase DHX16 as a potential pattern recognition receptor (PRR). Silencing of DHX16 in cells and in vivo diminished IFN-I responses against influenza virus. These effects extended to members of other virus families, including Zika and SARS-CoV-2. DHX16-dependent IFN-I production requires RIG-I and unanchored K48-poly-Ub synthesized by the E3-Ub ligase TRIM6. DHX16 recognizes a signal in influenza RNA segments that undergo splicing and requires its RNA helicase motif for direct, high-affinity interactions with specific viral RNAs. Our study establishes DHX16 as a PRR that partners with RIG-I for optimal activation of antiviral immunity requiring unanchored poly-Ub.
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Affiliation(s)
- Adam Hage
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Preeti Bharaj
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Sarah van Tol
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Maria I Giraldo
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Maria Gonzalez-Orozco
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Karl M Valerdi
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Abbey N Warren
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Leopoldo Aguilera-Aguirre
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Xuping Xie
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Steven G Widen
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Hong M Moulton
- Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR 97331, USA
| | - Benhur Lee
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jeffrey R Johnson
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Nevan J Krogan
- Department of Cellular and Molecular Pharmacology, University of California at San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), University of California at San Francisco, San Francisco, CA 94158, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA; Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX 77555, USA; Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA; Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Alexander N Freiberg
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA; Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX 77555, USA; Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Ricardo Rajsbaum
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA; Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX 77555, USA.
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17
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Chen Y, Chen X, Pan L, Huang Y, Cai Y, Li J, Li Y, Wang S. RNA helicase DHX15 decreases cell apoptosis by NF-κB signaling pathway in Burkitt lymphoma. Cancer Cell Int 2022; 22:92. [PMID: 35193582 PMCID: PMC8862312 DOI: 10.1186/s12935-021-02426-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 12/23/2021] [Indexed: 11/30/2022] Open
Abstract
Background DHX15 is one of the RNA helicase family members involving in several biological processes. Studies have reported that overexpression of DHX15 is related to cancer progression. However, the role of DHX15 in Burkitt lymphoma (BL) and latent Epstein-Barr virus (EBV) infection remains to be elucidated. Methods Expression of DHX15 was measured in BL patient by immunohistochemical staining. In vitro study, a CCK-8 assay was used to analyze cell proliferation and flow cytometry was performed to assess cell cycle, apoptosis and mitochondria membrane potential. Members of NF-κB signaling pathway and apoptotic-related proteins expression were measured by western-blot. EBV latent infection products and RNA polymerase III transcripts expression were determined by quantitative real-time PCR and western-blot. In vivo study, HE, IHC, TUNEL and ISH assays were used to analyze the effect of DHX15 on subcutaneous tumor nodes formation. Results DHX15 was overexpressed in Burkitt lymphoma patients and tends to be associated with poor progression-free survival and poor overall survival. Knockdown of DHX15 significantly inhibited BL tumor growth, reduced cell proliferation, induced cell cycle arrest and increased cell apoptosis. Further analysis showed that canonical NF-κB signaling and its downstream targets, mitochondria and Caspase were involved in the increased cell apoptosis after DHX15 gene knockdown. Furthermore, knockdown of DHX15 reduced EBV latent infection products expression and inhibited RNA polymerase III activity. Conclusion DHX15 may be an oncogene in the development of BL and a potential therapeutic target for the treatment of BL and latent EBV infection. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-021-02426-5.
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Affiliation(s)
- Yuan Chen
- Union Clinical Medical College, Fujian Medical University, Fuzhou, China
| | - Xianglei Chen
- Union Clinical Medical College, Fujian Medical University, Fuzhou, China
| | - Lili Pan
- Department of Hematology, Fujian Institute of Hematology, Fujian Medical University Union Hospital, Xinquan Road, No.29, Fuzhou, Fujian, China
| | - Yuanmao Huang
- Zhangzhou Affiliated Hospital of Fujian Medical University, Zhangzhou, P.R. China
| | - Yuanhua Cai
- Union Clinical Medical College, Fujian Medical University, Fuzhou, China
| | - Jinggang Li
- Department of Hematology, Fujian Institute of Hematology, Fujian Medical University Union Hospital, Xinquan Road, No.29, Fuzhou, Fujian, China
| | - Yang Li
- Department of Hematology, Fujian Institute of Hematology, Fujian Medical University Union Hospital, Xinquan Road, No.29, Fuzhou, Fujian, China
| | - Shaoyuan Wang
- Department of Hematology, Fujian Institute of Hematology, Fujian Medical University Union Hospital, Xinquan Road, No.29, Fuzhou, Fujian, China.
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Pan Y, Cai W, Cheng A, Wang M, Yin Z, Jia R. Flaviviruses: Innate Immunity, Inflammasome Activation, Inflammatory Cell Death, and Cytokines. Front Immunol 2022; 13:829433. [PMID: 35154151 PMCID: PMC8835115 DOI: 10.3389/fimmu.2022.829433] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 01/10/2022] [Indexed: 12/12/2022] Open
Abstract
The innate immune system is the host’s first line of defense against the invasion of pathogens including flavivirus. The programmed cell death controlled by genes plays an irreplaceable role in resisting pathogen invasion and preventing pathogen infection. However, the inflammatory cell death, which can trigger the overflow of a large number of pro-inflammatory cytokines and cell contents, will initiate a severe inflammatory response. In this review, we summarized the current understanding of the innate immune response, inflammatory cell death pathway and cytokine secretion regulation during Dengue virus, West Nile virus, Zika virus, Japanese encephalitis virus and other flavivirus infections. We also discussed the impact of these flavivirus and viral proteins on these biological processes. This not only provides a scientific basis for elucidating the pathogenesis of flavivirus, but also lays the foundation for the development of effective antiviral therapies.
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Affiliation(s)
- Yuhong Pan
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Wenjun Cai
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Anchun Cheng
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- *Correspondence: Renyong Jia, ; Anchun Cheng,
| | - Mingshu Wang
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Zhongqiong Yin
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Renyong Jia
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- *Correspondence: Renyong Jia, ; Anchun Cheng,
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DEAD/H-box helicases:Anti-viral and pro-viral roles during infections. Virus Res 2021; 309:198658. [PMID: 34929216 DOI: 10.1016/j.virusres.2021.198658] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 11/26/2021] [Accepted: 12/14/2021] [Indexed: 02/08/2023]
Abstract
DEAD/H-box RNA helicases make the prominent family of helicases super family-2 which take part in almost all RNA-related processes, from initiation of transcription to RNA decay pathways. In addition to these RNA-related activities, in recent years a certain number of these helicases are reported to play important roles in anti-viral immunity through various ways. Along with RLHs, endosomal TLRs, and cytosolic DNA receptors, many RNA helicases including DDX3, DHX9, DDX6, DDX41, DHX33, DDX60, DHX36 and DDX1-DDX21-DHX36 complex act as viral nucleic acid sensors or co-sensors. These helicases mostly follow RLHs-MAVS and STING mediated signaling cascades to trigger induction of type-I interferons and pro-inflammatory cytokines. Many of them also function as downstream adaptor molecules (DDX3), segments of stress and processing bodies (DDX3 and DDX6) or negative regulators (DDX19, DDX24, DDX25, DDX39A and DDX46). On the contrary, many studies indicated that several DEAD/H-box helicases such as DDX1, DDX3, DDX6, DDX24, and DHX9 could be exploited by viruses to evade innate immune responses, suggesting that these helicases seem to have a dual function as anti-viral innate immune mediators and viral replication cofactors. In this review, we summarized the current knowledge on several representative DEAD/H-box helicases, with an emphasis on their functions in innate immunity responses, involved in their anti-viral and pro-viral roles.
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20
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Su C, Tang YD, Zheng C. DExD/H-box helicases: multifunctional regulators in antiviral innate immunity. Cell Mol Life Sci 2021; 79:2. [PMID: 34910251 PMCID: PMC8671602 DOI: 10.1007/s00018-021-04072-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/29/2021] [Accepted: 12/01/2021] [Indexed: 02/07/2023]
Abstract
DExD/H-box helicases play critical roles in multiple cellular processes, including transcription, cellular RNA metabolism, translation, and infections. Several seminal studies over the past decades have delineated the distinct functions of DExD/H-box helicases in regulating antiviral innate immune signaling pathways, including Toll-like receptors, retinoic acid-inducible gene I-like receptors, cyclic GMP-AMP synthase-the stimulator of interferon gene, and NOD-like receptors signaling pathways. Besides the prominent regulatory roles, there is increasing attention on their functions as nucleic acid sensors involved in antiviral innate immunity. Here we summarize the complex regulatory roles of DExD/H-box helicases in antiviral innate immunity. A better understanding of the underlying molecular mechanisms of DExD/H-box helicases' regulatory roles is vital for developing new therapeutics targeting DExD/H-box helicases and their mediated signaling transduction in viral infectious diseases.
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Affiliation(s)
- Chenhe Su
- Department of Immunology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
- The Wistar Institute, Philadelphia, PA, USA
| | - Yan-Dong Tang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, China
| | - Chunfu Zheng
- Department of Immunology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China.
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada.
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21
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Xing J, Zhou X, Fang M, Zhang E, Minze LJ, Zhang Z. DHX15 is required to control RNA virus-induced intestinal inflammation. Cell Rep 2021; 35:109205. [PMID: 34161762 PMCID: PMC8276442 DOI: 10.1016/j.celrep.2021.109205] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 02/10/2021] [Accepted: 05/11/2021] [Indexed: 02/07/2023] Open
Abstract
RNA helicases play critical roles in various biological processes, including serving as viral RNA sensors in innate immunity. Here, we find that RNA helicase DEAH-box helicase 15 (DHX15) is essential for type I interferon (IFN-I, IFN-β), type III IFN (IFN-λ3), and inflammasome-derived cytokine IL-18 production by intestinal epithelial cells (IECs) in response to poly I:C and RNA viruses with preference of enteric RNA viruses, but not DNA virus. Importantly, we generate IEC-specific Dhx15-knockout mice and demonstrate that DHX15 is required for controlling intestinal inflammation induced by enteric RNA virus rotavirus in suckling mice and reovirus in adult mice in vivo, which owes to impaired IFN-β, IFN-λ3, and IL-18 production in IECs from Dhx15-deficient mice. Mechanistically, DHX15 interacts with NLRP6 to trigger NLRP6 inflammasome assembly and activation for inducing IL-18 secretion in IECs. Collectively, our report reveals critical roles for DHX15 in sensing enteric RNA viruses in IECs and controlling intestinal inflammation.
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Affiliation(s)
- Junji Xing
- Immunobiology and Transplant Science Center, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Xiaojing Zhou
- Immunobiology and Transplant Science Center, Houston Methodist Research Institute, Houston, TX 77030, USA; Department of Biochemistry, Clinical Medical College, Changchun University of Chinese Medicine, Changchun 130117, China
| | - Mingli Fang
- Immunobiology and Transplant Science Center, Houston Methodist Research Institute, Houston, TX 77030, USA; Department of Molecular Biology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China
| | - Evan Zhang
- Immunobiology and Transplant Science Center, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Laurie J Minze
- Immunobiology and Transplant Science Center, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Zhiqiang Zhang
- Immunobiology and Transplant Science Center, Houston Methodist Research Institute, Houston, TX 77030, USA; Department of Surgery, Weill Cornell Medical College of Cornell University, New York, NY 10065, USA.
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22
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Xing J, Zhang A, Du Y, Fang M, Minze LJ, Liu YJ, Li XC, Zhang Z. Identification of poly(ADP-ribose) polymerase 9 (PARP9) as a noncanonical sensor for RNA virus in dendritic cells. Nat Commun 2021; 12:2681. [PMID: 33976210 PMCID: PMC8113569 DOI: 10.1038/s41467-021-23003-4] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 04/09/2021] [Indexed: 01/17/2023] Open
Abstract
Innate immune cells are critical in protective immunity against viral infections, involved in sensing foreign viral nucleic acids. Here we report that the poly(ADP-ribose) polymerase 9 (PARP9), a member of PARP family, serves as a non-canonical sensor for RNA virus to initiate and amplify type I interferon (IFN) production. We find knockdown or deletion of PARP9 in human or mouse dendritic cells and macrophages inhibits type I IFN production in response to double strand RNA stimulation or RNA virus infection. Furthermore, mice deficient for PARP9 show enhanced susceptibility to infections with RNA viruses because of the impaired type I IFN production. Mechanistically, we show that PARP9 recognizes and binds viral RNA, with resultant recruitment and activation of the phosphoinositide 3-kinase (PI3K) and AKT3 pathway, independent of mitochondrial antiviral-signaling (MAVS). PI3K/AKT3 then activates the IRF3 and IRF7 by phosphorylating IRF3 at Ser385 and IRF7 at Ser437/438 mediating type I IFN production. Together, we reveal a critical role for PARP9 as a non-canonical RNA sensor that depends on the PI3K/AKT3 pathway to produce type I IFN. These findings may have important clinical implications in controlling viral infections and viral-induced diseases by targeting PARP9.
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Affiliation(s)
- Junji Xing
- Department of Surgery and Immunobiology and Transplant Science Center, Houston Methodist, Houston, TX, USA
| | - Ao Zhang
- Department of Surgery and Immunobiology and Transplant Science Center, Houston Methodist, Houston, TX, USA
- Department of Laboratory Medicine, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yong Du
- Department of Surgery and Immunobiology and Transplant Science Center, Houston Methodist, Houston, TX, USA
| | - Mingli Fang
- Department of Surgery and Immunobiology and Transplant Science Center, Houston Methodist, Houston, TX, USA
- Department of Molecular Biology, College of Basic Medical Sciences, Jilin University, Changchun, China
| | - Laurie J Minze
- Department of Surgery and Immunobiology and Transplant Science Center, Houston Methodist, Houston, TX, USA
| | | | - Xian Chang Li
- Department of Surgery and Immunobiology and Transplant Science Center, Houston Methodist, Houston, TX, USA
- Department of Surgery, Weill Cornell Medical College, Cornell University, New York, NY, USA
| | - Zhiqiang Zhang
- Department of Surgery and Immunobiology and Transplant Science Center, Houston Methodist, Houston, TX, USA.
- Department of Surgery, Weill Cornell Medical College, Cornell University, New York, NY, USA.
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23
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Jami R, Mérour E, Lamoureux A, Bernard J, Millet JK, Biacchesi S. Deciphering the Fine-Tuning of the Retinoic Acid-Inducible Gene-I Pathway in Teleost Fish and Beyond. Front Immunol 2021; 12:679242. [PMID: 33995423 PMCID: PMC8113963 DOI: 10.3389/fimmu.2021.679242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 04/07/2021] [Indexed: 11/13/2022] Open
Abstract
Interferons are the first lines of defense against viral pathogen invasion during the early stages of infection. Their synthesis is tightly regulated to prevent excessive immune responses and possible deleterious effects on the host organism itself. The RIG-I-like receptor signaling cascade is one of the major pathways leading to the production of interferons. This pathway amplifies danger signals and mounts an appropriate innate response but also needs to be finely regulated to allow a rapid return to immune homeostasis. Recent advances have characterized different cellular factors involved in the control of the RIG-I pathway. This has been most extensively studied in mammalian species; however, some inconsistencies remain to be resolved. The IFN system is remarkably well conserved in vertebrates and teleost fish possess all functional orthologs of mammalian RIG-I-like receptors as well as most downstream signaling molecules. Orthologs of almost all mammalian regulatory components described to date exist in teleost fish, such as the widely used zebrafish, making fish attractive and powerful models to study in detail the regulation and evolution of the RIG-I pathway.
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Affiliation(s)
- Raphaël Jami
- University Paris-Saclay, INRAE, UVSQ, VIM, Jouy-en-Josas, France
| | - Emilie Mérour
- University Paris-Saclay, INRAE, UVSQ, VIM, Jouy-en-Josas, France
| | - Annie Lamoureux
- University Paris-Saclay, INRAE, UVSQ, VIM, Jouy-en-Josas, France
| | - Julie Bernard
- University Paris-Saclay, INRAE, UVSQ, VIM, Jouy-en-Josas, France
| | - Jean K Millet
- University Paris-Saclay, INRAE, UVSQ, VIM, Jouy-en-Josas, France
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24
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The RNA helicase Dhx15 mediates Wnt-induced antimicrobial protein expression in Paneth cells. Proc Natl Acad Sci U S A 2021; 118:2017432118. [PMID: 33483420 PMCID: PMC7848544 DOI: 10.1073/pnas.2017432118] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
RNA helicases play roles in various essential biological processes such as RNA splicing and editing. Recent in vitro studies show that RNA helicases are involved in immune responses toward viruses, serving as viral RNA sensors or immune signaling adaptors. However, there is still a lack of in vivo data to support the tissue- or cell-specific function of RNA helicases owing to the lethality of mice with complete knockout of RNA helicases; further, there is a lack of evidence about the antibacterial role of helicases. Here, we investigated the in vivo role of Dhx15 in intestinal antibacterial responses by generating mice that were intestinal epithelial cell (IEC)-specific deficient for Dhx15 (Dhx15 f/f Villin1-cre, Dhx15ΔIEC). These mice are susceptible to infection with enteric bacteria Citrobacter rodentium (C. rod), owing to impaired α-defensin production by Paneth cells. Moreover, mice with Paneth cell-specific depletion of Dhx15 (Dhx15 f/f Defensinα6-cre, Dhx15ΔPaneth) are more susceptible to DSS (dextran sodium sulfate)-induced colitis, which phenocopy Dhx15ΔIEC mice, due to the dysbiosis of the intestinal microbiota. In humans, reduced protein levels of Dhx15 are found in ulcerative colitis (UC) patients. Taken together, our findings identify a key regulator of Wnt-induced α-defensins in Paneth cells and offer insights into its role in the antimicrobial response as well as intestinal inflammation.
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25
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Liu G, Gack MU. Distinct and Orchestrated Functions of RNA Sensors in Innate Immunity. Immunity 2020; 53:26-42. [PMID: 32668226 PMCID: PMC7367493 DOI: 10.1016/j.immuni.2020.03.017] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 03/07/2020] [Accepted: 03/07/2020] [Indexed: 12/21/2022]
Abstract
Faithful maintenance of immune homeostasis relies on the capacity of the cellular immune surveillance machinery to recognize "nonself", such as the presence of pathogenic RNA. Several families of pattern-recognition receptors exist that detect immunostimulatory RNA and then induce cytokine-mediated antiviral and proinflammatory responses. Here, we review the distinct features of bona fide RNA sensors, Toll-like receptors and retinoic-acid inducible gene-I (RIG-I)-like receptors in particular, with a focus on their functional specificity imposed by cell-type-dependent expression, subcellular localization, and ligand preference. Furthermore, we highlight recent advances on the roles of nucleotide-binding oligomerization domain (NOD)-like receptors and DEAD-box or DEAH-box RNA helicases in an orchestrated RNA-sensing network and also discuss the relevance of RNA sensor polymorphisms in human disease.
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Affiliation(s)
- GuanQun Liu
- Department of Microbiology, The University of Chicago, Chicago, IL 60637, USA
| | - Michaela U Gack
- Department of Microbiology, The University of Chicago, Chicago, IL 60637, USA.
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26
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Detanico T, Virgen-Slane R, Steen-Fuentes S, Lin WW, Rhode-Kurnow A, Chappell E, Correa RG, DiCandido MJ, Mbow ML, Li J, Ware CF. Co-expression Networks Identify DHX15 RNA Helicase as a B Cell Regulatory Factor. Front Immunol 2019; 10:2903. [PMID: 31921164 PMCID: PMC6915936 DOI: 10.3389/fimmu.2019.02903] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 11/26/2019] [Indexed: 12/30/2022] Open
Abstract
Genome-wide co-expression analysis is often used for annotating novel gene functions from high-dimensional data. Here, we developed an R package with a Shiny visualization app that creates immuno-networks from RNAseq data using a combination of Weighted Gene Co-expression Network Analysis (WGCNA), xCell immune cell signatures, and Bayesian Network Learning. Using a large publicly available RNAseq dataset we generated a Gene Module-Immune Cell (GMIC) network that predicted causal relationships between DEAH-box RNA helicase (DHX)15 and genes associated with humoral immunity, suggesting that DHX15 may regulate B cell fate. Deletion of DHX15 in mouse B cells led to impaired lymphocyte development, reduced peripheral B cell numbers, and dysregulated expression of genes linked to antibody-mediated immune responses similar to the genes predicted by the GMIC network. Moreover, antigen immunization of mice demonstrated that optimal primary IgG1 responses required DHX15. Intrinsic expression of DHX15 was necessary for proliferation and survival of activated of B cells. Altogether, these results support the use of co-expression networks to elucidate fundamental biological processes.
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Affiliation(s)
- Thiago Detanico
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States
| | - Richard Virgen-Slane
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States
| | - Seth Steen-Fuentes
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States
| | - Wai W. Lin
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States
| | - Antje Rhode-Kurnow
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States
| | - Elizabeth Chappell
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States
| | - Ricardo G. Correa
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States
| | - Michael J. DiCandido
- Department of Immunology & Respiratory Disease Research, Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, CT, United States
| | - M. Lamine Mbow
- Department of Immunology & Respiratory Disease Research, Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, CT, United States
| | - Jun Li
- Department of Immunology & Respiratory Disease Research, Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, CT, United States
| | - Carl F. Ware
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States
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27
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Mitochondria-localised ZNFX1 functions as a dsRNA sensor to initiate antiviral responses through MAVS. Nat Cell Biol 2019; 21:1346-1356. [PMID: 31685995 DOI: 10.1038/s41556-019-0416-0] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 09/26/2019] [Indexed: 12/30/2022]
Abstract
In the past two decades, emerging studies have suggested that DExD/H box helicases belonging to helicase superfamily 2 (SF2) play essential roles in antiviral innate immunity. However, the antiviral functions of helicase SF1, which shares a conserved helicase core with SF2, are little understood. Here we demonstrate that zinc finger NFX1-type containing 1 (ZNFX1), a helicase SF1, is an interferon (IFN)-stimulated, mitochondrial-localised dsRNA sensor that specifically restricts the replication of RNA viruses. Upon virus infection, ZNFX1 immediately recognizes viral RNA through its Armadillo-type fold and P-loop domain and then interacts with mitochondrial antiviral signalling protein to initiate the type I IFN response without depending on retinoic acid-inducible gene I-like receptors (RLRs). In short, as is the case with interferon-stimulated genes (ISGs) alone, ZNFX1 can induce IFN and ISG expression at an early stage of RNA virus infection to form a positively regulated loop of the well-known RLR signalling. This provides another layer of understanding of the complexity of antiviral immunity.
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28
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Yao G, Chen K, Qin Y, Niu Y, Zhang X, Xu S, Zhang C, Feng M, Wang K. Long Non-coding RNA JHDM1D-AS1 Interacts with DHX15 Protein to Enhance Non-Small-Cell Lung Cancer Growth and Metastasis. MOLECULAR THERAPY-NUCLEIC ACIDS 2019; 18:831-840. [PMID: 31739208 PMCID: PMC6861564 DOI: 10.1016/j.omtn.2019.09.028] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 09/04/2019] [Accepted: 09/21/2019] [Indexed: 01/16/2023]
Abstract
JHDM1D antisense 1 (JHDM1D-AS1), a long non-coding RNA (lncRNA), has been shown to promote pancreatic cancer growth by inducing an angiogenic response. However, its biological and clinical significance in non-small-cell lung cancer (NSCLC) is still unclear. In this study, we examined the expression and prognostic significance of JHDM1D-AS1 in NSCLC. The effects of JHDM1D-AS1 knockdown or overexpression on NSCLC growth and metastasis were investigated. We show that JHDM1D-AS1 is upregulated in NSCLC relative to adjacent normal lung tissues. High JHDM1D-AS1 expression is significantly correlated with advanced tumor, node, and metastasis (TNM) stage and lymph node metastasis. JHDM1D-AS1 expression serves as an independent prognostic factor for overall survival of patients with NSCLC. Functionally, JHDM1D-AS1 knockdown inhibits NSCLC cell aggressiveness both in vitro and in vivo, which is rescued by ectopic expression of JHDM1D-AS1. JHDM1D-AS1 binding stabilizes DHX15 protein in NSCLC cells. DHX15 overexpression enhances NSCLC cell proliferation and invasion, whereas knockdown of DHX15 exerts opposite effects. JHDM1D-AS1-mediated aggressive phenotype is impaired when DHX15 is silenced. Ectopic expression of DHX15 restores the defects in proliferation and invasion of JHDM1D-AS1-depleted NSCLC cells. Collectively, the interaction between JHDM1D-AS1 and DHX15 accounts for NSCLC growth and metastasis. This work provides potential additional therapeutic targets for treatment of NSCLC.
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Affiliation(s)
- Guodong Yao
- Department of Pathology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Kexin Chen
- Department of Pathology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Yu Qin
- Department of Pathology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Yangyang Niu
- Department of Pathology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Xuefang Zhang
- Department of Pathology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Shidong Xu
- Department of Thoracic Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Chi Zhang
- Brandeis University, Waltham, MA, USA
| | - Meiyan Feng
- Department of Pathology, Harbin Medical University Cancer Hospital, Harbin, China.
| | - Kuan Wang
- Department of Gastrointestinal Surgery, Harbin Medical University Cancer Hospital, Harbin, China.
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29
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Poynter SJ, Herrington-Krause S, DeWitte-Orr SJ. Two DExD/H-box helicases, DDX3 and DHX9, identified in rainbow trout are able to bind dsRNA. FISH & SHELLFISH IMMUNOLOGY 2019; 93:1056-1066. [PMID: 31340170 DOI: 10.1016/j.fsi.2019.07.054] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 07/15/2019] [Accepted: 07/18/2019] [Indexed: 06/10/2023]
Abstract
In mammals, the multifunctional DExH/D-box helicases, DDX3 and DHX9, are nucleic acid sensors with a role in antiviral immunity; their role in innate immunity in fish is not yet understood. In the present study, full-length DDX3 and DHX9 coding sequences were identified in rainbow trout (Oncorhynchus mykiss). Bioinformatic analysis demonstrated both deduced proteins were similar to those of other species, with ~80% identity to other fish species and ~70-75% identity to mammals, and both protein sequences had conserved domains found amongst all species. Phylogenetic analysis revealed clustering of DDX3 and DHX9 with corresponding proteins from other fish. Cellular localization of overexpressed DDX3 and DHX9 was performed using GFP-tagged proteins, and endogenous DDX3 localization was measured using immunocytochemistry. In the rainbow trout gonadal cell line, RTG-2, DHX9 localized mostly to the nucleus, while DDX3 was found mainly in the cytoplasm. Tissue distribution from healthy juvenile rainbow trout revealed ubiquitous constitutive expression, highest levels of DDX3 expression were seen in the liver and DHX9 levels were fairly consistent among all tissues tested. Stimulation of RTG-2 cells revealed that DDX3 and DHX9 transcripts were both significantly upregulated by treatment with the dsRNA molecule, poly I:C. A pull-down assay suggested both proteins were able to bind dsRNA. In addition to their roles in RNA metabolism, the conserved common domains found between the rainbow trout proteins and other species having defined antiviral roles, combined with the ability for the proteins to bind to dsRNA, suggest these proteins may play an important role in fish innate antiviral immunity. Future studies on both DDX3 and DHX9 function will contribute to a better understanding of teleost immunity.
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Affiliation(s)
- Sarah J Poynter
- Department of Biology, University of Waterloo, 200 University Ave W, Waterloo, ON, N2L 3G1, Canada
| | - Shanee Herrington-Krause
- Department of Biology, Wilfrid Laurier University, 75 University Ave W, Waterloo, ON, N2L 3C5, Canada
| | - Stephanie J DeWitte-Orr
- Department of Biology, Wilfrid Laurier University, 75 University Ave W, Waterloo, ON, N2L 3C5, Canada; Department of Health Sciences, Wilfrid Laurier University, 75 University Ave W, Waterloo, ON, N2L 3C5, Canada.
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30
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Ruan J, Cao Y, Ling T, Li P, Wu S, Peng D, Wang Y, Jia X, Chen S, Xu A, Yuan S. DDX23, an Evolutionary Conserved dsRNA Sensor, Participates in Innate Antiviral Responses by Pairing With TRIF or MAVS. Front Immunol 2019; 10:2202. [PMID: 31620127 PMCID: PMC6759578 DOI: 10.3389/fimmu.2019.02202] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 08/30/2019] [Indexed: 12/24/2022] Open
Abstract
DExD/H-box helicases play essential roles in RNA metabolism, and emerging data suggests that they have additional functions in antiviral immunity across species. However, little is known about this evolutionarily conserved family in antiviral responses in lower species. Here, through isolation of poly(I:C)-binding proteins in amphioxus, an extant basal chordate, we found that DExD/H-box helicases DHX9, DHX15, and DDX23 are responsible for cytoplasmic dsRNA detection in amphioxus. Since the antiviral roles of DDX23 have not been characterized in mammals, we performed further poly(I:C) pull-down assays and found that human DDX23 binds to LMW poly(I:C) through its N-terminal region, suggesting that DDX23 is an evolutionarily conserved dsRNA sensor. Knockdown of human DDX23 enhanced the replication of VSV and reduced the activation of the NF-κB and IRF3. Moreover, when stimulated with poly(I:C) or VSV, human DDX23 translocated from the nucleus to the cytoplasm and formed complexes with TRIF or MAVS to initiate downstream signaling. Collectively, this comparative immunological study not only defined DDX23 as an emerging nuclear pattern recognition receptor (PRR) for the innate sensing of an RNA virus, but also extended the essential role of the DExD/H helicase family in viral RNA sensing from mammals to basal chordates.
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Affiliation(s)
- Jie Ruan
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, College of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yange Cao
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, College of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Tao Ling
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, College of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Peiyi Li
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, College of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Shengpeng Wu
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, College of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Dezhi Peng
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, College of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yao Wang
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, College of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xin Jia
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, College of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Shangwu Chen
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, College of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Anlong Xu
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, College of Life Sciences, Sun Yat-sen University, Guangzhou, China.,School of Life Sciences, Beijing University of Chinese Medicine, Beijing, China
| | - Shaochun Yuan
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, College of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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Brisse M, Ly H. Comparative Structure and Function Analysis of the RIG-I-Like Receptors: RIG-I and MDA5. Front Immunol 2019; 10:1586. [PMID: 31379819 PMCID: PMC6652118 DOI: 10.3389/fimmu.2019.01586] [Citation(s) in RCA: 218] [Impact Index Per Article: 43.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 06/25/2019] [Indexed: 12/12/2022] Open
Abstract
RIG-I (Retinoic acid-inducible gene I) and MDA5 (Melanoma Differentiation-Associated protein 5), collectively known as the RIG-I-like receptors (RLRs), are key protein sensors of the pathogen-associated molecular patterns (PAMPs) in the form of viral double-stranded RNA (dsRNA) motifs to induce expression of type 1 interferons (IFN1) (IFNα and IFNβ) and other pro-inflammatory cytokines during the early stage of viral infection. While RIG-I and MDA5 share many genetic, structural and functional similarities, there is increasing evidence that they can have significantly different strategies to recognize different pathogens, PAMPs, and in different host species. This review article discusses the similarities and differences between RIG-I and MDA5 from multiple perspectives, including their structures, evolution and functional relationships with other cellular proteins, their differential mechanisms of distinguishing between host and viral dsRNAs and interactions with host and viral protein factors, and their immunogenic signaling. A comprehensive comparative analysis can help inform future studies of RIG-I and MDA5 in order to fully understand their functions in order to optimize potential therapeutic approaches targeting them.
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Affiliation(s)
- Morgan Brisse
- Biochemistry, Molecular Biology, and Biophysics Graduate Program, University of Minnesota, Twin Cities, St. Paul, MN, United States
- Department of Veterinary & Biomedical Sciences, University of Minnesota, Twin Cities, St. Paul, MN, United States
| | - Hinh Ly
- Department of Veterinary & Biomedical Sciences, University of Minnesota, Twin Cities, St. Paul, MN, United States
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32
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Pattabhi S, Knoll ML, Gale M, Loo YM. DHX15 Is a Coreceptor for RLR Signaling That Promotes Antiviral Defense Against RNA Virus Infection. J Interferon Cytokine Res 2019; 39:331-346. [PMID: 31090472 PMCID: PMC6590726 DOI: 10.1089/jir.2018.0163] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 03/01/2019] [Indexed: 12/23/2022] Open
Abstract
RNA helicases play an important role in the response to microbial infection. Retinoic acid inducible gene-I (RIG-I) and members of the RIG-I-like receptor (RLR) family of helicases function as cytoplasmic pattern recognition receptors (PRRs) whose actions are essential for recognition of RNA viruses. RIG-I association with pathogen-associated molecular patterns (PAMPs) within viral RNA leads to its activation and signaling via the mitochondrial antiviral signaling (MAVS) adapter protein. This interaction mediates downstream signaling events that drive the innate immune response to virus infection. Here we identify the DEAH-box RNA helicase DHX15 as a RLR binding partner and signaling cofactor. In human cells, DHX15 is required for virus-induced RLR signaling of innate immune gene expression. Knockdown of DHX15 increased susceptibility to infection by RNA viruses of diverse genera, including Paramyxoviridae, Rhabdoviridae, and Picornaviridae. DHX15 associates with RIG-I caspase activation and recruitment domains (CARDs) through its amino terminus, in which the complex is recruited to MAVS on virus infection. Importantly, although DHX15 cannot substitute for RIG-I in innate immune signaling, DHX15 selectively binds PAMP RNA to promote RIG-I ATP hydrolysis and signaling activation in response to viral RNA. Our results define DHX15 as a coreceptor required for RLR innate immune responses to control RNA virus infection.
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Affiliation(s)
- Sowmya Pattabhi
- Department of Global Health, University of Washington, Seattle, Washington
- Department of Immunology, Center for Innate Immunity and Immune Disease, University of Washington, Seattle, Washington
| | - Megan L. Knoll
- Department of Immunology, Center for Innate Immunity and Immune Disease, University of Washington, Seattle, Washington
- Department of Immunology, University of Washington, Seattle, Washington
| | - Michael Gale
- Department of Global Health, University of Washington, Seattle, Washington
- Department of Immunology, Center for Innate Immunity and Immune Disease, University of Washington, Seattle, Washington
- Department of Immunology, University of Washington, Seattle, Washington
| | - Yueh-Ming Loo
- Department of Immunology, Center for Innate Immunity and Immune Disease, University of Washington, Seattle, Washington
- Department of Immunology, University of Washington, Seattle, Washington
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33
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Bosisio D, Gianello V, Salvi V, Sozzani S. Extracellular miRNAs as activators of innate immune receptors. Cancer Lett 2019; 452:59-65. [PMID: 30910591 DOI: 10.1016/j.canlet.2019.03.021] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 03/04/2019] [Accepted: 03/08/2019] [Indexed: 12/15/2022]
Abstract
Since the discovery of the existence of microRNAs (miRNAs) in body fluids, the fascinating hypothesis that extracellular miRNAs may play a role in cell-to-cell signalling started to make its own way. In this review, we summarize the current knowledge that supports the role of miRNAs in the regulation of the immune response by an unconventional mechanism based on the activation of intracellular innate immune sensors of nucleic acids, namely the Toll-like receptors (TLRs). Such a mechanism of action has been now described to amplify and influence the pathogenesis of several inflammation-dependent pathological conditions, including cancer growth and metastasis, neurodegeneration, autoimmunity and cardiovascular diseases. The available data suggest that we have only begun to touch upon a complex system that is likely to involve many receptors and molecules. These findings may help to understand the pathogenesis of immune-mediated diseases and provide the basis for the identification of new potential therapeutic targets.
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Affiliation(s)
- Daniela Bosisio
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Veronica Gianello
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Valentina Salvi
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Silvano Sozzani
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy.
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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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Xie C, Liao H, Zhang C, Zhang S. Overexpression and clinical relevance of the RNA helicase DHX15 in hepatocellular carcinoma. Hum Pathol 2018; 84:213-220. [PMID: 30339968 DOI: 10.1016/j.humpath.2018.10.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Revised: 09/29/2018] [Accepted: 10/04/2018] [Indexed: 01/06/2023]
Abstract
DHX15 is an outstanding member of the DEAH-box RNA helicase family. A few studies suggest that DHX15 contributes to carcinogenesis in several tumor cell lines. However, whether DHX15 acts as an oncogene or tumor suppressor and its association with hepatocellular carcinoma (HCC) prognosis are still poorly understood. To address this question, we used immunohistochemistry to evaluate DHX15 expression patterns and their association with clinicopathological factors and the prognosis of patients with HCC. Our results showed that DHX15 expression was significantly higher in cancerous tissues than that in nontumor tissues (P < .0001). DHX15 expression in HCC patients was associated with differentiation status (P = .018), tumor number (P = .048), intrahepatic or extrahepatic metastasis (P = .001), serum α-fetoprotein (P = .006), hepatitis B virus level (P = .018), and recurrence (P < .001). In addition, the survival analysis revealed that the DHX15-high group had significantly decreased overall survival time (P = .004) and lower 1-year survival rates (P = .002) compared with the DHX15-low group. Furthermore, multivariate analysis identified DHX15 expression as an independent factor associated with poor prognosis in HCC (P = .036). In summary, these findings demonstrate, for the first time, that DHX15 is significantly upregulated in HCC and its high expression was correlated with poor prognosis, suggesting its pivotal role in the progression of HCC. The present results suggest that DHX15 may serve as a potential prognostic biomarker for HCC patients.
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Affiliation(s)
- Chengrong Xie
- Fujian Provincial Key Laboratory of Chronic Liver Disease and Hepatocellular Carcinoma (Xiamen University Affiliated Zhongshan Hospital), Fujian, China
| | - Hongfeng Liao
- Department of Pathology, Xiamen University Affiliated Zhongshan Hospital, Fujian, China
| | - Changmao Zhang
- School of Clinical Medicine, Fujian Medical University, Fujian, China
| | - Sheng Zhang
- Department of Pathology, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
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36
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Cao X, Xue YJ, Du JL, Xu Q, Yang XC, Zeng Y, Wang BB, Wang HZ, Liu J, Cai KZ, Ma ZR. Induction and Suppression of Innate Antiviral Responses by Hepatitis A Virus. Front Microbiol 2018; 9:1865. [PMID: 30174659 PMCID: PMC6107850 DOI: 10.3389/fmicb.2018.01865] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Accepted: 07/25/2018] [Indexed: 12/25/2022] Open
Abstract
Hepatitis A virus (HAV) belongs to the family Picornaviridae. It is the pathogen of acute viral hepatitis caused by fecal-oral transmission. RNA viruses are sensed by pathogen-associated pattern recognition receptors (PRRs) such as Toll-like receptor 3 (TLR3), retinoic acid-inducible gene I (RIG-I), and melanoma differentiation-associated gene 5 (MDA5). PRR activation leads to production of type 1 interferon (IFN-α/β), serving as the first line of defense against viruses. However, HAV has developed various strategies to compromise the innate immune system and promote viral propagation within the host cells. The long coevolution of HAV in hosts has prompted the development of effective immune antagonism strategies that actively fight against host antiviral responses. Proteases encoded by HAV can cleave the mitochondrial antiviral signaling protein (MAVS, also known as IPS-1, VISA, or Cardif), TIR domain- containing adaptor inducing IFN-β (TRIF, also known as TICAM-1) and nuclear factor-κB (NF-κB) essential modulator (NEMO), which are key adaptor proteins in RIG-I-like receptor (RLR), TLR3 and NF-κB signaling, respectively. In this mini-review, we summarize all the recent progress on the interaction between HAV and the host, especially focusing on how HAV abrogates the antiviral effects of the innate immune system.
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Affiliation(s)
- Xin Cao
- College of Life Science and Engineering, Northwest Minzu University, Engineering & Technology Research Center for Animal Cell, Lanzhou, China
- Key Laboratory of Bioengineering & Biotechnology of State Ethnic Affairs Commission, Lanzhou, China
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Yu-jia Xue
- College of Life Science and Engineering, Northwest Minzu University, Engineering & Technology Research Center for Animal Cell, Lanzhou, China
- Key Laboratory of Bioengineering & Biotechnology of State Ethnic Affairs Commission, Lanzhou, China
| | - Jiang-long Du
- College of Life Science and Engineering, Northwest Minzu University, Engineering & Technology Research Center for Animal Cell, Lanzhou, China
- Key Laboratory of Bioengineering & Biotechnology of State Ethnic Affairs Commission, Lanzhou, China
| | - Qiang Xu
- College of Life Science and Engineering, Northwest Minzu University, Engineering & Technology Research Center for Animal Cell, Lanzhou, China
- Key Laboratory of Bioengineering & Biotechnology of State Ethnic Affairs Commission, Lanzhou, China
| | - Xue-cai Yang
- College of Life Science and Engineering, Northwest Minzu University, Engineering & Technology Research Center for Animal Cell, Lanzhou, China
- Key Laboratory of Bioengineering & Biotechnology of State Ethnic Affairs Commission, Lanzhou, China
| | - Yan Zeng
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Bo-bo Wang
- College of Life Science and Engineering, Northwest Minzu University, Engineering & Technology Research Center for Animal Cell, Lanzhou, China
- Key Laboratory of Bioengineering & Biotechnology of State Ethnic Affairs Commission, Lanzhou, China
| | - Hai-zhen Wang
- Hebi Precision Medical Research Institute, People's Hospital of Hebi, Hebi, China
| | - Jing Liu
- Department of Medical OncologyPeople's Hospital of Hebi, Hebi, China
| | - Kui-zheng Cai
- College of Life Science and Engineering, Northwest Minzu University, Engineering & Technology Research Center for Animal Cell, Lanzhou, China
- Key Laboratory of Bioengineering & Biotechnology of State Ethnic Affairs Commission, Lanzhou, China
| | - Zhong-ren Ma
- College of Life Science and Engineering, Northwest Minzu University, Engineering & Technology Research Center for Animal Cell, Lanzhou, China
- Key Laboratory of Bioengineering & Biotechnology of State Ethnic Affairs Commission, Lanzhou, China
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Abstract
Pattern recognition receptors (PRRs) survey intra- and extracellular spaces for pathogen-associated molecular patterns (PAMPs) within microbial products of infection. Recognition and binding to cognate PAMP ligand by specific PRRs initiates signaling cascades that culminate in a coordinated intracellular innate immune response designed to control infection. In particular, our immune system has evolved specialized PRRs to discriminate viral nucleic acid from host. These are critical sensors of viral RNA to trigger innate immunity in the vertebrate host. Different families of PRRs of virus infection have been defined and reveal a diversity of PAMP specificity for wide viral pathogen coverage to recognize and extinguish virus infection. In this review, we discuss recent insights in pathogen recognition by the RIG-I-like receptors, related RNA helicases, Toll-like receptors, and other RNA sensor PRRs, to present emerging themes in innate immune signaling during virus infection.
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Affiliation(s)
- Kwan T Chow
- Center for Innate Immunity and Immune Disease and Department of Immunology, University of Washington, Seattle, Washington 98109, USA; , ,
| | - Michael Gale
- Center for Innate Immunity and Immune Disease and Department of Immunology, University of Washington, Seattle, Washington 98109, USA; , ,
| | - Yueh-Ming Loo
- Center for Innate Immunity and Immune Disease and Department of Immunology, University of Washington, Seattle, Washington 98109, USA; , ,
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Ito S, Koso H, Sakamoto K, Watanabe S. RNA helicase DHX15 acts as a tumour suppressor in glioma. Br J Cancer 2017; 117:1349-1359. [PMID: 28829764 PMCID: PMC5672939 DOI: 10.1038/bjc.2017.273] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2017] [Revised: 06/22/2017] [Accepted: 07/24/2017] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Glioblastoma is the most common form of malignant brain cancer and has a poor prognosis in adults. We identified Dhx15 as a candidate tumour suppressor gene in glioma by transposon-based mutagenesis. Dhx15 is an adenosine triphosphate (ATP)-dependent RNA helicase belonging to the DEAH-box (DHX) helicase family, but its role in cancer remains elusive. METHODS DHX15 expression levels were examined in glioma cell lines. DHX15 functions were examined by gain- and loss-of-function analyses. Protein motifs required for the function of DHX15 were investigated by the analysis of mutant proteins. RESULTS DHX15 expression was lower in human glioma cell lines than in normal neural stem cells. Dhx15 knockdown resulted in enhanced proliferation of primary immortalised mouse astrocytes, supporting the notion that DHX15 is a tumour suppressor. Retroviral-mediated transduction of DHX15 into glioma cell lines suppressed proliferation and foci formation in vitro. Moreover, DHX15 suppressed tumour formation in a xenograft mouse model. ATPase activity was not required for the growth-inhibitory function of DHX15; however, the Ia, Ib, IV, and V motifs, which act as RNA-binding domains in DHX15, were essential. qPCR analysis revealed that DHX15 suppressed expression of NF-κB downstream target genes as well as the genes involved in splicing. CONCLUSIONS These findings provide evidence that DHX15 acts as a tumour suppressor gene in glioma.
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Affiliation(s)
- Shingo Ito
- Division of Molecular and Developmental Biology, Institute of Medical Science, University of Tokyo, Tokyo 1088639, Japan
- Department of Coloproctological Surgery, Faculty of Medicine, Juntendo University, Tokyo 1138421, Japan
| | - Hideto Koso
- Division of Molecular and Developmental Biology, Institute of Medical Science, University of Tokyo, Tokyo 1088639, Japan
| | - Kazuhiro Sakamoto
- Department of Coloproctological Surgery, Faculty of Medicine, Juntendo University, Tokyo 1138421, Japan
| | - Sumiko Watanabe
- Division of Molecular and Developmental Biology, Institute of Medical Science, University of Tokyo, Tokyo 1088639, Japan
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Capitanio JS, Montpetit B, Wozniak RW. Nucleoplasmic Nup98 controls gene expression by regulating a DExH/D-box protein. Nucleus 2017; 9:1-8. [PMID: 28934014 PMCID: PMC5973140 DOI: 10.1080/19491034.2017.1364826] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The nucleoporin Nup98 has been linked to the regulation of transcription and RNA metabolism, 1-3 but the mechanisms by which Nup98 contributes to these processes remains largely undefined. Recently, we uncovered interactions between Nup98 and several DExH/D-box proteins (DBPs), a protein family well-known for modulating gene expression and RNA metabolism. 4-6 Analysis of Nup98 and one of these DBPs, DHX9, showed that they directly interact, their association is facilitated by RNA, and Nup98 binding stimulates DHX9 ATPase activity. 7 Furthermore, these proteins were dependent on one another for their proper association with a subset of gene loci to control transcription and modulate mRNA splicing. 7 On the basis of these observations, we proposed that Nup98 functions to regulate DHX9 activity within the nucleoplasm. 7 Since Nup98 is associated with several DBPs, regulation of DHX9 by Nup98 may represent a paradigm for understanding how Nup98, and possibly other FG-Nup proteins, could direct the diverse cellular activities of multiple DBPs.
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Affiliation(s)
| | - Ben Montpetit
- a Department of Cell Biology , University of Alberta , Edmonton , Canada.,b Department of Viticulture and Enology , University of California at Davis , Davis , CA , USA
| | - Richard W Wozniak
- a Department of Cell Biology , University of Alberta , Edmonton , Canada
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40
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DHX15 is associated with poor prognosis in acute myeloid leukemia (AML) and regulates cell apoptosis via the NF-kB signaling pathway. Oncotarget 2017; 8:89643-89654. [PMID: 29163777 PMCID: PMC5685698 DOI: 10.18632/oncotarget.20288] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 07/26/2017] [Indexed: 12/25/2022] Open
Abstract
The role of DHX15, a newly identified DEAH-box RNA helicase, in leukemogenesis remains elusive. Here, we identified a recurrent mutation in DHX15 (NM_001358:c.664C>G: p.(R222G)) in one familial AML patient and 4/240 sporadic AML patients. Additionally, DHX15 was commonly overexpressed in AML patients and associated with poor overall survival (OS) (P=0.019) and relapse-free survival (RFS) (P=0.032). In addition, we found a distinct expression pattern of DHX15. DHX15 was highly expressed in hematopoietic stem cells and leukemia cells but was lowly expressed in mature blood cells. DHX15 was down-regulated when AML patients achieved disease remission or when leukemia cell lines were induced to differentiate. DHX15 silencing greatly inhibited leukemia cell proliferation and induced cell apoptosis and G1-phase arrest. In contrast, the restoration of DHX15 expression rescued cell viability and reduced cell apoptosis. In addition, we found that DHX15 was down-regulated when cell apoptosis was induced by ATO (arsenic trioxide); overexpression of DHX15 caused dramatic resistance to ATO-induced cell apoptosis, suggesting an important role for DHX15 in cell apoptosis. We further explored the mechanism of DHX15 in apoptosis and found that overexpression of DHX15 activated NF-kB transcription. Knockdown of DHX15 inhibited the nuclear translocation and activation of the NF-kB subunit P65 in leukemia cells. Several downstream targets of the NF-kB pathway were also down-regulated, and apoptosis-associated genes CASP3 and PARP were activated. In conclusion, this study represents the first demonstration that DHX15 plays an important role in leukemogenesis via the NF-kB signaling pathway and may serve as an independent prognostic marker for AML.
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Murakami K, Nakano K, Shimizu T, Ohto U. The crystal structure of human DEAH-box RNA helicase 15 reveals a domain organization of the mammalian DEAH/RHA family. Acta Crystallogr F Struct Biol Commun 2017; 73:347-355. [PMID: 28580923 PMCID: PMC5458392 DOI: 10.1107/s2053230x17007336] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 05/17/2017] [Indexed: 12/31/2022] Open
Abstract
DEAH-box RNA helicase 15 (DHX15) plays important roles in RNA metabolism, including in splicing and in ribosome biogenesis. In addition, mammalian DHX15 also mediates the innate immune sensing of viral RNA. However, structural information on this protein is not available, although the structure of the fungal orthologue of this protein, Prp43, has been elucidated. Here, the crystal structure of the ADP-bound form of human DHX15 is reported at a resolution of 2.0 Å. This is the first structure to be revealed of a member of the mammalian DEAH-box RNA helicase (DEAH/RHA) family in a nearly complete form, including the catalytic core consisting of the two N-terminal RecA domains and the C-terminal regulatory domains (CTD). The ADP-bound form of DHX15 displayed a compact structure, in which the RecA domains made extensive contacts with the CTD. Notably, a potential RNA-binding site was found on the surface of a RecA domain with positive electrostatic potential. Almost all structural features were conserved between the fungal Prp43 and the human DHX15, suggesting that they share a fundamentally common mechanism of action and providing a better understanding of the specific mammalian functions of DHX15.
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Affiliation(s)
- Karin Murakami
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kenji Nakano
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Toshiyuki Shimizu
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Saitama 332-0012, Japan
| | - Umeharu Ohto
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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42
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Capitanio JS, Montpetit B, Wozniak RW. Human Nup98 regulates the localization and activity of DExH/D-box helicase DHX9. eLife 2017; 6. [PMID: 28221134 PMCID: PMC5338925 DOI: 10.7554/elife.18825] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 02/16/2017] [Indexed: 12/17/2022] Open
Abstract
Beyond their role at nuclear pore complexes, some nucleoporins function in the nucleoplasm. One such nucleoporin, Nup98, binds chromatin and regulates gene expression. To gain insight into how Nup98 contributes to this process, we focused on identifying novel binding partners and understanding the significance of these interactions. Here we report on the identification of the DExH/D-box helicase DHX9 as an intranuclear Nup98 binding partner. Various results, including in vitro assays, show that the FG/GLFG region of Nup98 binds to N- and C-terminal regions of DHX9 in an RNA facilitated manner. Importantly, binding of Nup98 stimulates the ATPase activity of DHX9, and a transcriptional reporter assay suggests Nup98 supports DHX9-stimulated transcription. Consistent with these observations, our analysis revealed that Nup98 and DHX9 bind interdependently to similar gene loci and their transcripts. Based on our results, we propose that Nup98 functions as a co-factor that regulates DHX9 and, potentially, other RNA helicases.
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Affiliation(s)
| | - Ben Montpetit
- Department of Cell Biology, University of Alberta, Edmonton, Canada.,Department of Viticulture and Enology, University of California, Davis, United states
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Tremblay N, Baril M, Chatel-Chaix L, Es-Saad S, Park AY, Koenekoop RK, Lamarre D. Spliceosome SNRNP200 Promotes Viral RNA Sensing and IRF3 Activation of Antiviral Response. PLoS Pathog 2016; 12:e1005772. [PMID: 27454487 PMCID: PMC4959778 DOI: 10.1371/journal.ppat.1005772] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 06/27/2016] [Indexed: 12/18/2022] Open
Abstract
Spliceosomal SNRNP200 is a Ski2-like RNA helicase that is associated with retinitis pigmentosa 33 (RP33). Here we found that SNRNP200 promotes viral RNA sensing and IRF3 activation through the ability of its amino-terminal Sec63 domain (Sec63-1) to bind RNA and to interact with TBK1. We show that SNRNP200 relocalizes into TBK1-containing cytoplasmic structures upon infection, in contrast to the RP33-associated S1087L mutant, which is also unable to rescue antiviral response of SNRNP200 knockdown cells. This functional rescue correlates with the Sec63-1-mediated binding of viral RNA. The hindered IFN-β production of knockdown cells was further confirmed in peripheral blood cells of RP33 patients bearing missense mutation in SNRNP200 upon infection with Sendai virus (SeV). This work identifies a novel immunoregulatory role of the spliceosomal SNRNP200 helicase as an RNA sensor and TBK1 adaptor for the activation of IRF3-mediated antiviral innate response. The innate immune system is the first line of defense against pathogens and relies on the recognition of molecular structures specific to pathogens by sensor receptors. These receptors activate a signaling cascade and induce a protective cellular innate immune response. In this study, we provide evidence for a role of the spliceosomal SNRNP200 RNA helicase in promoting antiviral response that is clearly distinguishable of the one in pre-mRNA splicing. The depletion of SNRNP200 in human cells resulted in a reduced interferon-β (IFNB1) production and increased susceptibility to viral infection. We showed that SNRNP200 positively regulates activation of the key transcription factor IRF3 via interaction with TANK kinase 1 (TBK1). Upon infection, SNRNP200 binds viral RNA and relocalizes into TBK1-containing cytoplasmic structures to promote IRF3 activation and IFNB1 production. Of clinical relevance, we observed a significantly hindered antiviral response of PBMCs from patients carrying a dominant SNRNP200 mutation associated with retina pigmentosa type 33 (RP33), an inherited degenerative eye disease. We showed that the RP33-associated S1087L SNRNP200 mutant has lost the ability to bind RNA and that its expression fails to rescue antiviral response in SNRNP200 silenced cells. Our study provides new insights into a role within the antiviral response for spliceosome SNRNP200 helicase as an RNA sensor and TBK1 adaptor in IRF3 signaling.
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Affiliation(s)
- Nicolas Tremblay
- Centre de Recherche du CHUM (CRCHUM), Montréal, Québec, Canada
- Faculté de Médecine, Université de Montréal, Montréal, Canada
| | - Martin Baril
- Centre de Recherche du CHUM (CRCHUM), Montréal, Québec, Canada
| | | | - Salwa Es-Saad
- Centre de Recherche du CHUM (CRCHUM), Montréal, Québec, Canada
| | - Alex Young Park
- Centre de Recherche du CHUM (CRCHUM), Montréal, Québec, Canada
- Faculté de Médecine, Université de Montréal, Montréal, Canada
| | - Robert K. Koenekoop
- Departments of Pediatric Surgery, Human Genetics and Ophthalmology, McGill University, Montréal, Canada
| | - Daniel Lamarre
- Centre de Recherche du CHUM (CRCHUM), Montréal, Québec, Canada
- Faculté de Médecine, Université de Montréal, Montréal, Canada
- * E-mail:
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Xia J, Qi X, Wu Y, Zhu B, Xu L, Zhang L, Gao X, Chen Y, Li J, Gao H. Genome-wide association study identifies loci and candidate genes for meat quality traits in Simmental beef cattle. Mamm Genome 2016; 27:246-55. [PMID: 27126640 DOI: 10.1007/s00335-016-9635-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Accepted: 04/11/2016] [Indexed: 12/13/2022]
Abstract
Improving meat quality is the best way to enhance profitability and strengthen competitiveness in beef industry. Identification of genetic variants that control beef quality traits can help breeders design optimal breeding programs to achieve this goal. We carried out a genome-wide association study for meat quality traits in 1141 Simmental cattle using the Illumina Bovine HD 770K SNP array to identify the candidate genes and genomic regions associated with meat quality traits for beef cattle, including fat color, meat color, marbling score, longissimus muscle area, and shear force. In our study, we identified twenty significant single-nucleotide polymorphisms (SNPs) (p < 1.47 × 10(-6)) associated with these five meat quality traits. Notably, we observed several SNPs were in or near eleven genes which have been reported previously, including TMEM236, SORL1, TRDN, S100A10, AP2S1, KCTD16, LOC506594, DHX15, LAMA4, PREX1, and BRINP3. We identified a haplotype block on BTA13 containing five significant SNPs associated with fat color trait. We also found one of 19 SNPs was associated with multiple traits (shear force and longissimus muscle area) on BTA7. Our results offer valuable insights to further explore the potential mechanism of meat quality traits in Simmental beef cattle.
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Affiliation(s)
- Jiangwei Xia
- Institute of Animal Science, Chinese Academy of Agricultural Science, No.2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Xin Qi
- Institute of Animal Science, Chinese Academy of Agricultural Science, No.2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Yang Wu
- Institute of Animal Science, Chinese Academy of Agricultural Science, No.2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Bo Zhu
- Institute of Animal Science, Chinese Academy of Agricultural Science, No.2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Lingyang Xu
- Institute of Animal Science, Chinese Academy of Agricultural Science, No.2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Lupei Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Science, No.2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Xue Gao
- Institute of Animal Science, Chinese Academy of Agricultural Science, No.2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Yan Chen
- Institute of Animal Science, Chinese Academy of Agricultural Science, No.2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Junya Li
- Institute of Animal Science, Chinese Academy of Agricultural Science, No.2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China.
| | - Huijiang Gao
- Institute of Animal Science, Chinese Academy of Agricultural Science, No.2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China.
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Suthar MK, Purva M, Maherchandani S, Kashyap SK. Identification and in silico analysis of cattle DExH/D box RNA helicases. SPRINGERPLUS 2016; 5:25. [PMID: 26783509 PMCID: PMC4705078 DOI: 10.1186/s40064-015-1640-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 12/20/2015] [Indexed: 12/16/2022]
Abstract
The helicases are motor proteins participating
in a range of nucleic acid metabolisms. RNA helicase families are characterized by the presence of conserved motifs. This article reports a comprehensive in silico analysis of Bos taurus DExH/D helicase members. Bovine helicases were identified using the helicase domain sequences including 38 DDX (DEAD box) and 16 DHX (DEAH box) members. Signature motifs were used for the validation of these proteins. Putative sub cellular localization and phylogenetic relationship for these RNA helicases were established. Comparative analysis of these proteins with human DDX and DHX members was carried out. These bovine helicase have been assigned putative physiological functions. Present study of cattle DExH/D helicase will provides an invaluable source for the detailed biochemical and physiological research on these members.
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Affiliation(s)
- Manish Kumar Suthar
- Department of Veterinary Microbiology and Biotechnology, Rajasthan University of Veterinary & Animal Sciences, Bikaner, Rajasthan 334001 India
| | - Mukul Purva
- Department of Veterinary Microbiology and Biotechnology, Rajasthan University of Veterinary & Animal Sciences, Bikaner, Rajasthan 334001 India
| | - Sunil Maherchandani
- Department of Veterinary Microbiology and Biotechnology, Rajasthan University of Veterinary & Animal Sciences, Bikaner, Rajasthan 334001 India
| | - Sudhir Kumar Kashyap
- Department of Veterinary Microbiology and Biotechnology, Rajasthan University of Veterinary & Animal Sciences, Bikaner, Rajasthan 334001 India
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Wang P, Zhu S, Yang L, Cui S, Pan W, Jackson R, Zheng Y, Rongvaux A, Sun Q, Yang G, Gao S, Lin R, You F, Flavell R, Fikrig E. Nlrp6 regulates intestinal antiviral innate immunity. Science 2015; 350:826-30. [PMID: 26494172 DOI: 10.1126/science.aab3145] [Citation(s) in RCA: 187] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 10/02/2015] [Indexed: 12/24/2022]
Abstract
The nucleotide-binding oligomerization domain-like receptor (Nlrp) 6 maintains gut microbiota homeostasis and regulates antibacterial immunity. We now report a role for Nlrp6 in the control of enteric virus infection. Nlrp6(-/-) and control mice systemically challenged with encephalomyocarditis virus had similar mortality; however, the gastrointestinal tract of Nlrp6(-/-) mice exhibited increased viral loads. Nlrp6(-/-) mice orally infected with encephalomyocarditis virus had increased mortality and viremia compared with controls. Similar results were observed with murine norovirus 1. Nlrp6 bound viral RNA via the RNA helicase Dhx15 and interacted with mitochondrial antiviral signaling protein to induce type I/III interferons (IFNs) and IFN-stimulated genes (ISGs). These data demonstrate that Nlrp6 functions with Dhx15 as a viral RNA sensor to induce ISGs, and this effect is especially important in the intestinal tract.
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Affiliation(s)
- Penghua Wang
- Section of Infectious Diseases, Yale University School of Medicine, 300 Cedar Street, New Haven, CT 06510, USA. Department of Microbiology and Immunology, New York Medical College, Valhalla, NY 10595, USA
| | - Shu Zhu
- Department of Immunobiology, Yale University School of Medicine, 300 Cedar Street, New Haven, CT 06510, USA
| | - Long Yang
- Section of Infectious Diseases, Yale University School of Medicine, 300 Cedar Street, New Haven, CT 06510, USA. Department of Microbiology and Immunology, New York Medical College, Valhalla, NY 10595, USA
| | - Shuang Cui
- Section of Infectious Diseases, Yale University School of Medicine, 300 Cedar Street, New Haven, CT 06510, USA
| | - Wen Pan
- Department of Genetics, Yale University School of Medicine, 300 Cedar Street, New Haven, CT 06510, USA
| | - Ruaidhri Jackson
- Department of Immunobiology, Yale University School of Medicine, 300 Cedar Street, New Haven, CT 06510, USA
| | - Yunjiang Zheng
- Department of Immunobiology, Yale University School of Medicine, 300 Cedar Street, New Haven, CT 06510, USA
| | - Anthony Rongvaux
- Department of Immunobiology, Yale University School of Medicine, 300 Cedar Street, New Haven, CT 06510, USA
| | - Qiangming Sun
- Section of Infectious Diseases, Yale University School of Medicine, 300 Cedar Street, New Haven, CT 06510, USA
| | - Guang Yang
- Section of Infectious Diseases, Yale University School of Medicine, 300 Cedar Street, New Haven, CT 06510, USA
| | - Shandian Gao
- Section of Infectious Diseases, Yale University School of Medicine, 300 Cedar Street, New Haven, CT 06510, USA
| | - Rongtuan Lin
- Lady Davis Institute, Department of Medicine, McGill University, Montreal, Quebec, Canada
| | - Fuping You
- Section of Infectious Diseases, Yale University School of Medicine, 300 Cedar Street, New Haven, CT 06510, USA
| | - Richard Flavell
- Department of Immunobiology, Yale University School of Medicine, 300 Cedar Street, New Haven, CT 06510, USA. Howard Hughes Medical Institute, Chevy Chase, MD 20815-6789, USA.
| | - Erol Fikrig
- Section of Infectious Diseases, Yale University School of Medicine, 300 Cedar Street, New Haven, CT 06510, USA. Howard Hughes Medical Institute, Chevy Chase, MD 20815-6789, USA.
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Regulation of DEAH/RHA helicases by G-patch proteins. BIOMED RESEARCH INTERNATIONAL 2015; 2015:931857. [PMID: 25692149 PMCID: PMC4322301 DOI: 10.1155/2015/931857] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Revised: 10/19/2014] [Accepted: 10/24/2014] [Indexed: 11/20/2022]
Abstract
RNA helicases from the DEAH/RHA family are present in all the processes of RNA metabolism. The function of two helicases from this family, Prp2 and Prp43, is regulated by protein partners containing a G-patch domain. The G-patch is a glycine-rich domain discovered by sequence alignment, involved in protein-protein and protein-nucleic acid interaction. Although it has been shown to stimulate the helicase's enzymatic activities, the precise role of the G-patch domain remains unclear. The role of G-patch proteins in the regulation of Prp43 activity has been studied in the two biological processes in which it is involved: splicing and ribosome biogenesis. Depending on the pathway, the activity of Prp43 is modulated by different G-patch proteins. A particular feature of the structure of DEAH/RHA helicases revealed by the Prp43 structure is the OB-fold domain in C-terminal part. The OB-fold has been shown to be a platform responsible for the interaction with G-patch proteins and RNA. Though there is still no structural data on the G-patch domain, in the current model, the interaction between the helicase, the G-patch protein, and RNA leads to a cooperative binding of RNA and conformational changes of the helicase.
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Leigh R, Proud D. Virus-induced modulation of lower airway diseases: pathogenesis and pharmacologic approaches to treatment. Pharmacol Ther 2014; 148:185-98. [PMID: 25550230 PMCID: PMC7173263 DOI: 10.1016/j.pharmthera.2014.12.005] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Accepted: 12/24/2014] [Indexed: 02/08/2023]
Abstract
Uncomplicated upper respiratory viral infections are the most common cause of days lost from work and school and exert a major economic burden. In susceptible individuals, however, common respiratory viruses, particularly human rhinoviruses, also can have a major impact on diseases that involve the lower airways, including asthma, chronic obstructive pulmonary diseases (COPD) and cystic fibrosis (CF). Respiratory virus-induced wheezing illnesses in early life are a significant risk factor for the subsequent development of asthma, and virus infections may also play a role in the development and progression of airway remodeling in asthma. It is clear that upper respiratory tract virus infections can spread to the lower airway and trigger acute attacks of asthma, COPD or CF. These exacerbations can be life-threatening, and exert an enormous burden on health care systems. In recent years we have gained new insights into the mechanisms by which respiratory viruses may induce acute exacerbations of lower airway diseases, as well as into host defense pathways that may regulate the outcomes to viral infections. In the current article we review the role of viruses in lower airway diseases, including our current understanding on pathways by which they may cause remodeling and trigger acute exacerbations. We also review the efficacy of current and emerging therapies used to treat these lower airway diseases on the outcomes due to viral infection, and discuss alternative therapeutic approaches for the management of virus-induced airway inflammation.
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Affiliation(s)
- Richard Leigh
- Airway Inflammation Research Group, Snyder Institute for Chronic Diseases and Department of Medicine, University of Calgary Faculty of Medicine, Calgary, Canada; Airway Inflammation Research Group, Snyder Institute for Chronic Diseases and Department of Physiology & Pharmacology, University of Calgary Faculty of Medicine, Calgary, Canada
| | - David Proud
- Airway Inflammation Research Group, Snyder Institute for Chronic Diseases and Department of Physiology & Pharmacology, University of Calgary Faculty of Medicine, Calgary, Canada.
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