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Yuan X, Shi J, Peng Z, Peng L, Zhou S, Wu C, Zhao J, Xu D, Li M, Wang Q, Zeng X. Global trends in research of melanoma differentiation-associated gene 5: a bibliometric analysis from 2002 to 2022. Clin Rheumatol 2024; 43:1111-1126. [PMID: 38182800 DOI: 10.1007/s10067-023-06851-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 12/11/2023] [Accepted: 12/16/2023] [Indexed: 01/07/2024]
Abstract
BACKGROUND Melanoma differentiation-associated gene 5 (MDA5), as a cytoplasmic sensor for viral double-stranded RNAs, has received increasing attention in recent years. Although considerable headway has been made on the functional role of MDA5 in antiviral immunity and autoimmune disease, the available literature is insufficient to assess the vast field. METHODS This study performed a bibliometric analysis to investigate current hotspots in the global scientific output of MDA5 over the past two decades. Related publications and recorded information from 2002 to 2022 in the Web of Science Core Collection (WoSCC) database were retrieved. VOSviewer and CiteSpace were used for quantitative evaluation and visualization. RESULTS A total of 2267 original articles and reviews were obtained, and the annual number of publications related to MDA5 was increasing rapidly. China has published the most papers, while the USA was the most influential country with the most citations and the highest H-index. The Chinese Academy of Sciences, the United States Department of Health and Human Services, and the Journal of Virology were the most prolific research affiliation, funding source, and journal, respectively. Fujita T (Kyoto University) was the most productive author with the highest H-index and had close cooperation with Kato H and Yoneyama M. The keywords "RIG-I," "MDA5," "innate immunity," "double-stranded-RNA," and "recognition" had the highest frequency, while "dermatomyositis" as well as "autoantibody" seemed to be the emerging hotspots. CONCLUSION This study comprehensively demonstrated the research frontiers of MDA5 and will provide a useful resource for scholars to conduct future decisions. KEY POINTS We conducted the first in-depth survey of the research frontiers on melanoma differentiation-associated gene 5 (MDA5) over the past two decades via bibliometric analysis. We found that many early breakthroughs have been made in the mechanism of MDA5-mediated antiviral immune responses, and the role of MDA5 in autoimmune and autoinflammatory diseases has raised the recent concern. We identified that the virus infection-associated pathogenesis and effective therapeutic strategy of anti-MDA5 antibody-positive dermatomyositis will remain the hotspots in the future.
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Affiliation(s)
- Xueting Yuan
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, China
- National Clinical Research Center for Dermatologic and Immunologic Diseases, Ministry of Science & Technology, Beijing, China
- State Key Laboratory of Complex Severe and Rare Diseases, Key Laboratory of Rheumatology & Clinical Immunology, Ministry of Education, Beijing, China
| | - Jia Shi
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, China
- National Clinical Research Center for Dermatologic and Immunologic Diseases, Ministry of Science & Technology, Beijing, China
- State Key Laboratory of Complex Severe and Rare Diseases, Key Laboratory of Rheumatology & Clinical Immunology, Ministry of Education, Beijing, China
| | - Zhao Peng
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, China
- National Clinical Research Center for Dermatologic and Immunologic Diseases, Ministry of Science & Technology, Beijing, China
- State Key Laboratory of Complex Severe and Rare Diseases, Key Laboratory of Rheumatology & Clinical Immunology, Ministry of Education, Beijing, China
| | - Liying Peng
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, China
- National Clinical Research Center for Dermatologic and Immunologic Diseases, Ministry of Science & Technology, Beijing, China
- State Key Laboratory of Complex Severe and Rare Diseases, Key Laboratory of Rheumatology & Clinical Immunology, Ministry of Education, Beijing, China
| | - Shuang Zhou
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, China
- National Clinical Research Center for Dermatologic and Immunologic Diseases, Ministry of Science & Technology, Beijing, China
- State Key Laboratory of Complex Severe and Rare Diseases, Key Laboratory of Rheumatology & Clinical Immunology, Ministry of Education, Beijing, China
| | - Chanyuan Wu
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, China
- National Clinical Research Center for Dermatologic and Immunologic Diseases, Ministry of Science & Technology, Beijing, China
- State Key Laboratory of Complex Severe and Rare Diseases, Key Laboratory of Rheumatology & Clinical Immunology, Ministry of Education, Beijing, China
| | - Jiuliang Zhao
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, China
- National Clinical Research Center for Dermatologic and Immunologic Diseases, Ministry of Science & Technology, Beijing, China
- State Key Laboratory of Complex Severe and Rare Diseases, Key Laboratory of Rheumatology & Clinical Immunology, Ministry of Education, Beijing, China
| | - Dong Xu
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, China
- National Clinical Research Center for Dermatologic and Immunologic Diseases, Ministry of Science & Technology, Beijing, China
- State Key Laboratory of Complex Severe and Rare Diseases, Key Laboratory of Rheumatology & Clinical Immunology, Ministry of Education, Beijing, China
| | - Mengtao Li
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, China
- National Clinical Research Center for Dermatologic and Immunologic Diseases, Ministry of Science & Technology, Beijing, China
- State Key Laboratory of Complex Severe and Rare Diseases, Key Laboratory of Rheumatology & Clinical Immunology, Ministry of Education, Beijing, China
| | - Qian Wang
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, China.
- National Clinical Research Center for Dermatologic and Immunologic Diseases, Ministry of Science & Technology, Beijing, China.
- State Key Laboratory of Complex Severe and Rare Diseases, Key Laboratory of Rheumatology & Clinical Immunology, Ministry of Education, Beijing, China.
- State Key Laboratory of Common Mechanism Research for Major Diseases, Beijing, China.
| | - Xiaofeng Zeng
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, China.
- National Clinical Research Center for Dermatologic and Immunologic Diseases, Ministry of Science & Technology, Beijing, China.
- State Key Laboratory of Complex Severe and Rare Diseases, Key Laboratory of Rheumatology & Clinical Immunology, Ministry of Education, Beijing, China.
- State Key Laboratory of Common Mechanism Research for Major Diseases, Beijing, China.
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Yuan H, Wu X, Wu Q, Chatoff A, Megill E, Gao J, Huang T, Duan T, Yang K, Jin C, Yuan F, Wang S, Zhao L, Zinn PO, Abdullah KG, Zhao Y, Snyder NW, Rich JN. Lysine catabolism reprograms tumour immunity through histone crotonylation. Nature 2023; 617:818-826. [PMID: 37198486 DOI: 10.1038/s41586-023-06061-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 04/06/2023] [Indexed: 05/19/2023]
Abstract
Cancer cells rewire metabolism to favour the generation of specialized metabolites that support tumour growth and reshape the tumour microenvironment1,2. Lysine functions as a biosynthetic molecule, energy source and antioxidant3-5, but little is known about its pathological role in cancer. Here we show that glioblastoma stem cells (GSCs) reprogram lysine catabolism through the upregulation of lysine transporter SLC7A2 and crotonyl-coenzyme A (crotonyl-CoA)-producing enzyme glutaryl-CoA dehydrogenase (GCDH) with downregulation of the crotonyl-CoA hydratase enoyl-CoA hydratase short chain 1 (ECHS1), leading to accumulation of intracellular crotonyl-CoA and histone H4 lysine crotonylation. A reduction in histone lysine crotonylation by either genetic manipulation or lysine restriction impaired tumour growth. In the nucleus, GCDH interacts with the crotonyltransferase CBP to promote histone lysine crotonylation. Loss of histone lysine crotonylation promotes immunogenic cytosolic double-stranded RNA (dsRNA) and dsDNA generation through enhanced H3K27ac, which stimulates the RNA sensor MDA5 and DNA sensor cyclic GMP-AMP synthase (cGAS) to boost type I interferon signalling, leading to compromised GSC tumorigenic potential and elevated CD8+ T cell infiltration. A lysine-restricted diet synergized with MYC inhibition or anti-PD-1 therapy to slow tumour growth. Collectively, GSCs co-opt lysine uptake and degradation to shunt the production of crotonyl-CoA, remodelling the chromatin landscape to evade interferon-induced intrinsic effects on GSC maintenance and extrinsic effects on immune response.
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Affiliation(s)
- Huairui Yuan
- Hillman Cancer Center and Department of Neurology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Xujia Wu
- Hillman Cancer Center and Department of Neurology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Qiulian Wu
- Hillman Cancer Center and Department of Neurology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Adam Chatoff
- Department of Cardiovascular Sciences, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, USA
| | - Emily Megill
- Department of Cardiovascular Sciences, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, USA
| | - Jinjun Gao
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL, USA
| | - Tengfei Huang
- Hillman Cancer Center and Department of Neurology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Tingting Duan
- Hillman Cancer Center and Department of Neurology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Kailin Yang
- Department of Radiation Oncology, Taussig Cancer Center, Cleveland Clinic, Cleveland, OH, USA
| | - Chunyu Jin
- Department and School of Medicine, University of California, San Diego, CA, USA
| | - Fanen Yuan
- Hillman Cancer Center and Department of Neurology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Shuai Wang
- Hillman Cancer Center and Department of Neurology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Linjie Zhao
- Hillman Cancer Center and Department of Neurology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Pascal O Zinn
- Hillman Cancer Center and Department of Neurology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
- Department of Neurosurgery, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Kalil G Abdullah
- Hillman Cancer Center and Department of Neurology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
- Department of Neurosurgery, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Yingming Zhao
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL, USA
| | - Nathaniel W Snyder
- Department of Cardiovascular Sciences, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, USA
| | - Jeremy N Rich
- Hillman Cancer Center and Department of Neurology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA.
- Department of Neurology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA.
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3
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Zhang T, Yin C, Fedorov A, Qiao L, Bao H, Beknazarov N, Wang S, Gautam A, Williams RM, Crawford JC, Peri S, Studitsky V, Beg AA, Thomas PG, Walkley C, Xu Y, Poptsova M, Herbert A, Balachandran S. ADAR1 masks the cancer immunotherapeutic promise of ZBP1-driven necroptosis. Nature 2022; 606:594-602. [PMID: 35614224 PMCID: PMC9373927 DOI: 10.1038/s41586-022-04753-7] [Citation(s) in RCA: 126] [Impact Index Per Article: 63.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 04/11/2022] [Indexed: 12/11/2022]
Abstract
Only a small proportion of patients with cancer show lasting responses to immune checkpoint blockade (ICB)-based monotherapies. The RNA-editing enzyme ADAR1 is an emerging determinant of resistance to ICB therapy and prevents ICB responsiveness by repressing immunogenic double-stranded RNAs (dsRNAs), such as those arising from the dysregulated expression of endogenous retroviral elements (EREs)1-4. These dsRNAs trigger an interferon-dependent antitumour response by activating A-form dsRNA (A-RNA)-sensing proteins such as MDA-5 and PKR5. Here we show that ADAR1 also prevents the accrual of endogenous Z-form dsRNA elements (Z-RNAs), which were enriched in the 3' untranslated regions of interferon-stimulated mRNAs. Depletion or mutation of ADAR1 resulted in Z-RNA accumulation and activation of the Z-RNA sensor ZBP1, which culminated in RIPK3-mediated necroptosis. As no clinically viable ADAR1 inhibitors currently exist, we searched for a compound that can override the requirement for ADAR1 inhibition and directly activate ZBP1. We identified a small molecule, the curaxin CBL0137, which potently activates ZBP1 by triggering Z-DNA formation in cells. CBL0137 induced ZBP1-dependent necroptosis in cancer-associated fibroblasts and reversed ICB unresponsiveness in mouse models of melanoma. Collectively, these results demonstrate that ADAR1 represses endogenous Z-RNAs and identifies ZBP1-mediated necroptosis as a new determinant of tumour immunogenicity masked by ADAR1. Therapeutic activation of ZBP1-induced necroptosis provides a readily translatable avenue for rekindling the immune responsiveness of ICB-resistant human cancers.
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Affiliation(s)
- Ting Zhang
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Chaoran Yin
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Aleksandr Fedorov
- Laboratory of Bioinformatics, Faculty of Computer Science, National Research University Higher School of Economics, Moscow, Russia
| | - Liangjun Qiao
- College of Basic Medicine, Chongqing Medical University, Chongqing, China
| | - Hongliang Bao
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, Kiyotake, Japan
| | - Nazar Beknazarov
- Laboratory of Bioinformatics, Faculty of Computer Science, National Research University Higher School of Economics, Moscow, Russia
| | - Shiyu Wang
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, Kiyotake, Japan
| | - Avishekh Gautam
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Riley M Williams
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | | | - Suraj Peri
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Vasily Studitsky
- Cancer Signaling and Epigenetics Program, Fox Chase Cancer Center, Philadelphia, PA, USA
- Biology Faculty, Lomonosov Moscow State University, Moscow, Russia
| | - Amer A Beg
- Department of Immunology and Thoracic Oncology, Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Paul G Thomas
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Carl Walkley
- Cancer & RNA Biology, St Vincent's Institute for Medical Research and Department of Medicine, St Vincent's Hospital, University of Melbourne, Fitzroy, Victoria, Australia
| | - Yan Xu
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, Kiyotake, Japan
| | - Maria Poptsova
- Laboratory of Bioinformatics, Faculty of Computer Science, National Research University Higher School of Economics, Moscow, Russia
| | - Alan Herbert
- Laboratory of Bioinformatics, Faculty of Computer Science, National Research University Higher School of Economics, Moscow, Russia.
- InsideOutBio, Charlestown, MA, USA.
| | - Siddharth Balachandran
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA, USA.
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Samms KA, Alkie TN, Jenik K, de Jong J, Klinger KM, DeWitte-Orr SJ. Oral delivery of a dsRNA-Phytoglycogen nanoparticle complex enhances both local and systemic innate immune responses in rainbow trout. Fish Shellfish Immunol 2022; 121:215-222. [PMID: 34999226 DOI: 10.1016/j.fsi.2021.12.038] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 12/21/2021] [Accepted: 12/22/2021] [Indexed: 06/14/2023]
Abstract
Salmonids are one of the most farmed fish species worldwide. These aquatic vertebrates rely heavily on their innate immune responses as the first line of defense to defend themselves against invading pathogens. Although commercial vaccines are available against some viral and bacterial pathogens affecting salmonids, their protective efficacy varies. Using a prophylactic inducer of local and systemic innate immune responses to limit infection could have significant implications in salmonid aquaculture. A potent inducer of innate immune responses in fish is double-stranded RNA (dsRNA), a molecule that all viruses make during their replicative cycle. Polyinosinic: polycytidylic acid (polyI:C) is a synthetic dsRNA commonly used to induce type I interferons (IFNs), interferon stimulated genes (ISGs) as well as an antiviral state in vertebrate species. Based on in vitro data it was hypothesized that both local and systemic innate immune responses, in salmonids, would be enhanced by orally delivering high molecular weight polyI:C (HMW polyI:C) using cationic phytoglycogen nanoparticles (NPs) as a delivery method. The present study investigates this hypothesis using two feed delivery methods. In the first in vivo study, to ensure an equal distribution of dose, individual rainbow trout (Oncorhynchus mykiss) were orally gavaged with feed moistened with a solution containing HMW-NP (polyI:C complexed with cationic phytoglycogen nanoparticles) or HMW polyI:C alone. In a second in vivo experiment, to better mimic a more realistic feeding scenario, rainbow trout were fed feed pellets to which HMW, or HMW-NP was added. The expression of IFN1 and ISGs (vig-3, Mx1) were quantified using real-time PCR in the intestine (local response) and head kidney (systemic response). The results of these studies indicate that HMW-NP induced a higher level of IFN1 and ISG expression in the intestine and head kidney compared to the HMW fed fish. The results of this study could lead to new advances in therapeutics for the aquaculture industry by utilizing the innate immune response against invading pathogens using an orally delivered stimulant.
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Affiliation(s)
- Kayla A Samms
- Department of Health Sciences, Wilfrid Laurier University, Waterloo, ON, Canada
| | - Tamiru N Alkie
- Department of Health Sciences, Wilfrid Laurier University, Waterloo, ON, Canada
| | - Kristof Jenik
- Department of Health Sciences, Wilfrid Laurier University, Waterloo, ON, Canada
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Zheng Y, Deng J, Han L, Zhuang MW, Xu Y, Zhang J, Nan ML, Xiao Y, Zhan P, Liu X, Gao C, Wang PH. SARS-CoV-2 NSP5 and N protein counteract the RIG-I signaling pathway by suppressing the formation of stress granules. Signal Transduct Target Ther 2022; 7:22. [PMID: 35075101 PMCID: PMC8785035 DOI: 10.1038/s41392-022-00878-3] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 12/17/2021] [Accepted: 01/10/2022] [Indexed: 02/06/2023] Open
Abstract
As a highly pathogenic human coronavirus, SARS-CoV-2 has to counteract an intricate network of antiviral host responses to establish infection and spread. The nucleic acid-induced stress response is an essential component of antiviral defense and is closely related to antiviral innate immunity. However, whether SARS-CoV-2 regulates the stress response pathway to achieve immune evasion remains elusive. In this study, SARS-CoV-2 NSP5 and N protein were found to attenuate antiviral stress granule (avSG) formation. Moreover, NSP5 and N suppressed IFN expression induced by infection of Sendai virus or transfection of a synthetic mimic of dsRNA, poly (I:C), inhibiting TBK1 and IRF3 phosphorylation, and restraining the nuclear translocalization of IRF3. Furthermore, HEK293T cells with ectopic expression of NSP5 or N protein were less resistant to vesicular stomatitis virus infection. Mechanistically, NSP5 suppressed avSG formation and disrupted RIG-I-MAVS complex to attenuate the RIG-I-mediated antiviral immunity. In contrast to the multiple targets of NSP5, the N protein specifically targeted cofactors upstream of RIG-I. The N protein interacted with G3BP1 to prevent avSG formation and to keep the cofactors G3BP1 and PACT from activating RIG-I. Additionally, the N protein also affected the recognition of dsRNA by RIG-I. This study revealed the intimate correlation between SARS-CoV-2, the stress response, and innate antiviral immunity, shedding light on the pathogenic mechanism of COVID-19.
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Affiliation(s)
- Yi Zheng
- Key Laboratory of Infection and Immunity of Shandong Province, Department of Immunology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China
| | - Jian Deng
- Key Laboratory for Experimental Teratology of Ministry of Education and Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China
| | - Lulu Han
- Key Laboratory of Infection and Immunity of Shandong Province, Department of Immunology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China
| | - Meng-Wei Zhuang
- Key Laboratory for Experimental Teratology of Ministry of Education and Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China
| | - Yanwen Xu
- Key Laboratory of Infection and Immunity of Shandong Province, Department of Immunology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China
| | - Jing Zhang
- Key Laboratory for Experimental Teratology of Ministry of Education and Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China
| | - Mei-Ling Nan
- Key Laboratory for Experimental Teratology of Ministry of Education and Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China
| | - Yang Xiao
- Key Laboratory for Experimental Teratology of Ministry of Education and Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012, Jinan, Shandong, PR China
- China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, 250012, Jinan, Shandong, PR China
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012, Jinan, Shandong, PR China
- China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, 250012, Jinan, Shandong, PR China
| | - Chengjiang Gao
- Key Laboratory of Infection and Immunity of Shandong Province, Department of Immunology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China.
| | - Pei-Hui Wang
- Key Laboratory for Experimental Teratology of Ministry of Education and Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China.
- Suzhou Research Institute, Shandong University, Shandong University, Suzhou, Jiangsu, 215123, China.
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Aune TM, Tossberg JT, Heinrich RM, Porter KP, Crooke PS. Alu RNA Structural Features Modulate Immune Cell Activation and A-to-I Editing of Alu RNAs Is Diminished in Human Inflammatory Bowel Disease. Front Immunol 2022; 13:818023. [PMID: 35126398 PMCID: PMC8813004 DOI: 10.3389/fimmu.2022.818023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 01/04/2022] [Indexed: 12/12/2022] Open
Abstract
Alu retrotransposons belong to the class of short interspersed nuclear elements (SINEs). Alu RNA is abundant in cells and its repetitive structure forms double-stranded RNAs (dsRNA) that activate dsRNA sensors and trigger innate immune responses with significant pathological consequences. Mechanisms to prevent innate immune activation include deamination of adenosines to inosines in dsRNAs, referred to as A-to-I editing, degradation of Alu RNAs by endoribonucleases, and sequestration of Alu RNAs by RNA binding proteins. We have previously demonstrated that widespread loss of Alu RNA A-to-I editing is associated with diverse human diseases including viral (COVID-19, influenza) and autoimmune diseases (multiple sclerosis). Here we demonstrate loss of A-to-I editing in leukocytes is also associated with inflammatory bowel diseases. Our structure-function analysis demonstrates that ability to activate innate immune responses resides in the left arm of Alu RNA, requires a 5’-PPP, RIG-I is the major Alu dsRNA sensor, and A-to-I editing disrupts both structure and function. Further, edited Alu RNAs inhibit activity of unedited Alu RNAs. Altering Alu RNA nucleotide sequence increases biological activity. Two classes of Alu RNAs exist, one class stimulates both IRF and NF-kB transcriptional activity and a second class only stimulates IRF transcriptional activity. Thus, Alu RNAs play important roles in human disease but may also have therapeutic potential.
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Affiliation(s)
- Thomas M. Aune
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, United States
- *Correspondence: Thomas M. Aune,
| | - John T. Tossberg
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Rachel M. Heinrich
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Krislyn P. Porter
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Philip S. Crooke
- Department of Mathematics, Vanderbilt University, Nashville, TN, United States
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7
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Bar Yaacov D. Functional analysis of ADARs in planarians supports a bilaterian ancestral role in suppressing double-stranded RNA-response. PLoS Pathog 2022; 18:e1010250. [PMID: 35041722 PMCID: PMC8797187 DOI: 10.1371/journal.ppat.1010250] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 01/28/2022] [Accepted: 01/06/2022] [Indexed: 11/18/2022] Open
Abstract
ADARs (adenosine deaminases acting on RNA) are known for their adenosine-to-inosine RNA editing activity, and most recently, for their role in preventing aberrant dsRNA-response by activation of dsRNA sensors (i.e., RIG-I-like receptor homologs). However, it is still unclear whether suppressing spurious dsRNA-response represents the ancestral role of ADARs in bilaterians. As a first step to address this question, we identified ADAR1 and ADAR2 homologs in the planarian Schmidtea mediterranea, which is evolutionarily distant from canonical lab models (e.g., flies and nematodes). Our results indicate that knockdown of either planarian adar1 or adar2 by RNA interference (RNAi) resulted in upregulation of dsRNA-response genes, including three planarian rig-I-like receptor (prlr) homologs. Furthermore, independent knockdown of adar1 and adar2 reduced the number of infected cells with a dsRNA virus, suggesting they suppress a bona fide anti-viral dsRNA-response activity. Knockdown of adar1 also resulted in lesion formation and animal lethality, thus attesting to its essentiality. Simultaneous knockdown of adar1 and prlr1 rescued adar1(RNAi)-dependent animal lethality and rescued the dsRNA-response, suggesting that it contributes to the deleterious effect of adar1 knockdown. Finally, we found that ADAR2, but not ADAR1, mediates mRNA editing in planarians, suggesting at least in part non-redundant activities for planarians ADARs. Our results underline the essential role of ADARs in suppressing activation of harmful dsRNA-response in planarians, thus supporting it as their ancestral role in bilaterians. Our work also set the stage to study further and better understand the regulatory mechanisms governing anti-viral dsRNA-responses from an evolutionary standpoint using planarians as a model. Today, more than ever, it is crucial to gain a deep understating of our anti-viral defenses. One of the ways to accomplish it is to study the principles governing anti-viral responses across various organisms. ADARs are a group of proteins that act on RNA molecules and alter their sequence compared to the genes that encode them (a process termed RNA editing). In recent years, ADARs have been shown to suppress abnormal anti-viral responses triggered by self-components of the cell (RNA encoded by the cell). Here, we show that the involvement of ADARs in anti-viral response regulation is conserved in planarians (free-living flatworms). We identified two ADAR proteins in planarians and showed that eliminating one (ADAR1) results in animal death and that an anti-viral response commenced in the absence of either ADAR1 or ADAR2. We further identified one of the proteins (PRLR1) that participate in initiating this anti-viral response in planarians, which its mammalian homolog (MDA5) serves a similar role. Thus, our work suggests that ADARs involvement in suppressing aberrant anti-viral response is an ancient evolutionary invention and is likely shared across multicellular organisms with bilateral symmetry.
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Affiliation(s)
- Dan Bar Yaacov
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- * E-mail:
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8
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Abstract
ADAR1-mediated deamination of adenosines in long double-stranded RNAs plays an important role in modulating the innate immune response. However, recent investigations based on metatranscriptomic samples of COVID-19 patients and SARS-COV-2-infected Vero cells have recovered contrasting findings. Using RNAseq data from time course experiments of infected human cell lines and transcriptome data from Vero cells and clinical samples, we prove that A-to-G changes observed in SARS-COV-2 genomes represent genuine RNA editing events, likely mediated by ADAR1. While the A-to-I editing rate is generally low, changes are distributed along the entire viral genome, are overrepresented in exonic regions, and are (in the majority of cases) nonsynonymous. The impact of RNA editing on virus-host interactions could be relevant to identify potential targets for therapeutic interventions.
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MESH Headings
- Adenosine/metabolism
- Adenosine Deaminase/genetics
- Adenosine Deaminase/immunology
- Animals
- COVID-19/genetics
- COVID-19/metabolism
- COVID-19/virology
- Cell Line, Tumor
- Chlorocebus aethiops
- DEAD Box Protein 58/genetics
- DEAD Box Protein 58/immunology
- Deamination
- Epithelial Cells/immunology
- Epithelial Cells/virology
- Genome, Viral
- Host-Pathogen Interactions/genetics
- Host-Pathogen Interactions/immunology
- Humans
- Immunity, Innate
- Inosine/metabolism
- Interferon-Induced Helicase, IFIH1/genetics
- Interferon-Induced Helicase, IFIH1/immunology
- Interferon-beta/genetics
- Interferon-beta/immunology
- RNA Editing
- RNA, Double-Stranded/genetics
- RNA, Double-Stranded/immunology
- RNA, Viral/genetics
- RNA, Viral/immunology
- RNA-Binding Proteins/genetics
- RNA-Binding Proteins/immunology
- Receptors, Immunologic/genetics
- Receptors, Immunologic/immunology
- SARS-CoV-2/genetics
- SARS-CoV-2/metabolism
- SARS-CoV-2/pathogenicity
- Transcriptome
- Vero Cells
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Affiliation(s)
- Ernesto Picardi
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari “Aldo Moro”, Via Orabona 4, 70125 Bari, Italy; (L.M.); (G.P.)
- Institute of Biomembranes and Bioenergetics, National Research Council, Via Amendola 122/O, 70126 Bari, Italy
- Consorzio Interuniversitario Biotecnologie (CIB), 34012 Trieste, Italy
| | - Luigi Mansi
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari “Aldo Moro”, Via Orabona 4, 70125 Bari, Italy; (L.M.); (G.P.)
| | - Graziano Pesole
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari “Aldo Moro”, Via Orabona 4, 70125 Bari, Italy; (L.M.); (G.P.)
- Institute of Biomembranes and Bioenergetics, National Research Council, Via Amendola 122/O, 70126 Bari, Italy
- Consorzio Interuniversitario Biotecnologie (CIB), 34012 Trieste, Italy
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9
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Wayment-Steele HK, Kim DS, Choe CA, Nicol JJ, Wellington-Oguri R, Watkins AM, Parra Sperberg RA, Huang PS, Participants E, Das R. Theoretical basis for stabilizing messenger RNA through secondary structure design. Nucleic Acids Res 2021; 49:10604-10617. [PMID: 34520542 PMCID: PMC8499941 DOI: 10.1093/nar/gkab764] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 08/17/2021] [Accepted: 08/27/2021] [Indexed: 01/08/2023] Open
Abstract
RNA hydrolysis presents problems in manufacturing, long-term storage, world-wide delivery and in vivo stability of messenger RNA (mRNA)-based vaccines and therapeutics. A largely unexplored strategy to reduce mRNA hydrolysis is to redesign RNAs to form double-stranded regions, which are protected from in-line cleavage and enzymatic degradation, while coding for the same proteins. The amount of stabilization that this strategy can deliver and the most effective algorithmic approach to achieve stabilization remain poorly understood. Here, we present simple calculations for estimating RNA stability against hydrolysis, and a model that links the average unpaired probability of an mRNA, or AUP, to its overall hydrolysis rate. To characterize the stabilization achievable through structure design, we compare AUP optimization by conventional mRNA design methods to results from more computationally sophisticated algorithms and crowdsourcing through the OpenVaccine challenge on the Eterna platform. We find that rational design on Eterna and the more sophisticated algorithms lead to constructs with low AUP, which we term 'superfolder' mRNAs. These designs exhibit a wide diversity of sequence and structure features that may be desirable for translation, biophysical size, and immunogenicity. Furthermore, their folding is robust to temperature, computer modeling method, choice of flanking untranslated regions, and changes in target protein sequence, as illustrated by rapid redesign of superfolder mRNAs for B.1.351, P.1 and B.1.1.7 variants of the prefusion-stabilized SARS-CoV-2 spike protein. Increases in in vitro mRNA half-life by at least two-fold appear immediately achievable.
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MESH Headings
- Algorithms
- Base Pairing
- Base Sequence
- COVID-19/prevention & control
- Humans
- Hydrolysis
- RNA Stability
- RNA, Double-Stranded/chemistry
- RNA, Double-Stranded/genetics
- RNA, Double-Stranded/immunology
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- RNA, Messenger/immunology
- RNA, Viral/chemistry
- RNA, Viral/genetics
- RNA, Viral/immunology
- SARS-CoV-2/genetics
- SARS-CoV-2/immunology
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
- Thermodynamics
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Affiliation(s)
- Hannah K Wayment-Steele
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
- Eterna Massive Open Laboratory
| | - Do Soon Kim
- Eterna Massive Open Laboratory
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - Christian A Choe
- Eterna Massive Open Laboratory
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | | | | | - Andrew M Watkins
- Eterna Massive Open Laboratory
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | | | - Po-Ssu Huang
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | | | - Rhiju Das
- Eterna Massive Open Laboratory
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
- Department of Physics, Stanford University, Stanford, CA 94305, USA
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10
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Dunker W, Ye X, Zhao Y, Liu L, Richardson A, Karijolich J. TDP-43 prevents endogenous RNAs from triggering a lethal RIG-I-dependent interferon response. Cell Rep 2021; 35:108976. [PMID: 33852834 PMCID: PMC8109599 DOI: 10.1016/j.celrep.2021.108976] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 02/01/2021] [Accepted: 03/19/2021] [Indexed: 12/16/2022] Open
Abstract
RIG-I-like receptors (RLRs) are involved in the discrimination of self versus non-self via the recognition of double-stranded RNA (dsRNA). Emerging evidence suggests that immunostimulatory dsRNAs are ubiquitously expressed but are disrupted or sequestered by cellular RNA binding proteins (RBPs). TDP-43 is an RBP associated with multiple neurological disorders and is essential for cell viability. Here, we demonstrate that TDP-43 regulates the accumulation of immunostimulatory dsRNA. The immunostimulatory RNA is identified as RNA polymerase III transcripts, including 7SL and Alu retrotransposons, and we demonstrate that the RNA-binding activity of TDP-43 is required to prevent immune stimulation. The dsRNAs activate a RIG-I-dependent interferon (IFN) response, which promotes necroptosis. Genetic inactivation of the RLR-pathway rescues the interferon-mediated cell death associated with loss of TDP-43. Collectively, our study describes a role for TDP-43 in preventing the accumulation of endogenous immunostimulatory dsRNAs and uncovers an intricate relationship between the control of cellular gene expression and IFN-mediated cell death.
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MESH Headings
- Adaptor Proteins, Signal Transducing/genetics
- Adaptor Proteins, Signal Transducing/immunology
- Alu Elements
- Cell Line, Tumor
- Cell Survival
- Cytokines/genetics
- Cytokines/immunology
- DEAD Box Protein 58/antagonists & inhibitors
- DEAD Box Protein 58/genetics
- DEAD Box Protein 58/immunology
- DNA-Binding Proteins/deficiency
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/immunology
- Epithelial Cells/immunology
- Epithelial Cells/virology
- Gene Expression Regulation
- HEK293 Cells
- Herpesvirus 8, Human/genetics
- Herpesvirus 8, Human/growth & development
- Herpesvirus 8, Human/immunology
- Humans
- Immunization
- Interferons/genetics
- Interferons/immunology
- Interleukin-6/genetics
- Interleukin-6/immunology
- Necroptosis/genetics
- Necroptosis/immunology
- Neurons/immunology
- Neurons/virology
- RNA Polymerase III/genetics
- RNA Polymerase III/immunology
- RNA, Double-Stranded/genetics
- RNA, Double-Stranded/immunology
- RNA, Messenger/genetics
- RNA, Messenger/immunology
- RNA, Small Cytoplasmic/genetics
- RNA, Small Cytoplasmic/immunology
- RNA, Viral/genetics
- RNA, Viral/immunology
- RNA-Binding Proteins/genetics
- RNA-Binding Proteins/immunology
- Receptors, Immunologic/antagonists & inhibitors
- Receptors, Immunologic/genetics
- Receptors, Immunologic/immunology
- Signal Recognition Particle/genetics
- Signal Recognition Particle/immunology
- Signal Transduction
- Tumor Necrosis Factor-alpha/genetics
- Tumor Necrosis Factor-alpha/immunology
- Ubiquitins/genetics
- Ubiquitins/immunology
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Affiliation(s)
- William Dunker
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232-2363, USA
| | - Xiang Ye
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232-2363, USA
| | - Yang Zhao
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232-2363, USA
| | - Lanxi Liu
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232-2363, USA
| | - Antiana Richardson
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232-2363, USA
| | - John Karijolich
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232-2363, USA; Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232-2363, USA; Vanderbilt-Ingram Cancer Center, Nashville, TN 37232-2363, USA; Vanderbilt Institute for Infection, Immunology and Inflammation, Nashville, TN 37232-2363, USA; Vanderbilt Center for Immunobiology, Nashville, TN 37232-2363, USA.
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11
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Lv X, Wang W, Zhao Q, Qiao X, Wang L, Yan Y, Han S, Liu Z, Wang L, Song L. A truncated intracellular Dicer-like molecule involves in antiviral immune recognition of oyster Crassostrea gigas. Dev Comp Immunol 2021; 116:103931. [PMID: 33220355 DOI: 10.1016/j.dci.2020.103931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 11/13/2020] [Accepted: 11/13/2020] [Indexed: 06/11/2023]
Abstract
The enzyme Dicer is best known for its role as an endoribonuclease in the small RNA pathway, playing a crucial role in recognizing viral double-stranded RNA (dsRNA) and inducing down-stream cascades to mediate anti-virus immunity. In the present study, a truncated Dicer-like gene was identified from oyster Crassostrea gigas, and its open reading frame (ORF) encoded a polypeptide (designed as CgDCL) of 530 amino acids. The CgDCL contained one N-terminal DEAD domain and a C-terminal helicase domain, but lack the conserved PAZ domain, ribonuclease domain (RIBOc) and dsRNA binding domain. The mRNA transcripts of CgDCL were detected in all the examined tissues with high expression levels in lip, gills and haemocytes, which were 62.06-fold, 48.91-fold and 47.13-fold (p < 0.05) of that in mantle, respectively. In the primarily cultured oyster haemocytes, the mRNA transcripts of CgDCL were significantly induced at 12 h after poly(I:C) stimulation, which were 4.04-fold (p < 0.05) of that in control group. The expression level of CgDCL mRNA in haemocytes was up-regulated significantly after dsRNA and recombinant interferon-like protein (rCgIFNLP) injection, which was 12.87-fold (p < 0.01) and 3.22-fold (p < 0.05) of that in control group, respectively. CgDCL proteins were mainly distributed in the cytoplasm of haemocytes. The recombinant CgDCL protein displayed binding activity to dsRNA and poly(I:C), but no obvious dsRNA cleavage activity. These results collectively suggest that truncated CgDCL from C. gigas was able to be activated by poly(I:C), dsRNA and CgIFNLP, and functioned as an intracellular recognition molecule to bind nucleic acid of virus, indicating a potential mutual cooperation between RNAi and IFN-like system in anti-virus immunity of oysters.
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Affiliation(s)
- Xiaojing Lv
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Laboratory of Marine Fisheries Science and Food Production Process, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China
| | - Weilin Wang
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Laboratory of Marine Fisheries Science and Food Production Process, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China
| | - Qi Zhao
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Laboratory of Marine Fisheries Science and Food Production Process, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China
| | - Xue Qiao
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Laboratory of Marine Fisheries Science and Food Production Process, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China
| | - Liyan Wang
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Laboratory of Marine Fisheries Science and Food Production Process, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China
| | - Yunchen Yan
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Laboratory of Marine Fisheries Science and Food Production Process, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China
| | - Shuo Han
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Laboratory of Marine Fisheries Science and Food Production Process, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China
| | - Zhaoqun Liu
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Laboratory of Marine Fisheries Science and Food Production Process, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China
| | - Lingling Wang
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Laboratory of Marine Fisheries Science and Food Production Process, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China.
| | - Linsheng Song
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Southern Laboratory of Ocean Science and Engineering (Guangdong,Zhuhai), Zhuhai, 519000, China; Laboratory of Marine Fisheries Science and Food Production Process, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China.
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12
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Sun B, Zeng H, Liang J, Zhang L, Hu H, Wang Q, Meng W, Li C, Ye F, Wang C, Zhu J. NSUN5 Facilitates Viral RNA Recognition by RIG-I Receptor. J Immunol 2020; 205:3408-3418. [PMID: 33177158 DOI: 10.4049/jimmunol.1901455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 10/14/2020] [Indexed: 11/19/2022]
Abstract
The RIG-I receptor induces the innate antiviral responses upon sensing RNA viruses. The mechanisms through which RIG-I optimizes the strength of the downstream signaling remain incompletely understood. In this study, we identified that NSUN5 could potentiate the RIG-I innate signaling pathway. Deficiency of NSUN5 enhanced RNA virus proliferation and inhibited the induction of the downstream antiviral genes. Consistently, NSUN5-deficient mice were more susceptible to RNA virus infection than their wild-type littermates. Mechanistically, NSUN5 bound directly to both viral RNA and RIG-I, synergizing the recognition of dsRNA by RIG-I. Collectively, to our knowledge, this study characterized NSUN5 as a novel RIG-I coreceptor, playing a vital role in restricting RNA virus infection.
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Affiliation(s)
- Boyue Sun
- State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing 211198, China
| | - Haoyang Zeng
- State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing 211198, China
| | - Jiaqian Liang
- State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing 211198, China
| | - Lele Zhang
- Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China; and
| | - Haiyang Hu
- State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing 211198, China
| | - Quanyi Wang
- State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing 211198, China
| | - Wei Meng
- State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing 211198, China
| | - Chenhui Li
- State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing 211198, China
| | - Fuqiang Ye
- Department of Disease Control and Prevention, Center for Disease Control and Prevention of Eastern Theater Command, Nanjing 210002, China
| | - Chen Wang
- State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing 211198, China;
| | - Juanjuan Zhu
- State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing 211198, China;
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13
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Tossberg JT, Heinrich RM, Farley VM, Crooke PS, Aune TM. Adenosine-to-Inosine RNA Editing of Alu Double-Stranded (ds)RNAs Is Markedly Decreased in Multiple Sclerosis and Unedited Alu dsRNAs Are Potent Activators of Proinflammatory Transcriptional Responses. J Immunol 2020; 205:2606-2617. [PMID: 33046502 PMCID: PMC7872017 DOI: 10.4049/jimmunol.2000384] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 09/14/2020] [Indexed: 12/27/2022]
Abstract
Sensors that detect dsRNA stimulate IFN responses as a defense against viral infection. IFN responses are also well documented in a variety of human autoimmune diseases, including relapsing-remitting multiple sclerosis (MS), in which increased IFN responses result from increased levels of double-stranded endogenous Alu RNAs. Mechanisms underlying increases in double-stranded Alu RNAs in MS are obscure. We find widespread loss of adenosine-to-inosine editing of Alu RNAs in MS. Unedited Alu RNAs are potent activators of both IFN and NF-κB responses via the dsRNA sensors, RIG-I, and TLR3. Minor editing of highly active Alu elements abrogates the ability to activate both transcriptional responses. Thus, adenosine-to-inosine editing may also represent an important defense against autoimmune diseases such as MS.
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Affiliation(s)
- John T Tossberg
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37212
| | - Rachel M Heinrich
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37212
| | - Virginia M Farley
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37212
| | - Philip S Crooke
- Department of Mathematics, Vanderbilt University, Nashville, TN 37212; and
| | - Thomas M Aune
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37212;
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37212
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14
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Salka K, Arroyo M, Chorvinsky E, Abutaleb K, Perez GF, Wolf S, Xuchen X, Weinstock J, Gutierrez MJ, Pérez-Losada M, Pillai DK, Nino G. Innate IFN-lambda responses to dsRNA in the human infant airway epithelium and clinical regulatory factors during viral respiratory infections in early life. Clin Exp Allergy 2020; 50:1044-1054. [PMID: 32623773 PMCID: PMC7484417 DOI: 10.1111/cea.13701] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 06/11/2020] [Accepted: 06/17/2020] [Indexed: 01/11/2023]
Abstract
INTRODUCTION IFN lambda (type III-IFN-λ1) is a molecule primarily produced by epithelial cells that provides an important first-line defence against viral respiratory infections and has been linked to the pathogenesis of viral-induced wheezing in early life. The goal of this study was to better understand the regulation of innate IFN-lambda responses in vitro in primary human infant airway epithelial cells (AECs) and in vivo using nasal aspirates during viral respiratory infections. METHODS IFN-lambda protein levels were quantified: (a) in human infant AECs exposed to (poly(I:C) dsRNA) under different experimental conditions (n = 8 donors); and (b) in nasal aspirates of young children (≤3 years) hospitalized with viral respiratory infection (n = 138) and in uninfected controls (n = 74). In vivo IFN-lambda airway levels during viral infections were correlated with individual characteristics and respiratory disease parameters. RESULTS Our in vitro experiments showed that the poly(I:C)-induced innate production of IFN lambda in human infant AECs is regulated by (a) p38-MAPK/NF-kB dependent mechanism; and (b) exposure to pro-inflammatory signals such as IL1β. Our in vivo studies demonstrated that (a) infants (<18 months) had higher virus-induced IFN-lambda airway secretion; (b) subjects with RSV infection showed the highest IFN-lambda airway levels; and (c) individuals with the highest virus-induced IFN-lambda levels (>90th percentile) had higher viral loads and were more likely to have respiratory sick visits within 12 months of discharge (OR = 5.8). CONCLUSION IFN-lambda responses to dsRNA in the human infant airway epithelium are regulated by p38-MAPK and NF-kB signalling. High in vivo IFN-lambda production is influenced by virus type and associated with recurrent respiratory sick visits in young children.
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Affiliation(s)
- Kyle Salka
- Division of Pediatric Pulmonary and Sleep Medicine. Children’s National Medical Center, George Washington University, Washington, D.C, USA
| | - Maria Arroyo
- Division of Pediatric Pulmonary and Sleep Medicine. Children’s National Medical Center, George Washington University, Washington, D.C, USA
| | - Elizabeth Chorvinsky
- Division of Pediatric Pulmonary and Sleep Medicine. Children’s National Medical Center, George Washington University, Washington, D.C, USA
| | - Karima Abutaleb
- Division of Pediatric Pulmonary and Sleep Medicine. Children’s National Medical Center, George Washington University, Washington, D.C, USA
| | - Geovanny F. Perez
- Division of Pediatric Pulmonary and Sleep Medicine. Children’s National Medical Center, George Washington University, Washington, D.C, USA
| | - Seth Wolf
- Division of Pediatric Pulmonary and Sleep Medicine. Children’s National Medical Center, George Washington University, Washington, D.C, USA
| | - Xilei Xuchen
- Division of Pediatric Pulmonary and Sleep Medicine. Children’s National Medical Center, George Washington University, Washington, D.C, USA
| | - Jered Weinstock
- Division of Pediatric Pulmonary and Sleep Medicine. Children’s National Medical Center, George Washington University, Washington, D.C, USA
| | - Maria J. Gutierrez
- Division of Pediatric Allergy and Immunology, Johns Hopkins University, Baltimore, MD
| | - Marcos Pérez-Losada
- Computational Biology Institute, Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, George Washington University, Washington, DC, 20052, USA
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal
| | - Dinesh K. Pillai
- Division of Pediatric Pulmonary and Sleep Medicine. Children’s National Medical Center, George Washington University, Washington, D.C, USA
| | - Gustavo Nino
- Division of Pediatric Pulmonary and Sleep Medicine. Children’s National Medical Center, George Washington University, Washington, D.C, USA
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15
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Gstalder C, Liu D, Miao D, Lutterbach B, DeVine AL, Lin C, Shettigar M, Pancholi P, Buchbinder EI, Carter SL, Manos MP, Rojas-Rudilla V, Brennick R, Gjini E, Chen PH, Lako A, Rodig S, Yoon CH, Freeman GJ, Barbie DA, Hodi FS, Miles W, Van Allen EM, Haq R. Inactivation of Fbxw7 Impairs dsRNA Sensing and Confers Resistance to PD-1 Blockade. Cancer Discov 2020; 10:1296-1311. [PMID: 32371478 PMCID: PMC8802534 DOI: 10.1158/2159-8290.cd-19-1416] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 04/04/2020] [Accepted: 04/30/2020] [Indexed: 11/16/2022]
Abstract
The molecular mechanisms leading to resistance to PD-1 blockade are largely unknown. Here, we characterize tumor biopsies from a patient with melanoma who displayed heterogeneous responses to anti-PD-1 therapy. We observe that a resistant tumor exhibited a loss-of-function mutation in the tumor suppressor gene FBXW7, whereas a sensitive tumor from the same patient did not. Consistent with a functional role in immunotherapy response, inactivation of Fbxw7 in murine tumor cell lines caused resistance to anti-PD-1 in immunocompetent animals. Loss of Fbxw7 was associated with altered immune microenvironment, decreased tumor-intrinsic expression of the double-stranded RNA (dsRNA) sensors MDA5 and RIG1, and diminished induction of type I IFN and MHC-I expression. In contrast, restoration of dsRNA sensing in Fbxw7-deficient cells was sufficient to sensitize them to anti-PD-1. Our results thus establish a new role for the commonly inactivated tumor suppressor FBXW7 in viral sensing and sensitivity to immunotherapy. SIGNIFICANCE: Our findings establish a role of the commonly inactivated tumor suppressor FBXW7 as a genomic driver of response to anti-PD-1 therapy. Fbxw7 loss promotes resistance to anti-PD-1 through the downregulation of viral sensing pathways, suggesting that therapeutic reactivation of these pathways could improve clinical responses to checkpoint inhibitors in genomically defined cancer patient populations.This article is highlighted in the In This Issue feature, p. 1241.
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MESH Headings
- Aged
- Animals
- Antibodies, Monoclonal, Humanized/pharmacology
- Antibodies, Monoclonal, Humanized/therapeutic use
- Cell Line, Tumor/transplantation
- DEAD Box Protein 58/genetics
- DEAD Box Protein 58/metabolism
- Disease Models, Animal
- Drug Resistance, Neoplasm/genetics
- F-Box-WD Repeat-Containing Protein 7/genetics
- F-Box-WD Repeat-Containing Protein 7/metabolism
- Gene Expression Regulation, Neoplastic/immunology
- HeLa Cells
- Humans
- Immune Checkpoint Inhibitors/pharmacology
- Immune Checkpoint Inhibitors/therapeutic use
- Interferon-Induced Helicase, IFIH1/genetics
- Interferon-Induced Helicase, IFIH1/metabolism
- Loss of Function Mutation
- Male
- Mice
- Mutagenesis, Site-Directed
- Programmed Cell Death 1 Receptor/antagonists & inhibitors
- RNA, Double-Stranded/immunology
- RNA, Double-Stranded/metabolism
- Receptors, Immunologic/genetics
- Receptors, Immunologic/metabolism
- Skin Neoplasms/drug therapy
- Skin Neoplasms/genetics
- Skin Neoplasms/immunology
- Skin Neoplasms/pathology
- Tumor Microenvironment/genetics
- Tumor Microenvironment/immunology
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Affiliation(s)
- Cécile Gstalder
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
- Division of Molecular and Cellular Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - David Liu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
- Division of Population Sciences, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Diana Miao
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Bart Lutterbach
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
- Division of Molecular and Cellular Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Alexander L DeVine
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
- Division of Molecular and Cellular Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Chenyu Lin
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio
| | - Megha Shettigar
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
- Division of Molecular and Cellular Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Priya Pancholi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
- Division of Molecular and Cellular Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Elizabeth I Buchbinder
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Scott L Carter
- Department of Data Sciences, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
- Division of Computational Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Michael P Manos
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Vanesa Rojas-Rudilla
- Department of CAMD Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Ryan Brennick
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Evisa Gjini
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Pei-Hsuan Chen
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Ana Lako
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Scott Rodig
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Charles H Yoon
- Department of Surgery, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Gordon J Freeman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - David A Barbie
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - F Stephen Hodi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Wayne Miles
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio
| | - Eliezer M Van Allen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Rizwan Haq
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.
- Division of Molecular and Cellular Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
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16
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Abstract
Double-stranded RNA (dsRNA) is a common pattern formed during the replication of both RNA and DNA viruses. Perception of virus-derived dsRNAs by specialized receptor molecules leads to the activation of various antiviral measures. In plants, these defensive processes include the adaptive RNA interference (RNAi) pathway and innate pattern-triggered immune (PTI) responses. While details of the former process have been well established in recent years, the latter are still only partially understood at the molecular level. Nonetheless, emerging data suggest extensive cross talk between the different antiviral mechanisms. Here, we demonstrate that dsRNA-binding protein 2 (DRB2) of Nicotiana benthamiana plays a direct role in potato virus X (PVX)-elicited systemic necrosis. These results establish that DRB2, a known component of RNAi, is also involved in a virus-induced PTI response. In addition, our findings suggest that RNA-dependent polymerase 6 (RDR6)-dependent dsRNAs play an important role in the triggering of PVX-induced systemic necrosis. Based on our data, a model is formulated whereby competition between different DRB proteins for virus-derived dsRNAs helps establish the dominant antiviral pathways that are activated in response to virus infection.IMPORTANCE Plants employ multiple defense mechanisms to restrict viral infections, among which RNA interference is the best understood. The activation of innate immunity often leads to both local and systemic necrotic responses, which confine the virus to the infected cells and can also provide resistance to distal, noninfected parts of the organism. Systemic necrosis, which is regarded as a special form of the local hypersensitive response, results in necrosis of the apical stem region, usually causing the death of the plant. Here, we provide evidence that the dsRNA-binding protein 2 of Nicotiana benthamiana plays an important role in virus-induced systemic necrosis. Our findings are not only compatible with the recent hypothesis that DRB proteins act as viral invasion sensors but also extends it by proposing that DRBs play a critical role in establishing the dominant antiviral measures that are triggered during virus infection.
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Affiliation(s)
- Károly Fátyol
- Agricultural Biotechnology Institute, National Agricultural Research and Innovation, Gödöllő, Hungary
| | - Katalin Anna Fekete
- Agricultural Biotechnology Institute, National Agricultural Research and Innovation, Gödöllő, Hungary
| | - Márta Ludman
- Agricultural Biotechnology Institute, National Agricultural Research and Innovation, Gödöllő, Hungary
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17
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Li CS, Kausar S, Gul I, Yao XX, Li MY, Chen CC, Abbas MN, Dai LS. Heat shock protein 20 from Procambarus clarkii is involved in the innate immune responses against microbial infection. Dev Comp Immunol 2020; 106:103638. [PMID: 32017956 DOI: 10.1016/j.dci.2020.103638] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 01/31/2020] [Accepted: 01/31/2020] [Indexed: 06/10/2023]
Abstract
Small heat shock proteins (shsps) are conserved across invertebrate species. They are implicated in the modulation of various biological processes, such as immune responses, abiotic stress tolerance metamorphosis, and embryonic development. Herein, we identified a heat shock protein 20 from the red swamp crayfish, Procambarus clarkii (named as Pc-Hsp20), and performed in vivo studies to elucidate its physiological functions in the innate immunity. The open reading frame of Pc-Hsp20 was 609 base pair, encoding a protein of 202 amino acid residues with a hsp20/alpha crystallin family domain. Pc-Hsp20 was ubiquitously expressed in various tissues; however, it was highest in the hepatopancreas. The challenge with immune elicitors remarkably enhanced the transcript level of Pc-Hsp20 in the hepatopancreas when compared with the control. Administration of double-stranded RNA could significantly reduce expression of the Pc-Hsp20 mRNAs, and most of the immune-related genes expression enhanced with a variable concentration in the hepatopancreas. Altogether, these results suggest that Pc-Hsp20 may participate in innate immunity against microbial pathogens.
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Affiliation(s)
- Chang-Sheng Li
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, 325035, PR China; School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, 325035, PR China
| | - Saima Kausar
- State Key Laboratory of Silkworm Genome Biology, College of Biotechnology, Southwest University, Chongqing, 400715, PR China; Department of Zoology and Fisheries, University of Agriculture, Faisalabad, 38000, Pakistan
| | - Isma Gul
- State Key Laboratory of Silkworm Genome Biology, College of Biotechnology, Southwest University, Chongqing, 400715, PR China; Department of Zoology and Fisheries, University of Agriculture, Faisalabad, 38000, Pakistan
| | - Xiao-Xiao Yao
- School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, 325035, PR China
| | - Meng-Yi Li
- School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, 325035, PR China
| | - Cheng-Chun Chen
- School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, 325035, PR China.
| | - Muhammad Nadeem Abbas
- State Key Laboratory of Silkworm Genome Biology, College of Biotechnology, Southwest University, Chongqing, 400715, PR China; Department of Zoology and Fisheries, University of Agriculture, Faisalabad, 38000, Pakistan.
| | - Li-Shang Dai
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, 325035, PR China.
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18
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Mateer EJ, Maruyama J, Card GE, Paessler S, Huang C. Lassa Virus, but Not Highly Pathogenic New World Arenaviruses, Restricts Immunostimulatory Double-Stranded RNA Accumulation during Infection. J Virol 2020; 94:e02006-19. [PMID: 32051278 PMCID: PMC7163147 DOI: 10.1128/jvi.02006-19] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 02/09/2020] [Indexed: 12/14/2022] Open
Abstract
The arenaviruses Lassa virus (LASV), Junín virus (JUNV), and Machupo virus (MACV) can cause severe and fatal diseases in humans. Although these pathogens are closely related, the host immune responses to these virus infections differ remarkably, with direct implications for viral pathogenesis. LASV infection is immunosuppressive, with a very low-level interferon response. In contrast, JUNV and MACV infections stimulate a robust interferon (IFN) response in a retinoic acid-inducible gene I (RIG-I)-dependent manner and readily activate protein kinase R (PKR), a known host double-stranded RNA (dsRNA) sensor. In response to infection with RNA viruses, host nonself RNA sensors recognize virus-derived dsRNA as danger signals and initiate innate immune responses. Arenavirus nucleoproteins (NPs) contain a highly conserved exoribonuclease (ExoN) motif, through which LASV NP has been shown to degrade virus-derived immunostimulatory dsRNA in biochemical assays. In this study, we for the first time present evidence that LASV restricts dsRNA accumulation during infection. Although JUNV and MACV NPs also have the ExoN motif, dsRNA readily accumulated in infected cells and often colocalized with dsRNA sensors. Moreover, LASV coinfection diminished the accumulation of dsRNA and the IFN response in JUNV-infected cells. The disruption of LASV NP ExoN with a mutation led to dsRNA accumulation and impaired LASV replication in minigenome systems. Importantly, both LASV NP and RNA polymerase L protein were required to diminish the accumulation of dsRNA and the IFN response in JUNV infection. For the first time, we discovered a collaboration between LASV NP ExoN and L protein in limiting dsRNA accumulation. Our new findings provide mechanistic insights into the differential host innate immune responses to highly pathogenic arenavirus infections.IMPORTANCE Arenavirus NPs contain a highly conserved DEDDh ExoN motif, through which LASV NP degrades virus-derived, immunostimulatory dsRNA in biochemical assays to eliminate the danger signal and inhibit the innate immune response. Nevertheless, the function of NP ExoN in arenavirus infection remains to be defined. In this study, we discovered that LASV potently restricts dsRNA accumulation during infection and minigenome replication. In contrast, although the NPs of JUNV and MACV also harbor the ExoN motif, dsRNA readily formed during JUNV and MACV infections, accompanied by IFN and PKR responses. Interestingly, LASV NP alone was not sufficient to limit dsRNA accumulation. Instead, both LASV NP and L protein were required to restrict immunostimulatory dsRNA accumulation. Our findings provide novel and important insights into the mechanism for the distinct innate immune response to these highly pathogenic arenaviruses and open new directions for future studies.
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Affiliation(s)
- Elizabeth J Mateer
- Department of Pathology, Galveston National Laboratory and Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, Texas, USA
| | - Junki Maruyama
- Department of Pathology, Galveston National Laboratory and Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, Texas, USA
| | - Galen E Card
- Department of Pathology, Galveston National Laboratory and Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, Texas, USA
| | - Slobodan Paessler
- Department of Pathology, Galveston National Laboratory and Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, Texas, USA
| | - Cheng Huang
- Department of Pathology, Galveston National Laboratory and Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, Texas, USA
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19
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Wiatrek DM, Candela ME, Sedmík J, Oppelt J, Keegan LP, O'Connell MA. Activation of innate immunity by mitochondrial dsRNA in mouse cells lacking p53 protein. RNA 2019; 25:713-726. [PMID: 30894411 PMCID: PMC6521600 DOI: 10.1261/rna.069625.118] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 03/16/2019] [Indexed: 05/27/2023]
Abstract
Viral and cellular double-stranded RNA (dsRNA) is recognized by cytosolic innate immune sensors, including RIG-I-like receptors. Some cytoplasmic dsRNA is commonly present in cells, and one source is mitochondrial dsRNA, which results from bidirectional transcription of mitochondrial DNA (mtDNA). Here we demonstrate that Trp53 mutant mouse embryonic fibroblasts contain immune-stimulating endogenous dsRNA of mitochondrial origin. We show that the immune response induced by this dsRNA is mediated via RIG-I-like receptors and leads to the expression of type I interferon and proinflammatory cytokine genes. The mitochondrial dsRNA is cleaved by RNase L, which cleaves all cellular RNA including mitochondrial mRNAs, increasing activation of RIG-I-like receptors. When mitochondrial transcription is interrupted there is a subsequent decrease in this immune-stimulatory dsRNA. Our results reveal that the role of p53 in innate immunity is even more versatile and complex than previously anticipated. Our study, therefore, sheds new light on the role of endogenous RNA in diseases featuring aberrant immune responses.
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MESH Headings
- Adaptor Proteins, Signal Transducing
- Adenosine Deaminase/deficiency
- Adenosine Deaminase/genetics
- Adenosine Deaminase/immunology
- Animals
- Carrier Proteins/genetics
- Carrier Proteins/immunology
- DEAD Box Protein 58/genetics
- DEAD Box Protein 58/immunology
- Embryo, Mammalian
- Endoribonucleases/genetics
- Endoribonucleases/immunology
- Fibroblasts/cytology
- Fibroblasts/immunology
- Immunity, Innate/genetics
- Interferon Regulatory Factor-7/genetics
- Interferon Regulatory Factor-7/immunology
- Interferon-Induced Helicase, IFIH1/genetics
- Interferon-Induced Helicase, IFIH1/immunology
- Intracellular Signaling Peptides and Proteins
- Mice
- Mice, Inbred C57BL
- Mice, Knockout
- Proteins/genetics
- Proteins/immunology
- RNA, Double-Stranded/genetics
- RNA, Double-Stranded/immunology
- RNA, Mitochondrial/genetics
- RNA, Mitochondrial/immunology
- RNA-Binding Proteins
- Transcription, Genetic
- Transfection
- Tumor Suppressor Protein p53/deficiency
- Tumor Suppressor Protein p53/genetics
- Tumor Suppressor Protein p53/immunology
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Affiliation(s)
| | | | - Jiří Sedmík
- CEITEC Masaryk University, 625 00 Brno, Czech Republic
| | - Jan Oppelt
- CEITEC Masaryk University, 625 00 Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
| | - Liam P Keegan
- CEITEC Masaryk University, 625 00 Brno, Czech Republic
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20
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Cadena C, Ahmad S, Xavier A, Willemsen J, Park S, Park JW, Oh SW, Fujita T, Hou F, Binder M, Hur S. Ubiquitin-Dependent and -Independent Roles of E3 Ligase RIPLET in Innate Immunity. Cell 2019; 177:1187-1200.e16. [PMID: 31006531 PMCID: PMC6525047 DOI: 10.1016/j.cell.2019.03.017] [Citation(s) in RCA: 119] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 01/28/2019] [Accepted: 03/07/2019] [Indexed: 01/22/2023]
Abstract
The conventional view posits that E3 ligases function primarily through conjugating ubiquitin (Ub) to their substrate molecules. We report here that RIPLET, an essential E3 ligase in antiviral immunity, promotes the antiviral signaling activity of the viral RNA receptor RIG-I through both Ub-dependent and -independent manners. RIPLET uses its dimeric structure and a bivalent binding mode to preferentially recognize and ubiquitinate RIG-I pre-oligomerized on dsRNA. In addition, RIPLET can cross-bridge RIG-I filaments on longer dsRNAs, inducing aggregate-like RIG-I assemblies. The consequent receptor clustering synergizes with the Ub-dependent mechanism to amplify RIG-I-mediated antiviral signaling in an RNA-length dependent manner. These observations show the unexpected role of an E3 ligase as a co-receptor that directly participates in receptor oligomerization and ligand discrimination. It also highlights a previously unrecognized mechanism by which the innate immune system measures foreign nucleic acid length, a common criterion for self versus non-self nucleic acid discrimination.
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Affiliation(s)
- Cristhian Cadena
- Program in Virology, Division of Medical Sciences, Harvard Medical School, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, MA 02115, USA
| | - Sadeem Ahmad
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, MA 02115, USA
| | - Audrey Xavier
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, MA 02115, USA; Institute of Chemistry and Biochemistry, Free University of Berlin, Germany
| | - Joschka Willemsen
- Research Group "Dynamics of Early Viral Infection and the Innate Antiviral Response" (division F170), German Cancer Research Center, 69120 Heidelberg, Germany
| | - Sehoon Park
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, MA 02115, USA
| | - Ji Woo Park
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, MA 02115, USA; Biology Department, Boston College, Chestnut Hill, MA, USA
| | - Seong-Wook Oh
- Laboratory of Molecular Genetics, Institute for Frontier Life and Medical Sciences, Kyoto University, Japan
| | - Takashi Fujita
- Laboratory of Molecular Genetics, Institute for Frontier Life and Medical Sciences, Kyoto University, Japan
| | - Fajian Hou
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, China
| | - Marco Binder
- Research Group "Dynamics of Early Viral Infection and the Innate Antiviral Response" (division F170), German Cancer Research Center, 69120 Heidelberg, Germany
| | - Sun Hur
- Program in Virology, Division of Medical Sciences, Harvard Medical School, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, MA 02115, USA.
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21
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Bou-Nader C, Gordon JM, Henderson FE, Zhang J. The search for a PKR code-differential regulation of protein kinase R activity by diverse RNA and protein regulators. RNA 2019; 25:539-556. [PMID: 30770398 PMCID: PMC6467004 DOI: 10.1261/rna.070169.118] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The interferon-inducible protein kinase R (PKR) is a key component of host innate immunity that restricts viral replication and propagation. As one of the four eIF2α kinases that sense diverse stresses and direct the integrated stress response (ISR) crucial for cell survival and proliferation, PKR's versatile roles extend well beyond antiviral defense. Targeted by numerous host and viral regulators made of RNA and proteins, PKR is subject to multiple layers of endogenous control and external manipulation, driving its rapid evolution. These versatile regulators include not only the canonical double-stranded RNA (dsRNA) that activates the kinase activity of PKR, but also highly structured viral, host, and artificial RNAs that exert a full spectrum of effects. In this review, we discuss our deepening understanding of the allosteric mechanism that connects the regulatory and effector domains of PKR, with an emphasis on diverse structured RNA regulators in comparison to their protein counterparts. Through this analysis, we conclude that much of the mechanistic details that underlie this RNA-regulated kinase await structural and functional elucidation, upon which we can then describe a "PKR code," a set of structural and chemical features of RNA that are both descriptive and predictive for their effects on PKR.
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Affiliation(s)
- Charles Bou-Nader
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland 20892, USA
| | - Jackson M Gordon
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland 20892, USA
| | - Frances E Henderson
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland 20892, USA
| | - Jinwei Zhang
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland 20892, USA
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22
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Vo NTK, Moore LC, Leis E, DeWitte-Orr SJ. Class A scavenger receptors mediate extracellular dsRNA sensing, leading to downstream antiviral gene expression in a novel American toad cell line, BufoTad. Dev Comp Immunol 2019; 92:140-149. [PMID: 30452932 DOI: 10.1016/j.dci.2018.11.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 11/15/2018] [Accepted: 11/15/2018] [Indexed: 06/09/2023]
Abstract
Viral double-stranded (ds)RNA is a potent pathogen-associated molecular pattern (PAMP), capable of inducing a strong antiviral state within the cell, protecting the cell from virus infection. In mammals and fish, sensing extracellular dsRNA is mediated by cell-surface class A scavenger receptors (SR-As). Currently, very little is known about SR-As in amphibians, including: sequence, expression patterns and function. To this end, SR-A expression and function was studied in a novel American toad (Anaxyrus americanus) tadpole cell line called BufoTad. BufoTad was derived from a whole tadpole. The cell line exhibits a cobblestone morphology and expresses abundant levels of transcripts for cytokeratin 19, vimentin, claudin 3, chemokine receptor CXCR4, and SR-AI, one of the five members of the SR-A family, collectively suggesting that BufoTad could be endothelial-like. BufoTad cells bound acetylated LDL, whereas the Xenopus laevis kidney epithelial A6 cell line did not, suggesting functional SR-A activity in BufoTad cells. Additionally, three SR-A competitive ligands (DxSO4, fucoidan, poly inosine (pI)) completely blocked AcLDL binding in BufoTad cells, whereas their three corresponding non-competitive ligands (ChSO4, fetuin, poly cytosine (pC)) did not. A commercial dsRNA, poly IC, induced robust expression of an Mx-like gene transcript, a possible antiviral protein in BufoTad cells. Employing the same SR-A ligand blocking assay used for AcLDL blocked dsRNA-induced ISG expression. This study is the first demonstration that amphibian SR-As have functional ligand binding activities in a live biological cellular model and that sensing extracellular dsRNA in amphibian cells leads to antiviral gene expression that is mediated by class A scavenger receptors.
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Affiliation(s)
- Nguyen T K Vo
- Department of Health Sciences, Wilfrid Laurier University, Waterloo, ON, Canada
| | - Levi C Moore
- Department of Health Sciences, Wilfrid Laurier University, Waterloo, ON, Canada
| | - Eric Leis
- La Crosse Fish Health Center, U.S. Fish and Wildlife Service, Midwest Fisheries Center, Onalaska, WI, USA
| | - Stephanie J DeWitte-Orr
- Department of Health Sciences, Wilfrid Laurier University, Waterloo, ON, Canada; Department of Biology, Wilfrid Laurier University, Waterloo, ON, Canada.
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23
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Mohapatra A, Parida S, Mohanty J, Sahoo PK. Identification and functional characterization of a g-type lysozyme gene of Labeo rohita, an Indian major carp species. Dev Comp Immunol 2019; 92:87-98. [PMID: 30439371 DOI: 10.1016/j.dci.2018.11.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 11/06/2018] [Accepted: 11/06/2018] [Indexed: 06/09/2023]
Abstract
Lysozyme, an important secretory innate immune component, possesses antimicrobial activity against broad spectrum of bacteria and viruses. In the present study, complete CDs (558 bps) of g-type lysozyme of rohu (Labeo rohita) was amplified and translated for a putative protein of 185 amino acids. The domain architecture and tertiary structure was also predicted for the protein. Its expression profile was studied in three infection models (bacteria: Aeromonas hydrophila, poly I:C, a dsRNA viral analogue and an ectoparasite: Argulus siamensis) in liver and kidney tissues of rohu. An up-regulation of 630-fold and 420-fold of the gene was observed at 48 h in liver and anterior kidney tissues respectively, after A. hydrophila infection. Significant increase in transcript level was noticed in both liver (0.8-fold) and kidney (480-fold) after 1 h and 12 h of poly I:C induction, respectively. Similarly, expression of lysozyme g transcripts was increased 6000-fold after 7 d of A. siamensis infection in liver tissue. The recombinant protein of g-type lysozyme of rohu (rLr-lysG) of 20.19 kDa was produced in Escherichia coli system and the lysozyme activity of rLr-lysG was found to be most active at pH 6.0 and temperature 35 °C. The potential lytic activity was found to be against A. hydrophila (UL = 0.53) followed by for E. tarda (UL = 0.45) whereas the lytic activity was the least against S. aureus (UL = 0.35) and M. lysodeikticus (UL = 0.34), at pH 6.0 and temperature 35 °C. The normal serum level of protein was estimated using indirect ELISA and was found to be very low (0.12-0.15 μg/ml). These results suggested that g-type lysozyme of rohu might be a potent immunostimulant against microbial infections, with a major role in innate immunity.
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Affiliation(s)
- Amruta Mohapatra
- Fish Health Management Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, 751002, India
| | - Sonali Parida
- Fish Health Management Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, 751002, India
| | - Jyotirmaya Mohanty
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, 751002, India
| | - P K Sahoo
- Fish Health Management Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, 751002, India.
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24
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Zheng J, Wang C, Chang MR, Devarkar SC, Schweibenz B, Crynen GC, Garcia-Ordonez RD, Pascal BD, Novick SJ, Patel SS, Marcotrigiano J, Griffin PR. HDX-MS reveals dysregulated checkpoints that compromise discrimination against self RNA during RIG-I mediated autoimmunity. Nat Commun 2018; 9:5366. [PMID: 30560918 PMCID: PMC6299088 DOI: 10.1038/s41467-018-07780-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 11/28/2018] [Indexed: 01/25/2023] Open
Abstract
Retinoic acid inducible gene-I (RIG-I) ensures immune surveillance of viral RNAs bearing a 5'-triphosphate (5'ppp) moiety. Mutations in RIG-I (C268F and E373A) lead to impaired ATPase activity, thereby driving hyperactive signaling associated with autoimmune diseases. Here we report, using hydrogen/deuterium exchange, mechanistic models for dysregulated RIG-I proofreading that ultimately result in the improper recognition of cellular RNAs bearing 7-methylguanosine and N1-2'-O-methylation (Cap1) on the 5' end. Cap1-RNA compromises its ability to stabilize RIG-I helicase and blunts caspase activation and recruitment domains (CARD) partial opening by threefold. RIG-I H830A mutation restores Cap1-helicase engagement as well as CARDs partial opening event to a level comparable to that of 5'ppp. However, E373A RIG-I locks the receptor in an ATP-bound state, resulting in enhanced Cap1-helicase engagement and a sequential CARDs stimulation. C268F mutation renders a more tethered ring architecture and results in constitutive CARDs signaling in an ATP-independent manner.
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MESH Headings
- Adenosine Triphosphatases/metabolism
- Autoimmunity/genetics
- Caspase Activation and Recruitment Domain/immunology
- DEAD Box Protein 58/chemistry
- DEAD Box Protein 58/genetics
- DEAD Box Protein 58/immunology
- DEAD Box Protein 58/metabolism
- Deuterium Exchange Measurement/methods
- Gain of Function Mutation
- Guanosine/analogs & derivatives
- Guanosine/chemistry
- Guanosine/immunology
- Guanosine/metabolism
- Immunity, Innate/genetics
- Interferon-Induced Helicase, IFIH1/immunology
- Interferon-Induced Helicase, IFIH1/metabolism
- Mass Spectrometry/methods
- Methylation
- Models, Molecular
- Mutagenesis, Site-Directed
- Protein Binding/genetics
- Protein Binding/immunology
- RNA Caps/chemistry
- RNA Caps/immunology
- RNA Caps/metabolism
- RNA, Double-Stranded/chemistry
- RNA, Double-Stranded/immunology
- RNA, Double-Stranded/metabolism
- RNA, Viral/immunology
- Receptors, Immunologic
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/immunology
- Recombinant Proteins/metabolism
- Signal Transduction/genetics
- Signal Transduction/immunology
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Affiliation(s)
- Jie Zheng
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, 33458, USA.
| | - Chen Wang
- Structural Virology Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Mi Ra Chang
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, 33458, USA
| | - Swapnil C Devarkar
- Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, 08854, USA
| | - Brandon Schweibenz
- Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, 08854, USA
| | - Gogce C Crynen
- The Center for Computational Biology, The Scripps Research Institute, Jupiter, FL, 33458, USA
| | - Ruben D Garcia-Ordonez
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, 33458, USA
| | - Bruce D Pascal
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, 33458, USA
- Omics Informatics LLC, Honolulu, HI 96813, USA
| | - Scott J Novick
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, 33458, USA
| | - Smita S Patel
- Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, 08854, USA
| | - Joseph Marcotrigiano
- Structural Virology Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - Patrick R Griffin
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, 33458, USA.
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25
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Semple SL, Vo NTK, Poynter SJ, Li M, Heath DD, DeWitte-Orr SJ, Dixon B. Extracellular dsRNA induces a type I interferon response mediated via class A scavenger receptors in a novel Chinook salmon derived spleen cell line. Dev Comp Immunol 2018; 89:93-101. [PMID: 30118734 DOI: 10.1016/j.dci.2018.08.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 08/13/2018] [Accepted: 08/13/2018] [Indexed: 06/08/2023]
Abstract
Despite increased global interest in Chinook salmon aquaculture, little is known of their viral immune defenses. This study describes the establishment and characterization of a continuous cell line derived from Chinook salmon spleen, CHSS, and its use in innate immune studies. Optimal growth was seen at 14-18 °C when grown in Leibovitz's L-15 media with 20% fetal bovine serum. DNA analyses confirmed that CHSS was Chinook salmon and genetically different from the only other available Chinook salmon cell line, CHSE-214. Unlike CHSE-214, CHSS could bind extracellular dsRNA, resulting in the rapid and robust expression of antiviral genes. Receptor/ligand blocking assays confirmed that class A scavenger receptors (SR-A) facilitated dsRNA binding and subsequent gene expression. Although both cell lines expressed three SR-A genes: SCARA3, SCARA4, and SCARA5, only CHSS appeared to have functional cell-surface SR-As for dsRNA. Collectively, CHSS is an excellent cell model to study dsRNA-mediated innate immunity in Chinook salmon.
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Affiliation(s)
- S L Semple
- Department of Biology, University of Waterloo, 200 University Ave W., Waterloo, ON, N2L 3G1, Canada
| | - N T K Vo
- Department of Biology, University of Waterloo, 200 University Ave W., Waterloo, ON, N2L 3G1, Canada
| | - S J Poynter
- Department of Biology, University of Waterloo, 200 University Ave W., Waterloo, ON, N2L 3G1, Canada
| | - M Li
- Department of Biology, University of Waterloo, 200 University Ave W., Waterloo, ON, N2L 3G1, Canada
| | - D D Heath
- Great Lakes Institute of Environmental Research, University of Windsor, 2990 Riverside Drive, West Windsor, Ontario, N9C 1A2, Canada
| | - S J DeWitte-Orr
- Department of Biology, Wilfrid Laurier University, Waterloo, Ontario, N2L 3C5, Canada; Department of Health Sciences, Wilfrid Laurier University, Waterloo, Ontario, N2L 3C5, Canada
| | - B Dixon
- Department of Biology, University of Waterloo, 200 University Ave W., Waterloo, ON, N2L 3G1, Canada.
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26
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Guanzon DAV, Maningas MBB. Functional elucidation of LvToll 3 receptor from P. vannamei through RNA interference and its potential role in the shrimp antiviral response. Dev Comp Immunol 2018; 84:172-180. [PMID: 29421160 DOI: 10.1016/j.dci.2018.01.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Revised: 01/26/2018] [Accepted: 01/27/2018] [Indexed: 06/08/2023]
Abstract
There is a continuing debate on whether an antiviral immunity similar to vertebrate interferon response exists in invertebrates. Recent advances in penaeid immunology identified several new members of the Toll receptor family and one of these is LvToll3 (Litopenaeus vannamei Toll3). It is hypothesized in this study that LvToll3 responds to pathogen associated molecular patterns (PAMPs) such as dsRNA, which then activates certain antiviral pathways in penaeids. RNA interference (RNAi) was used to determine differences in the expression levels of specific genes putatively involved in the antiviral response through qPCR. Results showed that LvToll3 upregulation could be elicited through the introduction of double stranded RNA (dsRNA) regardless of sequence relative to initial levels in the 3rd hour. Furthermore, statistically intriguing trend in the overall expression of Vago 4/5 and Interferon regulatory factor (IRF) suggests that both these genes are affected by the expression of LvToll3. Dicer showed no statistical difference between the experimentally treated (LvToll3-dsRNA), positive control (GFP-dsRNA), and control (PBS) samples corroborating the assertion that dicer is part of another antiviral mechanism that acts in concert with Toll system. These findings suggests that LvToll3 plays a critical role in penaeid antiviral immunity when molecular patterns associated with viruses are detected.
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Affiliation(s)
| | - Mary Beth B Maningas
- The Graduate School, University of Santo Tomas, España, 1015, Manila, Philippines; Department of Biological Sciences, College of Science, University of Santo Tomas, España, 1015, Manila, Philippines; Research Center for the Natural and Applied Sciences, Molecular Biology and Biotechnology Laboratory, University of Santo Tomas, España, 1015, Manila, Philippines.
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27
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Mu X, Greenwald E, Ahmad S, Hur S. An origin of the immunogenicity of in vitro transcribed RNA. Nucleic Acids Res 2018; 46:5239-5249. [PMID: 29534222 PMCID: PMC6007322 DOI: 10.1093/nar/gky177] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 02/12/2018] [Accepted: 02/28/2018] [Indexed: 12/24/2022] Open
Abstract
The emergence of RNA-based therapeutics demands robust and economical methods to produce RNA with few byproducts from aberrant activity. While in vitro transcription using the bacteriophage T7 RNA polymerase is one such popular method, its transcripts are known to display an immune-stimulatory activity that is often undesirable and uncontrollable. We here showed that the immune-stimulatory activity of T7 transcript is contributed by its aberrant activity to initiate transcription from a promoter-less DNA end. This activity results in the production of an antisense RNA that is fully complementary to the intended sense RNA product, and consequently a long double-stranded RNA (dsRNA) that can robustly stimulate a cytosolic pattern recognition receptor, MDA5. This promoter-independent transcriptional activity of the T7 RNA polymerase was observed for a wide range of DNA sequences and lengths, but can be suppressed by altering the transcription reaction with modified nucleotides or by reducing the Mg2+ concentration. The current work thus not only offers a previously unappreciated mechanism by which T7 transcripts stimulate the innate immune system, but also shows that the immune-stimulatory activity can be readily regulated.
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MESH Headings
- DEAD Box Protein 58/genetics
- DEAD Box Protein 58/immunology
- DNA-Directed RNA Polymerases/genetics
- DNA-Directed RNA Polymerases/metabolism
- HEK293 Cells
- Humans
- Immunity, Innate/physiology
- Interferon-Induced Helicase, IFIH1/genetics
- Interferon-Induced Helicase, IFIH1/immunology
- Interferon-Induced Helicase, IFIH1/metabolism
- Interferon-beta/genetics
- Magnesium/pharmacology
- Nucleotides/genetics
- Nucleotides/metabolism
- Promoter Regions, Genetic
- RNA, Double-Stranded/genetics
- RNA, Double-Stranded/immunology
- RNA, Double-Stranded/metabolism
- Receptors, Immunologic
- Transcription, Genetic/drug effects
- Viral Proteins/genetics
- Viral Proteins/metabolism
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Affiliation(s)
- Xin Mu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, MA 02115, USA
| | - Emily Greenwald
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, MA 02115, USA
| | - Sadeem Ahmad
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, MA 02115, USA
| | - Sun Hur
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, MA 02115, USA
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28
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Poynter SJ, DeWitte-Orr SJ. Understanding Viral dsRNA-Mediated Innate Immune Responses at the Cellular Level Using a Rainbow Trout Model. Front Immunol 2018; 9:829. [PMID: 29740439 PMCID: PMC5924774 DOI: 10.3389/fimmu.2018.00829] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 04/05/2018] [Indexed: 12/20/2022] Open
Abstract
Viruses across genome types produce long dsRNA molecules during replication [viral (v-) dsRNA]. dsRNA is a potent signaling molecule and inducer of type I interferon (IFN), leading to the production of interferon-stimulated genes (ISGs), and a protective antiviral state within the cell. Research on dsRNA-induced immune responses has relied heavily on a commercially available, and biologically irrelevant dsRNA, polyinosinic:polycytidylic acid (poly I:C). Alternatively, dsRNA can be produced by in vitro transcription (ivt-) dsRNA, with a defined sequence and length. We hypothesized that ivt-dsRNA, containing legitimate viral sequence and length, would be a more appropriate proxy for v-dsRNA, compared with poly I:C. This is the first study to investigate the effects of v-dsRNA on the innate antiviral response and to compare v-dsRNA to ivt-dsRNA-induced responses in fish cells, specifically rainbow trout. Previously, class A scavenger receptors (SR-As) were found to be surface receptors for poly I:C in rainbow trout cells. In this study, ivt-dsRNA binding was blocked by poly I:C and v-dsRNA, as well as SR-A competitive ligands, suggesting all three dsRNA molecules are recognized by SR-As. Downstream innate antiviral effects were determined by measuring IFN and ISG transcript levels using qRT-PCR and antiviral assays. Similar to what has been shown previously with ivt-dsRNA, v-dsRNA was able to induce IFN and ISG transcript production between 3 and 24 h, and its effects were length dependent (i.e., longer v-dsRNA produced a stronger response). Interestingly, when v-dsRNA and ivt-dsRNA were length and sequence matched both molecules induced statistically similar IFN and ISG transcript levels, which resulted in similar antiviral states against two aquatic viruses. To pursue sequence effects further, three ivt-dsRNA molecules of the same length but different sequences (including host and viral sequences) were tested for their ability to induce IFN/ISG transcripts and an antiviral state. All three induced responses similarly. This study is the first of its kind to look at the effects v-dsRNA in fish cells as well as to compare ivt-dsRNA to v-dsRNA, and suggests that ivt-dsRNA may be a good surrogate for v-dsRNA in the study of dsRNA-induced responses and potential future antiviral therapies.
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Affiliation(s)
- Sarah J. Poynter
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
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29
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Sarkis S, Lise MC, Darcissac E, Dabo S, Falk M, Chaulet L, Neuveut C, Meurs EF, Lavergne A, Lacoste V. Development of molecular and cellular tools to decipher the type I IFN pathway of the common vampire bat. Dev Comp Immunol 2018; 81:1-7. [PMID: 29122634 DOI: 10.1016/j.dci.2017.10.023] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 10/31/2017] [Accepted: 10/31/2017] [Indexed: 06/07/2023]
Abstract
Though the common vampire bat, Desmodus rotundus, is known as the main rabies virus reservoir in Latin America, no tools are available to investigate its antiviral innate immune system. To characterize the IFN-I pathway, we established an immortalized cell line from a D. rotundus fetal lung named FLuDero. Then we molecularly characterized some of the Toll-like receptors (TLR3, 7, 8 and 9), the three RIG-I-like receptor members, as well as IFNα1 and IFNβ. Challenging the FLuDero cell line with poly (I:C) resulted in an up-regulation of both IFNα1 and IFNβ and the induction of expression of the different pattern recognition receptors characterized. These findings provide evidence of the intact dsRNA recognition machinery and the IFN-I signaling pathway in our cellular model. Herein, we generated a sum of insightful specific molecular and cellular tools that will serve as a useful model to study virus-host interactions of the common vampire bat.
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Affiliation(s)
- Sarkis Sarkis
- Laboratoire des Interactions Virus-Hôtes, Institut Pasteur de La Guyane, Cayenne, French Guiana.
| | - Marie-Claude Lise
- Laboratoire des Interactions Virus-Hôtes, Institut Pasteur de La Guyane, Cayenne, French Guiana
| | - Edith Darcissac
- Laboratoire des Interactions Virus-Hôtes, Institut Pasteur de La Guyane, Cayenne, French Guiana
| | - Stéphanie Dabo
- Hepacivirus and Innate Immunity, Institut Pasteur, 75015 Paris, France
| | - Marcel Falk
- Laboratoire des Interactions Virus-Hôtes, Institut Pasteur de La Guyane, Cayenne, French Guiana
| | - Laura Chaulet
- Laboratoire des Interactions Virus-Hôtes, Institut Pasteur de La Guyane, Cayenne, French Guiana
| | - Christine Neuveut
- Hepacivirus and Innate Immunity, Institut Pasteur, 75015 Paris, France
| | - Eliane F Meurs
- Hepacivirus and Innate Immunity, Institut Pasteur, 75015 Paris, France
| | - Anne Lavergne
- Laboratoire des Interactions Virus-Hôtes, Institut Pasteur de La Guyane, Cayenne, French Guiana
| | - Vincent Lacoste
- Laboratoire des Interactions Virus-Hôtes, Institut Pasteur de La Guyane, Cayenne, French Guiana.
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30
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Basu S, Fowler BJ, Kerur N, Arnvig KB, Rao NA. NLRP3 inflammasome activation by mycobacterial ESAT-6 and dsRNA in intraocular tuberculosis. Microb Pathog 2017; 114:219-224. [PMID: 29180292 DOI: 10.1016/j.micpath.2017.11.044] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 11/23/2017] [Accepted: 11/23/2017] [Indexed: 01/08/2023]
Abstract
The molecular basis of intraocular tuberculosis (TB) is not well understood. In this study, we investigated the role of two constituents of viable Mycobacterium tuberculosis - Early Secreted Antigenic Target-6 (ESAT-6), and mycobacterial RNA- in inflammasome activation in the retinal pigment epithelium (RPE), a key site of inflammation in intraocular TB. We found that ESAT-6 induced caspase-1 activation and inflammasome priming in mouse RPE cells, substantially more in wild-type than in Tlr2/3/4/7/9-/-, Myd88-/- or Nlrp3-/- RPE cells. Sub-retinal ESAT-6 injection resulted in greater RPE degeneration in wild-type than in Nlrp3-/- mice. In human ocular TB tissue sections, NLRP3 staining was noted in retina as well as RPE. Mycobacterial RNA, specifically its double stranded component, also induced caspase-1 activation, and the double stranded RNA was immunolocalized to human ocular TB sections. Our observations suggest that inflammasome activation in RPE by viable M. tuberculosis could potentially contribute to human intraocular TB.
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MESH Headings
- Animals
- Antigens, Bacterial/genetics
- Antigens, Bacterial/immunology
- Bacterial Proteins/genetics
- Bacterial Proteins/immunology
- Caspase 1/genetics
- Caspase 1/immunology
- Host-Parasite Interactions
- Humans
- Inflammasomes/genetics
- Inflammasomes/immunology
- Mice
- Mice, Inbred C57BL
- Mycobacterium tuberculosis/genetics
- Mycobacterium tuberculosis/immunology
- NLR Family, Pyrin Domain-Containing 3 Protein/genetics
- NLR Family, Pyrin Domain-Containing 3 Protein/immunology
- RNA, Bacterial/genetics
- RNA, Bacterial/immunology
- RNA, Double-Stranded/genetics
- RNA, Double-Stranded/immunology
- Retinal Pigment Epithelium/immunology
- Retinal Pigment Epithelium/microbiology
- Tuberculosis, Ocular/genetics
- Tuberculosis, Ocular/immunology
- Tuberculosis, Ocular/microbiology
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Affiliation(s)
- Soumyava Basu
- L V Prasad Eye Institute, Mithu Tulsi Chanrai Campus, Bhubaneswar, India; Department of Ophthalmology and Visual Sciences, University of Kentucky, Lexington, KY, USA.
| | - Benjamin J Fowler
- Department of Ophthalmology and Visual Sciences, University of Kentucky, Lexington, KY, USA
| | | | - Kristine B Arnvig
- Institute of Structural and Molecular Biology, University College, London, UK
| | - Narsing A Rao
- USC Eye Institute, The Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
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31
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Cherepanova AV, Nazarkina ZK, Laktionov PP. Oligodeoxynucleotide Analogues of Circulating DNA Inhibit dsRNA-Induced Immune Response at the Early Stages of Signal Transduction Cascade in a Cell Type-Dependent Manner. Adv Exp Med Biol 2017; 924:105-107. [PMID: 27753028 DOI: 10.1007/978-3-319-42044-8_20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Oligodeoxynucleotide (ODN) analogues of cell-surface-bound circulating DNA inhibit the dsRNA-induced production of pro-inflammatory interleukin 6, interferon beta and antibacterial peptide beta-defensin 2 not only in human gingival fibroblasts, but also in human primary endothelial and transformed cells (Hela and A431). ODN analogues do not effect dendritic cells activation by poly(I:C). The data obtained indicate that the early stages of the signal transduction cascade are violated by ODN analogues and the effects depend on the cell type.
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Affiliation(s)
- Anna V Cherepanova
- Institute of Chemical Biology and FundamentalMedicine SB RAS, Lavrentiev ave., 8, Novosibirsk, 630090, Russia.
| | - Zhanna K Nazarkina
- Institute of Chemical Biology and FundamentalMedicine SB RAS, Lavrentiev ave., 8, Novosibirsk, 630090, Russia
| | - Pavel P Laktionov
- Institute of Chemical Biology and FundamentalMedicine SB RAS, Lavrentiev ave., 8, Novosibirsk, 630090, Russia
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32
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Yapp CW, Widaad Mohaimin A, Idris A. Poly I:C Delivery into J774.1 and RAW264.7 Macrophages Induces Rapid Cell Death. Iran J Immunol 2017; 14:250-256. [PMID: 28919588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
BACKGROUND Cytosolic double-stranded RNA (dsRNA) is an important 'molecular signature' for the detection of intracellular viral infections. Although intracellular dsRNA is a known potent inducer of apoptosis, the optimal time and dose for the onset of dsRNA-mediated apoptosis have not been studied in detail. OBJECTIVE To perform an accurate temporal assessment of the cell death responses in dsRNA-dependent cytotoxicity. METHODS Poly I:C (PIC), a synthetic dsRNA molecule was delivered intracellularly into J774.1 and RAW264.7 murine macrophages via electroporation. Cell viability was measured using the MTT assay and apoptosis was determined by sub-G0/G1 DNA content using flow cytometry. RESULTS Loss of cell viability was seen as early as 3h post-electroporation of macrophages. A significant increase in the sub-G0/G1 DNA content consistent with apoptosis was observed in PIC-electroporated macrophages as early as 3h post electroporation. CONCLUSION Intracellular PIC delivery induces rapid macrophage cell death.
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Affiliation(s)
- Cheah Wen Yapp
- PAPRSB Institute of Health Sciences, University of Brunei Darussalam, Brunei Darussalam
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33
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Dai X, Tohyama M, Murakami M, Sayama K. Epidermal keratinocytes sense dsRNA via the NLRP3 inflammasome, mediating interleukin (IL)-1β and IL-18 release. Exp Dermatol 2017; 26:904-911. [PMID: 28266737 DOI: 10.1111/exd.13334] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/22/2017] [Indexed: 12/22/2022]
Abstract
Skin epidermis, in addition to its barrier function, is able to actively sense harmful pathogens using pattern recognition receptors. In immune cells, the nucleotide-binding oligomerization domain, leucine-rich repeat and pyrin domain containing 3 (NLRP3) inflammasome can mediate innate immunity against viral infection via a mechanism involving viral dsRNA recognition. Epidermal keratinocytes express NLRP3 inflammasome, which can sense contact sensitizers and mite allergens, leading to pro-interleukin (IL)-1β and pro-IL-18 cleavage into their active forms. Skin often faces viral infection. However, it is unknown whether viral dsRNA can be detected by the keratinocyte NLRP3 inflammasome. We transfected polyinosinic:polycytidylic acid (poly I:C), a synthetic viral dsRNA analogue, into cultured primary human keratinocytes at the aid of Lipofectamine 2000, and found that transfected poly I:C activated caspase-1 and induced caspase-1-dependent release of IL-1β and IL-18, which were suppressed on transfection with NLRP3 siRNA. The activation of keratinocyte NLRP3 inflammasome by transfected poly I:C was dependent on dsRNA-induced protein kinase (PKR) activation, and priming with type I interferons upregulated NLRP3 inflammasome activation through promoting PKR activation in poly I:C-transfected keratinocytes. In conclusion, the NLRP3 inflammasome can act as a sensor of dsRNA in epidermal keratinocytes, which may be important in both skin innate immune defense against viral infection and skin inflammation.
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Affiliation(s)
- Xiuju Dai
- Department of Dermatology, Ehime University Graduate School of Medicine, Toon, Ehime, Japan
| | - Mikiko Tohyama
- Department of Dermatology, Ehime University Graduate School of Medicine, Toon, Ehime, Japan
| | - Masamoto Murakami
- Department of Dermatology, Ehime University Graduate School of Medicine, Toon, Ehime, Japan
| | - Koji Sayama
- Department of Dermatology, Ehime University Graduate School of Medicine, Toon, Ehime, Japan
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Rey S, Moiche V, Boltaña S, Teles M, MacKenzie S. Behavioural fever in zebrafish larvae. Dev Comp Immunol 2017; 67:287-292. [PMID: 27670815 DOI: 10.1016/j.dci.2016.09.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 09/15/2016] [Accepted: 09/15/2016] [Indexed: 06/06/2023]
Abstract
Behavioural fever has been reported in different species of mobile ectotherms including the zebrafish, Danio rerio, in response to exogenous pyrogens. In this study we report, to our knowledge for the first time, upon the ontogenic onset of behavioural fever in zebrafish (Danio rerio) larvae. For this, zebrafish larvae (from first feeding to juveniles) were placed in a continuous thermal gradient providing the opportunity to select their preferred temperature. The novel thermal preference aquarium was based upon a continuous vertical column system and allows for non-invasive observation of larvae vertical distribution under isothermal (TR at 28 °C) and thermal gradient conditions (TCH: 28-32 °C). Larval thermal preference was assessed under both conditions with or without an immersion challenge, in order to detect the onset of the behavioural fever response. Our results defined the onset of the dsRNA induced behavioural fever at 18-20 days post fertilization (dpf). Significant differences were observed in dsRNA challenged larvae, which prefer higher temperatures (1-4 °C increase) throughout the experimental period as compared to non-challenged larvae. In parallel we measured the abundance of antiviral transcripts; viperin, gig2, irf7, trim25 and Mxb mRNAs in dsRNA challenged larvae under both thermal regimes: TR and TCh. Significant increases in the abundance of all measured transcripts were recorded under thermal choice conditions signifying that thermo-coupling and the resultant enhancement of the immune response to dsRNA challenge occurs from 18 dpf onwards in the zebrafish. The results are of importance as they identify a key developmental stage where the neuro-immune interface matures in the zebrafish likely providing increased resistance to viral infection.
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Affiliation(s)
- Sonia Rey
- Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Barcelona, 08193 Bellaterra, Spain
| | - Visila Moiche
- Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Barcelona, 08193 Bellaterra, Spain
| | - Sebastian Boltaña
- Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Barcelona, 08193 Bellaterra, Spain
| | - Mariana Teles
- Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Barcelona, 08193 Bellaterra, Spain
| | - Simon MacKenzie
- Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Barcelona, 08193 Bellaterra, Spain.
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Vegna S, Gregoire D, Moreau M, Lassus P, Durantel D, Assenat E, Hibner U, Simonin Y. NOD1 Participates in the Innate Immune Response Triggered by Hepatitis C Virus Polymerase. J Virol 2016; 90:6022-6035. [PMID: 27099311 PMCID: PMC4907226 DOI: 10.1128/jvi.03230-15] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 04/13/2016] [Indexed: 02/07/2023] Open
Abstract
UNLABELLED Hepatitis C virus (HCV) triggers innate immunity signaling in the infected cell. Replication of the viral genome is dispensable for this phenotype, and we along with others have recently shown that NS5B, the viral RNA-dependent RNA polymerase, synthesizes double-stranded RNA (dsRNA) from cellular templates, thus eliciting an inflammatory response, notably via activation of type I interferon and lymphotoxin β. Here, we investigated intracellular signal transduction pathways involved in this process. Using HepaRG cells, a model that largely recapitulates the in vivo complexities of the innate immunity receptor signaling, we have confirmed that NS5B triggered increased expression of the canonical pattern recognition receptors (PRRs) specific for dsRNA, namely, RIG-I, MDA5, and Toll-like receptor 3 (TLR3). Unexpectedly, intracellular dsRNA also led to accumulation of NOD1, a receptor classically involved in recognition of bacterial peptidoglycans. NOD1 activation, confirmed by analysis of its downstream targets, was likely due to its interaction with dsRNA and was independent of RIG-I and mitochondrial antiviral signaling protein (MAVS/IPS-1/Cardif/VISA) signaling. It is likely to have a functional significance in the cellular response in the context of HCV infection since interference with the NOD1 pathway severely reduced the inflammatory response elicited by NS5B. IMPORTANCE In this study, we show that NOD1, a PRR that normally senses bacterial peptidoglycans, is activated by HCV viral polymerase, probably through an interaction with dsRNA, suggesting that NOD1 acts as an RNA ligand recognition receptor. In consequence, interference with NOD1-mediated signaling significantly weakens the inflammatory response to dsRNA. These results add a new level of complexity to the understanding of the cross talk between different classes of pattern recognition receptors and may be related to certain complications of chronic hepatitis C virus infection.
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Affiliation(s)
- Serena Vegna
- CNRS, UMR 5535, Institut de Génétique Moléculaire de Montpellier, Montpellier, France
- Université de Montpellier, Montpellier, France
| | - Damien Gregoire
- CNRS, UMR 5535, Institut de Génétique Moléculaire de Montpellier, Montpellier, France
- Université de Montpellier, Montpellier, France
| | - Marie Moreau
- CNRS, UMR 5535, Institut de Génétique Moléculaire de Montpellier, Montpellier, France
- Université de Montpellier, Montpellier, France
| | - Patrice Lassus
- CNRS, UMR 5535, Institut de Génétique Moléculaire de Montpellier, Montpellier, France
- Université de Montpellier, Montpellier, France
| | - David Durantel
- INSERM, U1052, Cancer Research Center of Lyon, University of Lyon, Lyon, France
| | - Eric Assenat
- CNRS, UMR 5535, Institut de Génétique Moléculaire de Montpellier, Montpellier, France
- Université de Montpellier, Montpellier, France
- Service d'Oncologie Médicale, CHU St. Eloi, Montpellier, France
| | - Urszula Hibner
- CNRS, UMR 5535, Institut de Génétique Moléculaire de Montpellier, Montpellier, France
- Université de Montpellier, Montpellier, France
| | - Yannick Simonin
- CNRS, UMR 5535, Institut de Génétique Moléculaire de Montpellier, Montpellier, France
- Université de Montpellier, Montpellier, France
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Abstract
The type I/III interferon (IFN)-inducible 2'-5'- oligoadenylate synthetase (OAS)/endoribonuclease L (RNase L) is a classical innate immune pathway that has been implicated in antiviral and antibacterial defense and also in hereditary prostate cancer. The OAS/RNase L pathway is activated when OAS senses double-stranded RNA and catalyzes the synthesis of 2'-5' linked oligodenylates (2-5A) from ATP. 2-5A then binds and activates RNase L, resulting cleavage of single-stranded RNAs. RNase L cleavage products are capable of activating RIG-like receptors such as RIG-I and MDA5 that leads to IFN-β expression during viral infection. Our recent findings suggest that beside the RLR pathway, RNase L cleavage products can also activate the NLRP3-inflammasome pathway, which requires DHX33 (DExD/H-box helicase) and the mitochondrial adaptor protein MAVS. Here we discuss this newly identified role of OAS-RNase L pathway in regulation of inflammasome signaling as an alternative antimicrobial mechanism that has potential as a target for development of new broad-spectrum antimicrobial and anti-inflammatory therapies.
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Affiliation(s)
- Shuvojit Banerjee
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA.
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Edwards MR, Liu G, Mire CE, Sureshchandra S, Luthra P, Yen B, Shabman RS, Leung DW, Messaoudi I, Geisbert TW, Amarasinghe GK, Basler CF. Differential Regulation of Interferon Responses by Ebola and Marburg Virus VP35 Proteins. Cell Rep 2016; 14:1632-1640. [PMID: 26876165 PMCID: PMC4767585 DOI: 10.1016/j.celrep.2016.01.049] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 12/16/2015] [Accepted: 01/13/2016] [Indexed: 12/31/2022] Open
Abstract
Suppression of innate immune responses during filoviral infection contributes to disease severity. Ebola (EBOV) and Marburg (MARV) viruses each encode a VP35 protein that suppresses RIG-I-like receptor signaling and interferon-α/β (IFN-α/β) production by several mechanisms, including direct binding to double stranded RNA (dsRNA). Here, we demonstrate that in cell culture, MARV infection results in a greater upregulation of IFN responses as compared to EBOV infection. This correlates with differences in the efficiencies by which EBOV and MARV VP35s antagonize RIG-I signaling. Furthermore, structural and biochemical studies suggest that differential recognition of RNA elements by the respective VP35 C-terminal IFN inhibitory domain (IID) rather than affinity for RNA by the respective VP35s is critical for this observation. Our studies reveal functional differences in EBOV versus MARV VP35 RNA binding that result in unexpected differences in the host response to deadly viral pathogens.
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Affiliation(s)
- Megan R Edwards
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Gai Liu
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Chad E Mire
- Department of Microbiology and Immunology, Galveston National Laboratory, University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
| | - Suhas Sureshchandra
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA 92521, USA
| | - Priya Luthra
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Benjamin Yen
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Reed S Shabman
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Virology Group, J. Craig Venter Institute, Rockville, MD 20850, USA
| | - Daisy W Leung
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Ilhem Messaoudi
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA 92521, USA
| | - Thomas W Geisbert
- Department of Microbiology and Immunology, Galveston National Laboratory, University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
| | - Gaya K Amarasinghe
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA.
| | - Christopher F Basler
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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Abstract
Mammalian cells have the ability to recognize virus infection and mount a powerful antiviral response. Pattern recognition receptor proteins detect molecular signatures of virus infection and activate antiviral signaling. The RIG-I-like receptor (RLR) proteins are expressed in the cytoplasm of nearly all cells and specifically recognize virus-derived RNA species as a molecular feature discriminating the pathogen from the host. The RLR family is composed of three homologous proteins, RIG-I, MDA5, and LGP2. All RLRs have the ability to detect virus-derived dsRNA and hydrolyze ATP, but display individual differences in enzymatic activity, intrinsic ability to recognize RNA, and mechanisms of activation. Emerging evidence suggests that MDA5 and RIG-I utilize distinct mechanisms to form oligomeric complexes along dsRNA. Aligning of their signaling domains creates a platform capable of propagating and amplifying antiviral signaling responses. LGP2 with intact ATP hydrolysis is critical for the MDA5-mediated antiviral response, but LGP2 lacks the domains essential for activation of antiviral signaling, leaving the role of LGP2 in antiviral signaling unclear. Recent studies revealed a mechanistic basis of synergy between LGP2 and MDA5 leading to enhanced antiviral signaling. This review briefly summarizes the RLR system, and focuses on the relationship between LGP2 and MDA5, describing in detail how these two proteins work together to detect foreign RNA and generate a fully functional antiviral response.
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Affiliation(s)
- Annie M Bruns
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA.
| | - Curt M Horvath
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
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Maralit BA, Komatsu M, Hipolito SG, Hirono I, Kondo H. Microarray Analysis of Immunity Against WSSV in Response to Injection of Non-specific Long dsRNA in Kuruma Shrimp, Marsupenaeus japonicus. Mar Biotechnol (NY) 2015; 17:493-501. [PMID: 25953417 DOI: 10.1007/s10126-015-9637-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 04/13/2015] [Indexed: 06/04/2023]
Abstract
Injection of shrimp with non-specific double-stranded RNA (dsRNA) of diverse lengths, sequences, and base compositions is known to induce non-specific immunity and protect against lethal disease, although the mechanisms are unclear. Previous shrimp studies examined the effects of non-specific RNA on particular pathways, while their global effects have not been examined. To understand the global effects of non-specific RNA in shrimp, we injected kuruma shrimp (Marsupenaeus japonicus) with a dsRNA and a small interfering RNA (siRNA) that is not specific to any gene in the shrimp genome and then examined global gene expression at 24 and 48 h with a microarray. For the non-specific RNA, we chose double-stranded green fluorescent protein (dsGFP) and siGFP because they are commonly used as mock controls and their effects on shrimp have not yet been studied. Injection of PBS was used as a control. The microarray results showed that many genes were up-regulated and some were down-regulated by dsGFP. In addition, dsGFP injection increased survival following WSSV challenge. The changes in expression for several genes were confirmed by quantitative PCR. The up-regulated genes included genes for eight immune-related proteins: c-type lectin 2, hemocyte homeostasis-associated protein, viral responsive protein, fibrinogen-related protein 1, sid-1 like protein, argonaute 2, Dicer 2, and heat shock protein 90. These results show that injection of shrimp with non-specific dsRNA hinders viral accumulation and prevents significant mortalities.
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Affiliation(s)
- Benedict Arias Maralit
- Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, Konan 4-5-7, Minato-ku, Tokyo, 108-8477, Japan
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Taju G, Madan N, Abdul Majeed S, Kumar TR, Thamizhvanan S, Otta SK, Sahul Hameed AS. Immune responses of whiteleg shrimp, Litopenaeus vannamei (Boone, 1931), to bacterially expressed dsRNA specific to VP28 gene of white spot syndrome virus. J Fish Dis 2015; 38:451-465. [PMID: 24917208 DOI: 10.1111/jfd.12256] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 04/07/2014] [Accepted: 04/16/2014] [Indexed: 06/03/2023]
Abstract
In this study, dsRNA specific to VP28 gene of white spot syndrome virus (WSSV) of shrimp was synthesized in Escherichia coli in large scale and studied the immune response of shrimp to dsRNA-VP28. The haematological parameters such as clotting time and total haemocytes counts, and immunological parameters such as prophenoloxidase (proPO), superoxide dismutase (SOD), superoxide anion (SOA) and malondialdehyde content, as well as the mRNA expression of ten immune-related genes were examined to estimate the effect of dsRNA-VP28 on the innate immunity of Litopenaeus vannamei. The activities of proPO, SOA and SOD significantly increased in haemocyte after dsRNA-VP28 treatment, whereas MDA content did not change significantly. Among the ten immune-related genes examined, only the mRNA expression of proPO, cMnSOD, haemocyanin, crustin, BGBP, lipopolysaccharides (LPs), lectin and lysozyme in haemocytes, gill and hepatopancreas of L. vannamei, was significantly upregulated at 12 h after dsRNA-VP28 treatment, while no significant expression changes were observed in Toll receptor and tumour receptor genes. The increase of proPO and SOD activities, and SOA level and mRNA expression level of proPO, cMnSOD, haemocyanin, crustin, BGBP, LPs, lectin and lysozyme after dsRNA-VP28 stimulation indicate that these immune-related genes were involved in dsRNA-VP28-induced innate immunity in shrimp.
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Affiliation(s)
- G Taju
- OIE Reference Laboratory for WTD, PG & Research Department of Zoology, C. Abdul Hakeem College, Melvisharam, Vellore District, Tamilnadu, India
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Heyam A, Lagos D, Plevin M. Dissecting the roles of TRBP and PACT in double-stranded RNA recognition and processing of noncoding RNAs. Wiley Interdiscip Rev RNA 2015; 6:271-89. [PMID: 25630541 PMCID: PMC7169789 DOI: 10.1002/wrna.1272] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Revised: 10/08/2014] [Accepted: 10/09/2014] [Indexed: 12/27/2022]
Abstract
HIV TAR RNA-binding protein (TRBP) and Protein Activator of PKR (PACT) are double-stranded (ds) RNA-binding proteins that participate in both small regulatory RNA biogenesis and the response to viral dsRNA. Despite considerable progress toward understanding the structure-function relationship of TRBP and PACT, their specific roles in these seemingly distinct cellular pathways remain unclear. Both proteins are composed of three copies of the double-stranded RNA-binding domain, two of which interact with dsRNA, while the C-terminal copy mediates protein-protein interactions. PACT and TRBP are found in a complex with the endonuclease Dicer and facilitate processing of immature microRNAs. Their precise contribution to the Dicing step has not yet been defined: possibilities include precursor recruitment, rearrangement of dsRNA within the complex, loading the processed microRNA into the RNA-induced silencing complex, and distinguishing different classes of small dsRNA. TRBP and PACT also interact with the viral dsRNA sensors retinoic acid-inducible gene I (RIG-I) and double-stranded RNA-activated protein kinase (PKR). Current models suggest that PACT enables RIG-I to detect a wider range of viral dsRNAs, while TRBP and PACT exert opposing regulatory effects on PKR. Here, the evidence that implicates TRBP and PACT in regulatory RNA processing and viral dsRNA sensing is reviewed and discussed in the context of their molecular structure. The broader implications of a link between microRNA biogenesis and the innate antiviral response pathway are also considered.
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MESH Headings
- Amino Acid Sequence
- Carboxypeptidases/chemistry
- Carboxypeptidases/metabolism
- Carboxypeptidases/physiology
- Models, Genetic
- Models, Molecular
- Molecular Sequence Data
- Protein Structure, Tertiary
- RNA, Double-Stranded/chemistry
- RNA, Double-Stranded/immunology
- RNA, Double-Stranded/metabolism
- RNA, Untranslated/metabolism
- RNA, Viral/chemistry
- RNA, Viral/immunology
- RNA, Viral/metabolism
- RNA-Binding Proteins/chemistry
- RNA-Binding Proteins/metabolism
- RNA-Binding Proteins/physiology
- Ribonuclease III/chemistry
- Ribonuclease III/metabolism
- Ribonuclease III/physiology
- Structure-Activity Relationship
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Affiliation(s)
- Alex Heyam
- Department of Biology, University of York, York, UK
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Uchida L, Espada-Murao LA, Takamatsu Y, Okamoto K, Hayasaka D, Yu F, Nabeshima T, Buerano CC, Morita K. The dengue virus conceals double-stranded RNA in the intracellular membrane to escape from an interferon response. Sci Rep 2014; 4:7395. [PMID: 25491663 PMCID: PMC4261170 DOI: 10.1038/srep07395] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 11/11/2014] [Indexed: 12/11/2022] Open
Abstract
The dengue virus (DENV) circulates between humans and mosquitoes and requires no other mammals or birds for its maintenance in nature. The virus is well-adapted to humans, as reflected by high-level viraemia in patients. To investigate its high adaptability, the DENV induction of host type-I interferon (IFN) was assessed in vitro in human-derived HeLa cells and compared with that induced by the Japanese encephalitis virus (JEV), a closely related arbovirus that generally exhibits low viraemia in humans. A sustained viral spread with a poor IFN induction was observed in the DENV-infected cells, whereas the JEV infection resulted in a self-limiting and abortive infection with a high IFN induction. There was no difference between DENV and JEV double-stranded RNA (dsRNA) as IFN inducers. Instead, the dsRNA was poorly exposed in the cytosol as late as 48 h post-infection (p.i.), despite the high level of DENV replication in the infected cells. In contrast, the JEV-derived dsRNA appeared in the cytosol as early as 24 h p.i. Our results provided evidence for the first time in DENV, that concealing dsRNA in the intracellular membrane diminishes the effect of the host defence mechanism, a strategy that differs from an active suppression of IFN activity.
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Affiliation(s)
- Leo Uchida
- Department of Virology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Lyre Anni Espada-Murao
- Department of Virology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
| | - Yuki Takamatsu
- Department of Virology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
| | - Kenta Okamoto
- Department of Virology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
| | - Daisuke Hayasaka
- Department of Virology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
| | - Fuxun Yu
- Department of Virology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
| | - Takeshi Nabeshima
- Department of Virology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
| | - Corazon C. Buerano
- Department of Virology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
- Department of Molecular Epidemiology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
| | - Kouichi Morita
- Department of Virology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
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Wang GQ, Zhu ZX, Cao WJ, Liu L, Zheng HX. [Recent progress of the mechanisms for RNA viruses to block the recognition of dsRNA with RIG-I-like receptors]. Bing Du Xue Bao 2014; 30:704-12. [PMID: 25868287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
RIG-I-like receptors (RLRs) belong to pattern recognition receptors, which perform significant roles in antiviral responses. RLRs can initiate a cascade of signaling transduction that induces the production of type I interferon and activates the interferon signaling pathway, ultimately resulting in antiviral responses. In the course of evolution, viruses have been constantly counteracting host immune systems to facilitate their own survival and replication, and have developed a set of antagonistic strategies. These mainly comprise elusion, disguise and attack strategies to eliminate the activation of RLRs. In virus-infected cells, RLRs recognize viral RNA and then induce antiviral responses. A better understanding of viral antagonistic strategies against RLRs will provide insights into the development of new antiviral medicines. This mini-review concludes that there are three main antagonistic strategies by which RNA viruses can counteract the activation of the RLRs pathway. It aims to provide references and insights for similar studies on viral antagonism in an array of RNA viruses.
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Green TJ, Benkendorff K, Robinson N, Raftos D, Speck P. Anti-viral gene induction is absent upon secondary challenge with double-stranded RNA in the Pacific oyster, Crassostrea gigas. Fish Shellfish Immunol 2014; 39:492-497. [PMID: 24945571 DOI: 10.1016/j.fsi.2014.06.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 06/04/2014] [Accepted: 06/09/2014] [Indexed: 06/03/2023]
Abstract
Oyster farming is one of the most important aquaculture industries in the world. However, its productivity is increasingly limited by viral disease and we do not yet have management practices, such as protective vaccination, that can control these disease outbreaks. Hence, in the current study we investigated the expression of known anti-viral genes in oysters (Crassostrea gigas) in response to primary and secondary encounter with a virus associated molecular pattern (dsRNA), and tested whether a common form of epigenetic gene regulation (DNA methylation) was associated with the expression of these anti-viral genes. Injection of dsRNA into the adductor muscle resulted in the rapid and transient expression of virus recognition receptors (TLR & MDA5), whereas several anti-viral signalling (IRF & SOC-1) and effector (PKR & viperin) genes were still up-regulated at one week post primary challenge (p < 0.05). This primary encounter with dsRNA appeared to deplete the immune system because anti-viral gene induction was absent in the gills when oysters were given a second injection of dsRNA at 1-week post-primary injection. The expression of DNA methylation genes (DNMT1, DNMT3b, TDG, TET2) and DNA methylation profiles up-stream of specific anti-viral genes (STING, SOC-1 & Viperin) did not change in response to dsRNA injection (p > 0.05). These results collectively suggest that C. gigas does not have an enhanced anti-viral gene response (immune-priming) to secondary dsRNA challenge and that the sustained up-regulation of anti-viral signalling and effector genes following primary challenge is unlikely to be associated with upstream DNA methylation levels.
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Affiliation(s)
- Timothy J Green
- School of Biological Sciences and Australian Seafood Cooperative Research Centre, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia.
| | - Kirsten Benkendorff
- Marine Ecology Research Centre, Southern Cross University, P.O. Box 157, Lismore, NSW 2480, Australia
| | - Nick Robinson
- School of Biological Sciences and Australian Seafood Cooperative Research Centre, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia; Nofima, P.O. Box 210, N-1431 Ås, Norway
| | - David Raftos
- Department of Biological Sciences, Macquarie University, NSW 2109, Australia
| | - Peter Speck
- School of Biological Sciences and Australian Seafood Cooperative Research Centre, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia
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45
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Weber M, Weber F. Segmented negative-strand RNA viruses and RIG-I: divide (your genome) and rule. Curr Opin Microbiol 2014; 20:96-102. [PMID: 24930021 DOI: 10.1016/j.mib.2014.05.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Revised: 05/02/2014] [Accepted: 05/11/2014] [Indexed: 11/18/2022]
Abstract
The group of negative-stranded RNA viruses (NSVs) with a segmented genome comprises pathogens like influenza virus (eight segments), Rift Valley fever virus and Hantavirus (three segments), or Lassa virus (two segments). Partitioning the genome allows rapid evolution of new strains by reassortment. Each segment carries a short double-stranded (ds) 'panhandle' structure which serves as promoter. Similar dsRNA structures, however, represent the optimal ligand for RIG-I, a cytoplasmic pathogen sensor of the antiviral interferon response. Thus, segmenting a virus genome can entail an increased RIG-I sensitivity. Here, we outline the astonishingly diverse and efficient strategies by which segmented NSVs are compensating for the elevated number of RIG-I ligands in their genome.
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Affiliation(s)
- Michaela Weber
- Institute for Virology, Philipps-University Marburg, D-35043 Marburg, Germany
| | - Friedemann Weber
- Institute for Virology, Philipps-University Marburg, D-35043 Marburg, Germany.
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46
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Bertolusso R, Tian B, Zhao Y, Vergara L, Sabree A, Iwanaszko M, Lipniacki T, Brasier AR, Kimmel M. Dynamic cross talk model of the epithelial innate immune response to double-stranded RNA stimulation: coordinated dynamics emerging from cell-level noise. PLoS One 2014; 9:e93396. [PMID: 24710104 PMCID: PMC3977818 DOI: 10.1371/journal.pone.0093396] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Accepted: 03/04/2014] [Indexed: 01/01/2023] Open
Abstract
We present an integrated dynamical cross-talk model of the epithelial innate immune response (IIR) incorporating RIG-I and TLR3 as the two major pattern recognition receptors (PRR) converging on the RelA and IRF3 transcriptional effectors. bioPN simulations reproduce biologically relevant gene-and protein abundance measurements in response to time course, gene silencing and dose-response perturbations both at the population and single cell level. Our computational predictions suggest that RelA and IRF3 are under auto- and cross-regulation. We predict, and confirm experimentally, that RIG-I mRNA expression is controlled by IRF7. We also predict the existence of a TLR3-dependent, IRF3-independent transcription factor (or factors) that control(s) expression of MAVS, IRF3 and members of the IKK family. Our model confirms the observed dsRNA dose-dependence of oscillatory patterns in single cells, with periods of 1-3 hr. Model fitting to time series, matched by knockdown data suggests that the NF-κB module operates in a different regime (with different coefficient values) than in the TNFα-stimulation experiments. In future studies, this model will serve as a foundation for identification of virus-encoded IIR antagonists and examination of stochastic effects of viral replication. Our model generates simulated time series, which reproduce the noisy oscillatory patterns of activity (with 1-3 hour period) observed in individual cells. Our work supports the hypothesis that the IIR is a phenomenon that emerged by evolution despite highly variable responses at an individual cell level.
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Affiliation(s)
- Roberto Bertolusso
- Department of Statistics, Rice University, Houston, Texas, United States of America
| | - Bing Tian
- Department of Internal Medicine, University of Texas Medical Branch (UTMB), Galveston, Texas, United States of America
| | - Yingxin Zhao
- Department of Internal Medicine, University of Texas Medical Branch (UTMB), Galveston, Texas, United States of America
- Sealy Center for Molecular Medicine, UTMB, Galveston, Texas, United States of America
- Institute for Translational Sciences, UTMB, Galveston, Texas, United States of America
| | - Leoncio Vergara
- Center for Biomedical Engineering, UTMB, Galveston, Texas, United States of America
| | - Aqeeb Sabree
- Department of Statistics, Rice University, Houston, Texas, United States of America
| | - Marta Iwanaszko
- Systems Engineering Group, Silesian University of Technology, Gliwice, Poland
| | - Tomasz Lipniacki
- Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, Poland
| | - Allan R. Brasier
- Department of Internal Medicine, University of Texas Medical Branch (UTMB), Galveston, Texas, United States of America
- Sealy Center for Molecular Medicine, UTMB, Galveston, Texas, United States of America
- Institute for Translational Sciences, UTMB, Galveston, Texas, United States of America
| | - Marek Kimmel
- Department of Statistics, Rice University, Houston, Texas, United States of America
- Systems Engineering Group, Silesian University of Technology, Gliwice, Poland
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47
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Yoo JS, Takahasi K, Ng CS, Ouda R, Onomoto K, Yoneyama M, Lai JC, Lattmann S, Nagamine Y, Matsui T, Iwabuchi K, Kato H, Fujita T. DHX36 enhances RIG-I signaling by facilitating PKR-mediated antiviral stress granule formation. PLoS Pathog 2014; 10:e1004012. [PMID: 24651521 PMCID: PMC3961341 DOI: 10.1371/journal.ppat.1004012] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Accepted: 02/04/2014] [Indexed: 12/14/2022] Open
Abstract
RIG-I is a DExD/H-box RNA helicase and functions as a critical cytoplasmic sensor for RNA viruses to initiate antiviral interferon (IFN) responses. Here we demonstrate that another DExD/H-box RNA helicase DHX36 is a key molecule for RIG-I signaling by regulating double-stranded RNA (dsRNA)-dependent protein kinase (PKR) activation, which has been shown to be essential for the formation of antiviral stress granule (avSG). We found that DHX36 and PKR form a complex in a dsRNA-dependent manner. By forming this complex, DHX36 facilitates dsRNA binding and phosphorylation of PKR through its ATPase/helicase activity. Using DHX36 KO-inducible MEF cells, we demonstrated that DHX36 deficient cells showed defect in IFN production and higher susceptibility in RNA virus infection, indicating the physiological importance of this complex in host defense. In summary, we identify a novel function of DHX36 as a critical regulator of PKR-dependent avSG to facilitate viral RNA recognition by RIG-I-like receptor (RLR).
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Affiliation(s)
- Ji-Seung Yoo
- Laboratory of Molecular Genetics, Institute for Virus Research, Kyoto University, Kyoto, Japan
- Laboratory of Molecular Cell Biology, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Kiyohiro Takahasi
- Laboratory of Molecular Genetics, Institute for Virus Research, Kyoto University, Kyoto, Japan
- Institute for Innovative NanoBio Drug Discovery and Development, Graduate School of Pharmaceutical Science, Kyoto University, Kyoto, Japan
| | - Chen Seng Ng
- Laboratory of Molecular Genetics, Institute for Virus Research, Kyoto University, Kyoto, Japan
- Laboratory of Molecular Cell Biology, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Ryota Ouda
- Laboratory of Molecular Genetics, Institute for Virus Research, Kyoto University, Kyoto, Japan
- Laboratory of Molecular Cell Biology, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Koji Onomoto
- Division of Molecular Immunology, Medical Mycology Research Center, Chiba University, Chuo-ku, Chiba, Japan
| | - Mitsutoshi Yoneyama
- Division of Molecular Immunology, Medical Mycology Research Center, Chiba University, Chuo-ku, Chiba, Japan
| | - Janice Ching Lai
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Simon Lattmann
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Yoshikuni Nagamine
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Tadashi Matsui
- Department of Biochemistry I, School of Medicine, Kanazawa Medical University, Uchinada, Ishikawa, Japan
| | - Kuniyoshi Iwabuchi
- Department of Biochemistry I, School of Medicine, Kanazawa Medical University, Uchinada, Ishikawa, Japan
| | - Hiroki Kato
- Laboratory of Molecular Genetics, Institute for Virus Research, Kyoto University, Kyoto, Japan
- Laboratory of Molecular Cell Biology, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Takashi Fujita
- Laboratory of Molecular Genetics, Institute for Virus Research, Kyoto University, Kyoto, Japan
- Laboratory of Molecular Cell Biology, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
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48
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Karlikow M, Goic B, Saleh MC. RNAi and antiviral defense in Drosophila: setting up a systemic immune response. Dev Comp Immunol 2014; 42:85-92. [PMID: 23684730 DOI: 10.1016/j.dci.2013.05.004] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Revised: 05/03/2013] [Accepted: 05/06/2013] [Indexed: 06/02/2023]
Abstract
RNA interference (RNAi) controls gene expression in eukaryotic cells and thus, cellular homeostasis. In addition, in plants, nematodes and arthropods it is a central antiviral effector mechanism. Antiviral RNAi has been well described as a cell autonomous response, which is triggered by double-stranded RNA (dsRNA) molecules. This dsRNA is the precursor for the silencing of viral RNA in a sequence-specific manner. In plants, systemic antiviral immunity has been demonstrated, however much less is known in animals. Recently, some evidence for a systemic antiviral response in arthropods has come to light. Cell autonomous RNAi may not be sufficient to reach an efficient antiviral response, and the organism might rely on the spread and uptake of an RNAi signal of unknown origin. In this review, we offer a perspective on how RNAi-mediated antiviral immunity could confer systemic protection in insects and we propose directions for future research to understand the mechanism of RNAi-immune signal sorting, spreading and amplification.
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Affiliation(s)
- Margot Karlikow
- Institut Pasteur, Viruses and RNA Interference, Centre National de la Recherche Scientifique UMR3569, Paris, France
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49
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Abstract
Toll-like receptor 3 (TLR3) activation plays an important role in the innate immune responses to viral infections. We show here that the activation of TLR3 signaling pathway by poly I:C, a synthetic mimic of dsRNA, could induce high-level expression of interferon (IFN)-λ1 in a hepatoma cell line. The induced IFN-λ1 contributed to poly I:C-mediated inhibition of hepatitis C virus (HCV) Japanese fulminant hepatitis-1 (JFH-1) replication in Huh7 cells. This inhibitory effect of poly I:C on HCV replication, however, was compromised by HCV infection of Huh7 cells. Investigation of the mechanisms showed that HCV infection suppressed the expression of poly I:C-induced IFN-λ1 and IFN-stimulated genes [IFN-stimulated gene 56 (ISG-56), myxovirus resistance A (MxA) and 2'-5'-oligoadenylate synthetase 1 (OAS-1))], the key antiviral elements in IFN signaling pathway. Among the HCV nonstructural (NS) proteins tested, NS3/4A, NS5A and NS5B had the ability to inhibit poly I:C-induced IFN-λ1 expression in Huh7 cells. These observations provide the experimental evidence that HCV and its proteins impair TLR3 signaling and inhibit intracellular IFN-λ1/ISG expression in a hepatoma cell line, which may account for HCV persistence in the liver.
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Affiliation(s)
- Yizhong Wang
- The Center for Animal Experiment/ABSL-3 Laboratory, Wuhan University, Hubei, People’s Republic of China
- Department of Pathology and Laboratory Medicine, Temple University School of Medicine, Philadelphia, PA, USA
| | - Jieliang Li
- Department of Pathology and Laboratory Medicine, Temple University School of Medicine, Philadelphia, PA, USA
| | - Xu Wang
- Department of Pathology and Laboratory Medicine, Temple University School of Medicine, Philadelphia, PA, USA
| | - Li Ye
- The Center for Animal Experiment/ABSL-3 Laboratory, Wuhan University, Hubei, People’s Republic of China
| | - Yu Zhou
- Department of Pathology and Laboratory Medicine, Temple University School of Medicine, Philadelphia, PA, USA
| | - Rebecca M Thomas
- Department of Pathology and Laboratory Medicine, Temple University School of Medicine, Philadelphia, PA, USA
| | - Wenzhe Ho
- The Center for Animal Experiment/ABSL-3 Laboratory, Wuhan University, Hubei, People’s Republic of China
- Department of Pathology and Laboratory Medicine, Temple University School of Medicine, Philadelphia, PA, USA
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50
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Chen Y, Zhang Y, Huang Z, Xu Q, Zhu Z, Tong Y, Yu Q, Ding J, Chen G. Molecular characterization, expression patterns, and subcellular localization of RIG-I in the Jinding duck (Anas platyrhynchos domesticus). Dev Comp Immunol 2013; 41:766-771. [PMID: 23916689 DOI: 10.1016/j.dci.2013.07.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2013] [Revised: 07/16/2013] [Accepted: 07/24/2013] [Indexed: 06/02/2023]
Abstract
Retinoic acid-inducible gene I (RIG-I)-like receptors (RLRs) have recently been identified as cytoplasmic sensors for RNA virus. Recent research has shown that RIG-I, a member of this family, play an important role in innate immunity. In this study, we cloned the RIG-I gene from Jinding duck by reverse transcription polymerase chain reaction (RT-PCR) and rapid amplification of cDNA ends (RACE). We determined that the cDNA of duRIG-I contains a 14-bp 5' UTR, a 2802-bp open reading frame, and alternative 3' UTRs (295-bp and 927-bp) and encodes a polypeptide of 933 amino acids. Based on this sequence, the duRIG-I protein is predicted to have conserved domains typical of RLRs. In addition, duRIG-I was found to be distributed throughout DF1 cells by indirect immunofluorescence, as predicted. duRIG-I mRNA was scarcely detected in healthy tissues by semi-quantitative RT-PCR (sqRT-PCR). To study the role of RIG-I in innate immunity, we used synthetic double-stranded RNA to mimic viral infection in vivo and detected duRIG-I transcripts in spleen and liver by quantitative real-time PCR (qRT-PCR). The expression of duRIG-I mRNA was significantly elevated at 8h post-injection (P < 0.05) and was indistinguishable from control levels at other time points (P > 0.05). These results suggest that duRIG-I plays an important role in innate immune responses to double-stranded RNA viruses and warrant further studies to reveal the possible mechanism.
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Affiliation(s)
- Yang Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009 Jiangsu, PR China
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