1
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Sestan M, Arsov T, Kifer N, Frkovic M, Grguric D, Ellyard J, Cook M, Vinuesa CG, Jelusic M. Whole exome sequencing in patients with childhood-onset systemic lupus erythematosus: Results from a Croatian national study. Scand J Immunol 2024:e13411. [PMID: 39380326 DOI: 10.1111/sji.13411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 09/15/2024] [Accepted: 09/24/2024] [Indexed: 10/10/2024]
Abstract
The purpose of this study was to identify new and low-frequency gene variants using whole exome sequencing (WES) in patients with childhood-onset systemic lupus erythematosus (cSLE), that may be involved in the pathogenesis of SLE. We performed WES on selected 17 trios (in some cases including other informative family members) in which the proband presented with severe, atypical clinical features, resistance to conventional therapy, a family pattern of occurrence and/or syndromic characteristics. After performing WES and analysis of gene variants, 17 novel and/or low-frequency variants were identified in 7 patients. One variant was classified as pathogenic (KMT2D, NM_003482.3:c.8626delC, predicted to truncate the protein p.(Gln2876Serfs*34)) and two as likely pathogenic according to the American College of Medical Genetics and Genomics classification guidelines (ADAR, NM_001111.3:c.2815A>G, predicted to encode p.(Ile939Val); BLK, NM_001715.2:c.211G>A, predicted to encode p.(Ala71Thr)). The other variants remain of uncertain significance at this point of time. WES is an important diagnostic and research instrument, producing a growing list of likely genes and gene variants that may be of relevance in the pathogenesis of cSLE and potentially point to novel therapeutic targets.
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Affiliation(s)
- Mario Sestan
- Department of Paediatrics, University of Zagreb School of Medicine, University Hospital Centre Zagreb, Zagreb, Croatia
| | - Todor Arsov
- Faculty of Medical Sciences, University Goce Delchev, Shtip, North Macedonia
- The Francis Crick Institute, London, UK
| | - Nastasia Kifer
- Department of Paediatrics, University of Zagreb School of Medicine, University Hospital Centre Zagreb, Zagreb, Croatia
| | - Marijan Frkovic
- Department of Paediatrics, University of Zagreb School of Medicine, University Hospital Centre Zagreb, Zagreb, Croatia
| | - Danica Grguric
- Department of Paediatrics, University of Zagreb School of Medicine, University Hospital Centre Zagreb, Zagreb, Croatia
| | - Julia Ellyard
- Department of Immunology and Infectious Diseases, The John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Matthew Cook
- Department of Immunology and Infectious Diseases, The John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
- University of Cambridge, Cambridge, UK
| | - Carola G Vinuesa
- The Francis Crick Institute, London, UK
- Department of Immunology and Infectious Diseases, The John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Marija Jelusic
- Department of Paediatrics, University of Zagreb School of Medicine, University Hospital Centre Zagreb, Zagreb, Croatia
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2
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Heruye SH, Myslinski J, Zeng C, Zollman A, Makino S, Nanamatsu A, Mir Q, Janga SC, Doud EH, Eadon MT, Maier B, Hamada M, Tran TM, Dagher PC, Hato T. Inflammation primes the murine kidney for recovery by activating AZIN1 adenosine-to-inosine editing. J Clin Invest 2024; 134:e180117. [PMID: 38954486 PMCID: PMC11364396 DOI: 10.1172/jci180117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 06/25/2024] [Indexed: 07/04/2024] Open
Abstract
The progression of kidney disease varies among individuals, but a general methodology to quantify disease timelines is lacking. Particularly challenging is the task of determining the potential for recovery from acute kidney injury following various insults. Here, we report that quantitation of post-transcriptional adenosine-to-inosine (A-to-I) RNA editing offers a distinct genome-wide signature, enabling the delineation of disease trajectories in the kidney. A well-defined murine model of endotoxemia permitted the identification of the origin and extent of A-to-I editing, along with temporally discrete signatures of double-stranded RNA stress and adenosine deaminase isoform switching. We found that A-to-I editing of antizyme inhibitor 1 (AZIN1), a positive regulator of polyamine biosynthesis, serves as a particularly useful temporal landmark during endotoxemia. Our data indicate that AZIN1 A-to-I editing, triggered by preceding inflammation, primes the kidney and activates endogenous recovery mechanisms. By comparing genetically modified human cell lines and mice locked in either A-to-I-edited or uneditable states, we uncovered that AZIN1 A-to-I editing not only enhances polyamine biosynthesis but also engages glycolysis and nicotinamide biosynthesis to drive the recovery phenotype. Our findings implicate that quantifying AZIN1 A-to-I editing could potentially identify individuals who have transitioned to an endogenous recovery phase. This phase would reflect their past inflammation and indicate their potential for future recovery.
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Affiliation(s)
- Segewkal Hawaze Heruye
- Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Jered Myslinski
- Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Chao Zeng
- Faculty of Science and Engineering, Waseda University, Tokyo, Japan
| | - Amy Zollman
- Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Shinichi Makino
- Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Azuma Nanamatsu
- Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Quoseena Mir
- Luddy School of Informatics, Computing, and Engineering, Indiana University, Indianapolis, Indiana, USA
| | - Sarath Chandra Janga
- Luddy School of Informatics, Computing, and Engineering, Indiana University, Indianapolis, Indiana, USA
| | - Emma H. Doud
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Michael T. Eadon
- Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Bernhard Maier
- Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Michiaki Hamada
- Faculty of Science and Engineering, Waseda University, Tokyo, Japan
- AIST–Waseda University Computational Bio Big-Data Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
- Graduate School of Medicine, Nippon Medical School, Tokyo, Japan
| | - Tuan M. Tran
- Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Richard L. Roudebush Veterans Affairs Medical Center, Indianapolis, Indiana, USA
| | - Pierre C. Dagher
- Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Takashi Hato
- Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Richard L. Roudebush Veterans Affairs Medical Center, Indianapolis, Indiana, USA
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
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Gualandi N, Minisini M, Bertozzo A, Brancolini C. Dissecting transposable elements and endogenous retroviruses upregulation by HDAC inhibitors in leiomyosarcoma cells: Implications for the interferon response. Genomics 2024; 116:110909. [PMID: 39103003 DOI: 10.1016/j.ygeno.2024.110909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 07/22/2024] [Accepted: 07/31/2024] [Indexed: 08/07/2024]
Abstract
Transposable elements (TEs) are of interest as immunomodulators for cancer therapies. TEs can fold into dsRNAs that trigger the interferon response. Here, we investigated the effect of different HDAC inhibitors (HDACIs) on the expression of TEs in leiomyosarcoma cells. Our data show that endogenous retroviruses (ERVs), especially ERV1 elements, are upregulated after treatment with HDAC1/2/3-specific inhibitors. Surprisingly, the interferon response was not activated. We observed an increase in A-to-I editing of upregulated ERV1. This could have an impact on the stability of dsRNAs and the activation of the interferon response. We also found that H3K27ac levels are increased in the LTR12 subfamilies, which could be regulatory elements controlling the expression of proapoptotic genes such as TNFRSF10B. In summary, we provide a detailed characterization of TEs modulation in response to HDACIs and suggest the use of HDACIs in combination with ADAR inhibitors to induce cell death and support immunotherapy in cancer.
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Affiliation(s)
- Nicolò Gualandi
- Department of Medicine, Università degli Studi di Udine, P.le Kolbe 4, 33100 Udine, Italy
| | - Martina Minisini
- Department of Medicine, Università degli Studi di Udine, P.le Kolbe 4, 33100 Udine, Italy
| | - Alessio Bertozzo
- Department of Medicine, Università degli Studi di Udine, P.le Kolbe 4, 33100 Udine, Italy
| | - Claudio Brancolini
- Department of Medicine, Università degli Studi di Udine, P.le Kolbe 4, 33100 Udine, Italy.
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Smart A, Gilmer O, Caliskan N. Translation Inhibition Mediated by Interferon-Stimulated Genes during Viral Infections. Viruses 2024; 16:1097. [PMID: 39066259 PMCID: PMC11281336 DOI: 10.3390/v16071097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 07/04/2024] [Accepted: 07/04/2024] [Indexed: 07/28/2024] Open
Abstract
Viruses often pose a significant threat to the host through the exploitation of cellular machineries for their own benefit. In the context of immune responses, myriad host factors are deployed to target viral RNAs and inhibit viral protein translation, ultimately hampering viral replication. Understanding how "non-self" RNAs interact with the host translation machinery and trigger immune responses would help in the development of treatment strategies for viral infections. In this review, we explore how interferon-stimulated gene products interact with viral RNA and the translation machinery in order to induce either global or targeted translation inhibition.
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Affiliation(s)
- Alexandria Smart
- Helmholtz Institute for RNA-Based Infection Research, Helmholtz Centre for Infection Research (HIRI-HZI), Josef-Schneider-Strasse 2, 97080 Würzburg, Germany; (A.S.); (O.G.)
| | - Orian Gilmer
- Helmholtz Institute for RNA-Based Infection Research, Helmholtz Centre for Infection Research (HIRI-HZI), Josef-Schneider-Strasse 2, 97080 Würzburg, Germany; (A.S.); (O.G.)
| | - Neva Caliskan
- Helmholtz Institute for RNA-Based Infection Research, Helmholtz Centre for Infection Research (HIRI-HZI), Josef-Schneider-Strasse 2, 97080 Würzburg, Germany; (A.S.); (O.G.)
- Regensburg Center for Biochemistry (RCB), University of Regensburg, 93053 Regensburg, Germany
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5
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Gionco JT, Bernstein AI. Emerging Role of Environmental Epitranscriptomics and RNA Modifications in Parkinson's Disease. JOURNAL OF PARKINSON'S DISEASE 2024; 14:643-656. [PMID: 38578904 PMCID: PMC11191529 DOI: 10.3233/jpd-230457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 03/10/2024] [Indexed: 04/07/2024]
Abstract
Environmental risk factors and gene-environment interactions play a critical role in Parkinson's disease (PD). However, the relatively large contribution of environmental risk factors in the overwhelming majority of PD cases has been widely neglected in the field. A "PD prevention agenda" proposed in this journal laid out a set of research priorities focused on preventing PD through modification of environmental risk factors. This agenda includes a call for preclinical studies to employ new high-throughput methods for analyzing transcriptomics and epigenomics to provide a deeper understanding of the effects of exposures linked to PD. Here, we focus on epitranscriptomics as a novel area of research with the potential to add to our understanding of the interplay between genes and environmental exposures in PD. Both epigenetics and epitranscriptomics have been recognized as potential mediators of the complex relationship between genes, environment, and disease. Multiple studies have identified epigenetic alterations, such as DNA methylation, associated with PD and PD-related exposures in human studies and preclinical models. In addition, recent technological advancements have made it possible to study epitranscriptomic RNA modifications, such as RNA N6-methyladenosine (m6A), and a handful of recent studies have begun to explore epitranscriptomics in PD-relevant exposure models. Continued exploration of epitranscriptomic mechanisms in environmentally relevant PD models offers the opportunity to identify biomarkers, pre-degenerative changes that precede symptom onset, and potential mitigation strategies for disease prevention and treatment.
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Affiliation(s)
- John T. Gionco
- Graduate Program in Cell and Developmental Biology, Rutgers University, Piscataway, NJ, USA
| | - Alison I. Bernstein
- Department of Pharmacology and Toxicology, Rutgers University, Piscataway, NJ, USA
- Environmental and Occupational Health Sciences Institute, Rutgers University, Piscataway, NJ, USA
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6
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Lee HL, Squire E, Fotio Y, Mabou Tagne A, Lee J, Yoon JJ, Hong Y, Kim LH, Jung KM, Piomelli D. Frequent low-impact exposure to THC during adolescence causes persistent sexually dimorphic alterations in the response to viral infection in mice. Pharmacol Res 2024; 199:107049. [PMID: 38159785 DOI: 10.1016/j.phrs.2023.107049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 12/11/2023] [Accepted: 12/27/2023] [Indexed: 01/03/2024]
Abstract
Adolescent exposure to Δ9-tetrahydrocannabinol (THC) has enduring effects on energy metabolism and immune function. Prior work showed that daily administration of a low-impact dose of THC (5 mg/kg, intraperitoneal) during adolescence alters transcription in adult microglia and disrupts their response to bacterial endotoxin or social stress. To explore the lasting impact of adolescent THC exposure on the brain's reaction to viral infection, we administered THC (5 mg/kg, intraperitoneal) in male and female mice once daily on postnatal day (PND) 30-43. When the mice reached adulthood (PND 70), we challenged them with the viral mimic, polyinosinic acid:polycytidylic acid [Poly(I:C)], and assessed sickness behavior (motor activity, body temperature) and whole brain gene transcription. Poly(I:C) caused an elevation in body temperature which was lessened by prior THC exposure in female but not male mice. Adolescent THC exposure did not affect the locomotor response to Poly(I:C) in either sex. Transcriptomic analyses showed that Poly(I:C) produced a substantial upregulation of immune-related genes in the brain, which was decreased by THC in females. Additionally, the viral mimic caused a male-selective downregulation in transcription of genes involved in neurodevelopment and synaptic transmission, which was abrogated by adolescent THC treatment. The results indicate that Poly(I:C) produces complex transcriptional alterations in the mouse brain, which are sexually dimorphic and differentially affected by early-life THC exposure. In particular, adolescent THC dampens the brain's antiviral response to Poly(I:C) in female mice and prevents the transcriptional downregulation of neuron-related genes caused by the viral mimic in male mice.
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Affiliation(s)
- Hye-Lim Lee
- Department of Anatomy and Neurobiology, University of California, Irvine, USA
| | - Erica Squire
- Department of Anatomy and Neurobiology, University of California, Irvine, USA
| | - Yannick Fotio
- Department of Anatomy and Neurobiology, University of California, Irvine, USA
| | - Alex Mabou Tagne
- Department of Anatomy and Neurobiology, University of California, Irvine, USA
| | - Jungyeon Lee
- Department of Anatomy and Neurobiology, University of California, Irvine, USA
| | - John Jeongwoo Yoon
- Department of Anatomy and Neurobiology, University of California, Irvine, USA
| | - Yedam Hong
- Department of Anatomy and Neurobiology, University of California, Irvine, USA
| | - Laura Hyunseo Kim
- Department of Anatomy and Neurobiology, University of California, Irvine, USA
| | - Kwang-Mook Jung
- Department of Anatomy and Neurobiology, University of California, Irvine, USA
| | - Daniele Piomelli
- Department of Anatomy and Neurobiology, University of California, Irvine, USA; Department of Biological Chemistry, University of California, Irvine, USA; Department of Pharmaceutical Sciences, University of California, Irvine, USA.
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7
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Heruye S, Myslinski J, Zeng C, Zollman A, Makino S, Nanamatsu A, Mir Q, Janga SC, Doud EH, Eadon MT, Maier B, Hamada M, Tran TM, Dagher PC, Hato T. Inflammation primes the kidney for recovery by activating AZIN1 A-to-I editing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.09.566426. [PMID: 37986799 PMCID: PMC10659426 DOI: 10.1101/2023.11.09.566426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
The progression of kidney disease varies among individuals, but a general methodology to quantify disease timelines is lacking. Particularly challenging is the task of determining the potential for recovery from acute kidney injury following various insults. Here, we report that quantitation of post-transcriptional adenosine-to-inosine (A-to-I) RNA editing offers a distinct genome-wide signature, enabling the delineation of disease trajectories in the kidney. A well-defined murine model of endotoxemia permitted the identification of the origin and extent of A-to-I editing, along with temporally discrete signatures of double-stranded RNA stress and Adenosine Deaminase isoform switching. We found that A-to-I editing of Antizyme Inhibitor 1 (AZIN1), a positive regulator of polyamine biosynthesis, serves as a particularly useful temporal landmark during endotoxemia. Our data indicate that AZIN1 A-to-I editing, triggered by preceding inflammation, primes the kidney and activates endogenous recovery mechanisms. By comparing genetically modified human cell lines and mice locked in either A-to-I edited or uneditable states, we uncovered that AZIN1 A-to-I editing not only enhances polyamine biosynthesis but also engages glycolysis and nicotinamide biosynthesis to drive the recovery phenotype. Our findings implicate that quantifying AZIN1 A-to-I editing could potentially identify individuals who have transitioned to an endogenous recovery phase. This phase would reflect their past inflammation and indicate their potential for future recovery.
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Affiliation(s)
- Segewkal Heruye
- Department of Medicine, Indiana University School of Medicine
| | - Jered Myslinski
- Department of Medicine, Indiana University School of Medicine
| | - Chao Zeng
- Faculty of Science and Engineering, Waseda University, Tokyo
| | - Amy Zollman
- Department of Medicine, Indiana University School of Medicine
| | - Shinichi Makino
- Department of Medicine, Indiana University School of Medicine
| | - Azuma Nanamatsu
- Department of Medicine, Indiana University School of Medicine
| | - Quoseena Mir
- Luddy School of Informatics, Computing, and Engineering, Indiana University
| | | | - Emma H Doud
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine
| | - Michael T Eadon
- Department of Medicine, Indiana University School of Medicine
| | - Bernhard Maier
- Department of Medicine, Indiana University School of Medicine
| | - Michiaki Hamada
- Faculty of Science and Engineering, Waseda University, Tokyo
- AIST-Waseda University Computational Bio Big-Data Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, Tokyo
- Graduate School of Medicine, Nippon Medical School, Tokyo
| | - Tuan M Tran
- Department of Medicine, Indiana University School of Medicine
- Richard L. Roudebush Veterans Affairs Medical Center, Indianapolis
| | - Pierre C Dagher
- Department of Medicine, Indiana University School of Medicine
| | - Takashi Hato
- Department of Medicine, Indiana University School of Medicine
- Richard L. Roudebush Veterans Affairs Medical Center, Indianapolis
- Department of Medical and Molecular Genetics, Indiana University School of Medicine
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8
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Imran K, Iqbal MJ, Abid R, Ahmad MM, Calina D, Sharifi-Rad J, Cho WC. Cellular signaling modulated by miRNA-3652 in ovarian cancer: unveiling mechanistic pathways for future therapeutic strategies. Cell Commun Signal 2023; 21:289. [PMID: 37845675 PMCID: PMC10577948 DOI: 10.1186/s12964-023-01330-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 09/21/2023] [Indexed: 10/18/2023] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNA molecules that play pivotal roles in regulating gene expression and have been implicated in the pathogenesis of numerous cancers. miRNA-3652, though relatively less explored, has recently emerged as a potential key player in ovarian cancer's molecular landscape. This review aims to delineate the functional significance and tumor progression role of miRNA-3652 in ovarian cancer, shedding light on its potential as both a diagnostic biomarker and therapeutic target. A comprehensive literature search was carried out using established databases, the focus was on articles that reported the role of miRNA-3652 in ovarian cancer, encompassing mechanistic insights, functional studies, and its association with clinical outcomes. This updated review highlighted that miRNA-3652 is intricately involved in ovarian cancer cell proliferation, migration, and invasion, its dysregulation was linked to altered expression of critical genes involved in tumor growth and metastasis; furthermore, miRNA-3652 expression levels were found to correlate with clinical stages, prognosis, and response to therapy in ovarian cancer patients. miRNA-3652 holds significant promise as a vital molecular player in ovarian cancer's pathophysiology. Its functional role and impact on tumor progression make it a potential candidate for diagnostic and therapeutic applications in ovarian cancer. Given the pivotal role of miRNA-3652 in ovarian cancer, future studies should emphasize in-depth mechanistic explorations, utilizing advanced genomic and proteomic tools. Collaboration between basic scientists and clinicians will be vital to translating these findings into innovative diagnostic and therapeutic strategies, ultimately benefiting ovarian cancer patients. Video Abstract.
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Affiliation(s)
- Komal Imran
- Department of Biotechnology, Faculty of Sciences, University of Sialkot, Sialkot, Pakistan
| | - Muhammad Javed Iqbal
- Department of Biotechnology, Faculty of Sciences, University of Sialkot, Sialkot, Pakistan
| | - Rameesha Abid
- Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Muhammad Mushtaq Ahmad
- Department of Allied Health Sciences, International Institute of Science, Art and Technology, Gujranwala, Pakistan
| | - Daniela Calina
- Department of Clinical Pharmacy, University of Medicine and Pharmacy of Craiova, 200349, Craiova, Romania.
| | | | - William C Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Kowloon, Hong Kong.
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9
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Datta R, Adamska JZ, Bhate A, Li JB. A-to-I RNA editing by ADAR and its therapeutic applications: From viral infections to cancer immunotherapy. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 15:e1817. [PMID: 37718249 PMCID: PMC10947335 DOI: 10.1002/wrna.1817] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 08/29/2023] [Accepted: 08/29/2023] [Indexed: 09/19/2023]
Abstract
ADAR deaminases catalyze adenosine-to-inosine (A-to-I) editing on double-stranded RNA (dsRNA) substrates that regulate an umbrella of biological processes. One of the two catalytically active ADAR enzymes, ADAR1, plays a major role in innate immune responses by suppression of RNA sensing pathways which are orchestrated through the ADAR1-dsRNA-MDA5 axis. Unedited immunogenic dsRNA substrates are potent ligands for the cellular sensor MDA5. Upon activation, MDA5 leads to the induction of interferons and expression of hundreds of interferon-stimulated genes with potent antiviral activity. In this way, ADAR1 acts as a gatekeeper of the RNA sensing pathway by striking a fine balance between innate antiviral responses and prevention of autoimmunity. Reduced editing of immunogenic dsRNA by ADAR1 is strongly linked to the development of common autoimmune and inflammatory diseases. In viral infections, ADAR1 exhibits both antiviral and proviral effects. This is modulated by both editing-dependent and editing-independent functions, such as PKR antagonism. Several A-to-I RNA editing events have been identified in viruses, including in the insidious viral pathogen, SARS-CoV-2 which regulates viral fitness and infectivity, and could play a role in shaping viral evolution. Furthermore, ADAR1 is an attractive target for immuno-oncology therapy. Overexpression of ADAR1 and increased dsRNA editing have been observed in several human cancers. Silencing ADAR1, especially in cancers that are refractory to immune checkpoint inhibitors, is a promising therapeutic strategy for cancer immunotherapy in conjunction with epigenetic therapy. The mechanistic understanding of dsRNA editing by ADAR1 and dsRNA sensing by MDA5 and PKR holds great potential for therapeutic applications. This article is categorized under: RNA Processing > RNA Editing and Modification RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Rohini Datta
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Julia Z Adamska
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Amruta Bhate
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Jin Billy Li
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
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10
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Ma Q, Che L, Chen Y, Gu Z. Identification of five novel variants of ADAR1 in dyschromatosis symmetrica hereditaria by next-generation sequencing. Front Pediatr 2023; 11:1161502. [PMID: 37476031 PMCID: PMC10354868 DOI: 10.3389/fped.2023.1161502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 06/13/2023] [Indexed: 07/22/2023] Open
Abstract
Background Dyschromatosis symmetrica hereditaria (DSH) is a rare autosomal dominant inherited pigmentary dermatosis characterized by a mixture of hyperpigmented and hypopigmented freckles on the dorsal aspect of the distal extremities. To date, pathogenic mutations causing DSH have been identified in the adenosine deaminase acting on RNA1 gene (ADAR1), which is mapped to chromosome 1q21. Objective The present study aimed to investigate the underlying pathological mechanism in 14 patients with DSH from five unrelated Chinese families. Next-generation sequencing (NGS) and direct sequencing were performed on a proband with DSH to identify causative mutations. All coding, adjacent intronic, and 5'- and 3'-untranslated regions of ADAR1 were screened, and variants were identified. Result These mutations consisted of three missense mutations (NM_001025107: c.716G>A, NM_001111.5: c.3384G>C, and NM_001111.5: c.3385T>G), one nonsense mutation (NM_001111.5:c.511G>T), and one splice-site mutation (NM_001111.5: c.2080-1G>T) located in exon 2, exon 14, and the adjacent intronic region according to recommended Human Genome Variation Society (HGVS) nomenclature. Moreover, using polymerase chain reaction and Sanger sequencing, we identified five novel ADAR1 variants, which can be predicted to be pathogenic by in silico genome sequence analysis. Among the mutations, the missense mutations had no significant effect on the spatial structure of the protein, while the stop codon introduced by the nonsense mutation truncated the protein. Conclusion Our results highlighted that the advent of NGS has facilitated high-throughput screening for the identification of disease-causing mutations with high accuracy, stability, and specificity. Five novel genetic mutations were found in five unrelated families, thereby extending the pathogenic mutational spectrum of ADAR1 in DSH and providing new insights into this complex genetic disorder.
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Affiliation(s)
- Qian Ma
- Genetic and Prenatal Diagnosis Center, Department of Gynecology and Obstetrics, The First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Lingyi Che
- Genetic and Prenatal Diagnosis Center, Department of Gynecology and Obstetrics, The First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Yibing Chen
- Genetic and Prenatal Diagnosis Center, Department of Gynecology and Obstetrics, The First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Zhuoyu Gu
- Department of Thoracic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
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11
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Yuan J, Xu L, Bao HJ, Wang JL, Zhao Y, Chen S. Biological roles of A-to-I editing: implications in innate immunity, cell death, and cancer immunotherapy. J Exp Clin Cancer Res 2023; 42:149. [PMID: 37328893 DOI: 10.1186/s13046-023-02727-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 06/02/2023] [Indexed: 06/18/2023] Open
Abstract
Adenosine-to-inosine (A-to-I) editing, a key RNA modification widely found in eukaryotes, is catalyzed by adenosine deaminases acting on RNA (ADARs). Such RNA editing destabilizes endogenous dsRNAs, which are subsequently recognized by the sensors of innate immune and other proteins as autologous dsRNAs. This prevents the activation of innate immunity and type I interferon-mediated responses, thereby reducing the downstream cell death induced by the activation of the innate immune sensing system. ADARs-mediated editing can also occur in mRNAs and non-coding RNAs (ncRNAs) in different species. In mRNAs, A-to-I editing may lead to missense mutations and the selective splicing of coding regions. Meanwhile, in ncRNAs, A-to-I editing may affect targeting and disrupt ncRNAs maturation, leading to anomalous cell proliferation, invasion, and responses to immunotherapy. This review highlights the biological functions of A-to-I editing, its role in regulating innate immunity and cell death, and its potential molecular significance in tumorigenesis and cancer targeted therapy and immunotherapy.
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Affiliation(s)
- Jing Yuan
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Guangzhou Key Laboratory of Targeted Therapy for Gynecologic Oncology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, No.63 Duobao Road, Liwan District, Guangzhou City, Guangdong Province, 510150, P. R. China
| | - Li Xu
- Department of Laboratory Medicine, The First Hospital of China Medical University, Shenyang, 110001, China
| | - Hai-Juan Bao
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Guangzhou Key Laboratory of Targeted Therapy for Gynecologic Oncology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, No.63 Duobao Road, Liwan District, Guangzhou City, Guangdong Province, 510150, P. R. China
| | - Jie-Lin Wang
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Guangzhou Key Laboratory of Targeted Therapy for Gynecologic Oncology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, No.63 Duobao Road, Liwan District, Guangzhou City, Guangdong Province, 510150, P. R. China
| | - Yang Zhao
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Guangzhou Key Laboratory of Targeted Therapy for Gynecologic Oncology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, No.63 Duobao Road, Liwan District, Guangzhou City, Guangdong Province, 510150, P. R. China.
| | - Shuo Chen
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Guangzhou Key Laboratory of Targeted Therapy for Gynecologic Oncology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, No.63 Duobao Road, Liwan District, Guangzhou City, Guangdong Province, 510150, P. R. China.
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12
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Wang Y, Liu Y, Zhao Z, Wu X, Lin J, Li Y, Yan W, Wu Y, Shi Y, Wu X, Xue Y, He J, Liu S, Zhang X, Xu H, Tang Y, Yin S. The involvement of ADAR1 in chronic unpredictable stress-induced cognitive impairment by targeting DARPP-32 with miR-874-3p in BALB/c mice. Front Cell Dev Biol 2023; 11:919297. [PMID: 37123418 PMCID: PMC10132208 DOI: 10.3389/fcell.2023.919297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 03/07/2023] [Indexed: 05/02/2023] Open
Abstract
Introduction: Chronic stress exposure is the main environmental factor leading to cognitive impairment, but the detailed molecular mechanism is still unclear. Adenosine Deaminase acting on double-stranded RNA1(ADAR1) is involved in the occurrence of chronic stress-induced cognitive impairment. In addition, dopamine and Adenosine 3'5'-monophosphate-regulated phospho-protein (DARPP-32) gene variation affects cognitive function. Therefore, we hypothesized that ADAR1 plays a key role in chronic stress-induced cognitive impairment by acting on DARPP-32. Methods: In this study, postnatal 21-day-old male BALB/c mice were exposed to chronic unpredictable stressors. After that, the mice were treated with ADAR1 inducer/inhibitor. The cognitive ability and cerebral DARPP-32 protein expression of BALB/c mice were evaluated. In order to explore the link between ADAR1 and DARPP-32, the effects of ADAR1 high/low expression on DARPP-32 protein expression in vitro were detected. Results: ADAR1 inducer alleviates cognitive impairment and recovers decreased DARPP-32 protein expression of the hippocampus and prefrontal cortex in BALB/c mice with chronic unpredictable stress exposure. In vivo and in vitro studies confirm the results predicted by bio-informatics; that is, ADAR1 affects DARPP-32 expression via miR-874-3p. Discussion: The results in this study demonstrate that ADAR1 affects the expression of DARPP-32 via miR-874-3p, which is involved in the molecular mechanism of pathogenesis in chronic unpredictable stress-induced cognitive impairment. The new findings of this study provide a new therapeutic strategy for the prevention and treatment of stress cognitive impairment from epigenetics.
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Affiliation(s)
- Yanfang Wang
- College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Yingxin Liu
- College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Ziwei Zhao
- College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Xinyu Wu
- College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Jiabin Lin
- College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Yufei Li
- National and Local Joint Engineering Research Center for Drug Research and Development of Neurodegenerative Diseases, Dalian, China
| | - Wei Yan
- College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Yi Wu
- College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Yanfei Shi
- College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Xindi Wu
- College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Ying Xue
- College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Jiaqian He
- College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Shuqi Liu
- College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Xiaonan Zhang
- College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Hong Xu
- College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Yiyuan Tang
- College of Health Solutions, Phoenix, AZ, United States
| | - Shengming Yin
- College of Basic Medical Sciences, Dalian Medical University, Dalian, China
- *Correspondence: Shengming Yin,
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Welden JR, Margvelani G, Arizaca Maquera KA, Gudlavalleti B, Miranda Sardón S, Campos A, Robil N, Lee D, Hernandez A, Wang WX, Di J, de la Grange P, Nelson P, Stamm S. RNA editing of microtubule-associated protein tau circular RNAs promotes their translation and tau tangle formation. Nucleic Acids Res 2022; 50:12979-12996. [PMID: 36533443 PMCID: PMC9825173 DOI: 10.1093/nar/gkac1129] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 10/06/2022] [Accepted: 11/09/2022] [Indexed: 12/23/2022] Open
Abstract
Aggregation of the microtubule-associated protein tau characterizes tauopathies, including Alzheimer's disease and frontotemporal lobar degeneration (FTLD-Tau). Gene expression regulation of tau is complex and incompletely understood. Here we report that the human tau gene (MAPT) generates two circular RNAs (circRNAs) through backsplicing of exon 12 to either exon 7 (12→7 circRNA) or exon 10 (12→10 circRNA). Both circRNAs lack stop codons. The 12→7 circRNA contains one start codon and is translated in a rolling circle, generating a protein consisting of multimers of the microtubule-binding repeats R1-R4. For the 12→10 circRNA, a start codon can be introduced by two FTLD-Tau mutations, generating a protein consisting of multimers of the microtubule-binding repeats R2-R4, suggesting that mutations causing FTLD may act in part through tau circRNAs. Adenosine to inosine RNA editing dramatically increases translation of circRNAs and, in the 12→10 circRNA, RNA editing generates a translational start codon by changing AUA to AUI. Circular tau proteins self-aggregate and promote aggregation of linear tau proteins. Our data indicate that adenosine to inosine RNA editing initiates translation of human circular tau RNAs, which may contribute to tauopathies.
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Affiliation(s)
| | - Giorgi Margvelani
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA
| | | | - Bhavani Gudlavalleti
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA
| | - Sandra C Miranda Sardón
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA
| | - Alexandre Rosa Campos
- Sanford Burnham Prebys Medical Discovery Institute Proteomics Core, La Jolla, CA, USA
| | | | - Daniel C Lee
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA,Alzheimer's Disease Research Center Neuroscience, University of Kentucky, Lexington, KY, USA
| | | | - Wang-Xia Wang
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA,Alzheimer's Disease Research Center and Department of Pathology and Laboratory Medicine, University of Kentucky, Lexington, KY, USA
| | - Jing Di
- Alzheimer's Disease Research Center and Department of Pathology and Laboratory Medicine, University of Kentucky, Lexington, KY, USA
| | | | - Peter T Nelson
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA,Alzheimer's Disease Research Center and Department of Pathology and Laboratory Medicine, University of Kentucky, Lexington, KY, USA
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14
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Karmon M, Kopel E, Barzilai A, Geva P, Eisenberg E, Levanon EY, Greenberger S. Altered RNA Editing in Atopic Dermatitis Highlights the Role of Double-Stranded RNA for Immune Surveillance. J Invest Dermatol 2022; 143:933-943.e8. [PMID: 36502941 DOI: 10.1016/j.jid.2022.11.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 10/03/2022] [Accepted: 11/10/2022] [Indexed: 12/13/2022]
Abstract
Atopic dermatitis (AD) is associated with dysregulated type 1 IFN‒mediated responses, in parallel with the dominant type 2 inflammation. However, the pathophysiology of this dysregulation is largely unknown. Adenosine-to-inosine RNA editing plays a critical role in immune regulation by preventing double-stranded RNA recognition by MDA5 and IFN activation. We studied global adenosine-to-inosine editing in AD to elucidate the role played by altered editing in the pathophysiology of this disease. Analysis of three RNA-sequencing datasets of AD skin samples revealed reduced levels of adenosine-to-inosine RNA editing in AD. This reduction was seen globally throughout Alu repeats as well as in coding genes and in specific pre-mRNA loci expected to create long double-stranded RNA, the main substrate of MDA5 leading to type I IFN activation. Consistently, IFN signature genes were upregulated. In contrast, global editing was not altered in systemic lupus erythematosus and systemic sclerosis, despite IFN activation. Our results indicate that altered editing leading to impairment of the innate immune response may be involved in the pathogenesis of AD. Possibly, it may be relevant for additional autoimmune and inflammatory diseases.
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Affiliation(s)
- Miriam Karmon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Eli Kopel
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Aviv Barzilai
- Department of Dermatology, Sheba Medical Center, Tel Hashomer, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Polina Geva
- Department of Dermatology, Sheba Medical Center, Tel Hashomer, Israel
| | - Eli Eisenberg
- Raymond & Beverly Sackler School of Physics & Astronomy, Raymond & Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Erez Y Levanon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Shoshana Greenberger
- Department of Dermatology, Sheba Medical Center, Tel Hashomer, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
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15
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Kim K, Calabrese P, Wang S, Qin C, Rao Y, Feng P, Chen XS. The roles of APOBEC-mediated RNA editing in SARS-CoV-2 mutations, replication and fitness. Sci Rep 2022; 12:14972. [PMID: 36100631 PMCID: PMC9470679 DOI: 10.1038/s41598-022-19067-x] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 08/24/2022] [Indexed: 11/15/2022] Open
Abstract
During COVID-19 pandemic, mutations of SARS-CoV-2 produce new strains that can be more infectious or evade vaccines. Viral RNA mutations can arise from misincorporation by RNA-polymerases and modification by host factors. Analysis of SARS-CoV-2 sequence from patients showed a strong bias toward C-to-U mutation, suggesting a potential mutational role by host APOBEC cytosine deaminases that possess broad anti-viral activity. We report the first experimental evidence demonstrating that APOBEC3A, APOBEC1, and APOBEC3G can edit on specific sites of SARS-CoV-2 RNA to produce C-to-U mutations. However, SARS-CoV-2 replication and viral progeny production in Caco-2 cells are not inhibited by the expression of these APOBECs. Instead, expression of wild-type APOBEC3 greatly promotes viral replication/propagation, suggesting that SARS-CoV-2 utilizes the APOBEC-mediated mutations for fitness and evolution. Unlike the random mutations, this study suggests the predictability of all possible viral genome mutations by these APOBECs based on the UC/AC motifs and the viral genomic RNA structure.
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Affiliation(s)
- Kyumin Kim
- Molecular and Computational Biology Section, University of Southern California, Los Angeles, CA, 90089, USA
| | - Peter Calabrese
- Quantitative and Computational Biology Department, University of Southern California, Los Angeles, CA, 90089, USA
| | - Shanshan Wang
- Molecular and Computational Biology Section, University of Southern California, Los Angeles, CA, 90089, USA
| | - Chao Qin
- Section of Infection and Immunity, Herman Ostrow School of Dentistry, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, 90089, USA
| | - Youliang Rao
- Section of Infection and Immunity, Herman Ostrow School of Dentistry, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, 90089, USA
| | - Pinghui Feng
- Section of Infection and Immunity, Herman Ostrow School of Dentistry, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, 90089, USA
| | - Xiaojiang S Chen
- Molecular and Computational Biology Section, University of Southern California, Los Angeles, CA, 90089, USA.
- Genetic, Molecular and Cellular Biology Program, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA.
- Center of Excellence in NanoBiophysics, University of Southern California, Los Angeles, CA, 90089, USA.
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, 90089, USA.
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16
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Identification and validation of candidate genes for high calcium content in finger millet [Eleusine coracana (L.) Gaertn.] through genome-wide association study. J Cereal Sci 2022. [DOI: 10.1016/j.jcs.2022.103517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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17
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Evidence against the Human Metapneumovirus G, SH, and M2-2 Proteins as Bona Fide Interferon Antagonists. J Virol 2022; 96:e0072322. [PMID: 35975999 PMCID: PMC9472654 DOI: 10.1128/jvi.00723-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The production of type I interferon (IFN) is the hallmark of the innate immune response. Most, if not all, mammalian viruses have a way to circumvent this response. Fundamental knowledge on viral evasion of innate immune responses may facilitate the design of novel antiviral therapies. To investigate how human metapneumovirus (HMPV) interacts with the innate immune response, recombinant viruses lacking G, short hydrophobic (SH), or M2-2 protein expression were assessed for IFN induction in A549 cells. HMPV lacking G or SH protein expression induced similarly low levels of IFN, compared to the wild-type virus, whereas HMPV lacking M2-2 expression induced significantly more IFN than the wild-type virus. However, sequence analysis of the genomes of M2-2 mutant viruses revealed large numbers of mutations throughout the genome. Over 70% of these nucleotide substitutions were A-to-G and T-to-C mutations, consistent with the properties of the adenosine deaminase acting on RNA (ADAR) protein family. Knockdown of ADAR1 by CRISPR interference confirmed the role of ADAR1 in the editing of M2-2 deletion mutant virus genomes. More importantly, Northern blot analyses revealed the presence of defective interfering RNAs (DIs) in M2-2 mutant viruses and not in the wild-type virus or G and SH deletion mutant viruses. DIs are known to be potent inducers of the IFN response. The presence of DIs in M2-2 mutant virus stocks and hypermutated virus genomes interfere with studies on HMPV and the innate immune response and should be addressed in future studies. IMPORTANCE Understanding the interaction between viruses and the innate immune response is one of the barriers to the design of antiviral therapies. Here, we investigated the role of the G, SH, and M2-2 proteins of HMPV as type I IFN antagonists. In contrast to other studies, no IFN-antagonistic functions could be observed for the G and SH proteins. HMPV with a deletion of the M2-2 protein did induce type I IFN production upon infection of airway epithelial cells. However, during generation of virus stocks, these viruses rapidly accumulated DIs, which are strong activators of the type I IFN response. Additionally, the genomes of these viruses were hypermutated, which was prevented by generating stocks in ADAR knockdown cells, confirming a role for ADAR in hypermutation of HMPV genomes or DIs. These data indicate that a role of the HMPV M2-2 protein as a bona fide IFN antagonist remains elusive.
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18
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Liu J, Wang F, Zhang Y, Liu J, Zhao B. ADAR1-Mediated RNA Editing and Its Role in Cancer. Front Cell Dev Biol 2022; 10:956649. [PMID: 35898396 PMCID: PMC9309331 DOI: 10.3389/fcell.2022.956649] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 06/23/2022] [Indexed: 11/13/2022] Open
Abstract
It is well known that the stability of RNA, the interaction between RNA and protein, and the correct translation of protein are significant forces that drive the transition from normal cell to malignant tumor. Adenosine deaminase acting on RNA 1 (ADAR1) is an RNA editing enzyme that catalyzes the deamination of adenosine to inosine (A-to-I), which is one dynamic modification that in a combinatorial manner can give rise to a very diverse transcriptome. ADAR1-mediated RNA editing is essential for survival in mammals and its dysregulation results in aberrant editing of its substrates that may affect the phenotypic changes in cancer. This overediting phenomenon occurs in many cancers, such as liver, lung, breast, and esophageal cancers, and promotes tumor progression in most cases. In addition to its editing role, ADAR1 can also play an editing-independent role, although current research on this mechanism is relatively shallowly explored in tumors. In this review, we summarize the nature of ADAR1, mechanisms of ADAR1 editing-dependent and editing-independent and implications for tumorigenesis and prognosis, and pay special attention to effects of ADAR1 on cancers by regulating non-coding RNA formation and function.
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Affiliation(s)
- Jizhe Liu
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, China
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, China
| | - Fei Wang
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, China
- Mengchao Med-X Center, Fuzhou University, Fuzhou, China
| | - Yindan Zhang
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, China
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, China
| | - Jingfeng Liu
- Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou, China
- *Correspondence: Jingfeng Liu, ; Bixing Zhao,
| | - Bixing Zhao
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, China
- Mengchao Med-X Center, Fuzhou University, Fuzhou, China
- *Correspondence: Jingfeng Liu, ; Bixing Zhao,
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Rajendren S, Karijolich J. The Impact of RNA modifications on the Biology of DNA Virus Infection. Eur J Cell Biol 2022; 101:151239. [PMID: 35623231 PMCID: PMC9549750 DOI: 10.1016/j.ejcb.2022.151239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 05/15/2022] [Accepted: 05/16/2022] [Indexed: 11/26/2022] Open
Abstract
Approximately 170 RNA modifications have been identified and these are critical for determining the fate and function of cellular RNAs. Similar to human transcripts, viral RNAs possess an extensive RNA modification landscape. While initial efforts largely focused on investigating the RNA modification landscape in the context of RNA virus infection, a growing body of work has explored the impact of RNA modifications on DNA virus biology. These studies have revealed roles for RNA modifications in DNA virus infection, including gene regulation and viral pathogenesis. In this review, we will discuss the current knowledge on how RNA modifications impact DNA virus biology.
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20
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Tassinari V, Cerboni C, Soriani A. Self or Non-Self? It Is also a Matter of RNA Recognition and Editing by ADAR1. BIOLOGY 2022; 11:biology11040568. [PMID: 35453767 PMCID: PMC9024829 DOI: 10.3390/biology11040568] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 04/01/2022] [Accepted: 04/06/2022] [Indexed: 01/19/2023]
Abstract
Simple Summary A fundamental feature of innate immune cells is to detect the presence of non-self, such as potentially harmful nucleic acids, by germline-encoded specialized receptors called pattern recognition receptors (PRRs). ADAR1 is one key enzyme avoiding aberrant type I interferon (IFN-I) production and immune cell activation by the conversion of adenosine to inosine (A-to-I) in double-stranded RNA (dsRNA) structures that arise in self mRNA containing specific repetitive elements. This review intends to give an up-to-date and detailed overview of the ADAR1-mediated ability to modulate the immune response in autoimmune diseases and cancer progression. Abstract A-to-I editing is a post-transcriptional mechanism affecting coding and non-coding dsRNAs, catalyzed by the adenosine deaminases acting on the RNA (ADAR) family of enzymes. A-to-I modifications of endogenous dsRNA (mainly derived from Alu repetitive elements) prevent their recognition by cellular dsRNA sensors, thus avoiding the induction of antiviral signaling and uncontrolled IFN-I production. This process, mediated by ADAR1 activity, ensures the activation of an innate immune response against foreign (non-self) but not self nucleic acids. As a consequence, ADAR1 mutations or its de-regulated activity promote the development of autoimmune diseases and strongly impact cell growth, also leading to cancer. Moreover, the excessive inflammation promoted by Adar1 ablation also impacts T and B cell maturation, as well as the development of dendritic cell subsets, revealing a new role of ADAR1 in the homeostasis of the immune system.
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Kim K, Calabrese P, Wang S, Qin C, Rao Y, Feng P, Chen XS. The Roles of APOBEC-mediated RNA Editing in SARS-CoV-2 Mutations, Replication and Fitness.. [PMID: 34981048 PMCID: PMC8722585 DOI: 10.1101/2021.12.18.473309] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
During COVID-19 pandemic, mutations of SARS-CoV-2 produce new strains that can be more infectious or evade vaccines. Viral RNA mutations can arise from misincorporation by RNA-polymerases and modification by host factors. Analysis of SARS-CoV-2 sequence from patients showed a strong bias toward C-to-U mutation, suggesting a potential mutational role by host APOBEC cytosine deaminases that possess broad anti-viral activity. We report the first experimental evidence demonstrating that APOBEC3A, APOBEC1, and APOBEC3G can edit on specific sites of SARS-CoV-2 RNA to produce C-to-U mutations. However, SARS-CoV-2 replication and viral progeny production in Caco-2 cells are not inhibited by the expression of these APOBECs. Instead, expression of wild-type APOBEC3 greatly promotes viral replication/propagation, suggesting that SARS-CoV-2 utilizes the APOBEC-mediated mutations for fitness and evolution. Unlike the random mutations, this study suggests the predictability of all possible viral genome mutations by these APOBECs based on the UC/AC motifs and the viral genomic RNA structure. Efficient Editing of SARS-CoV-2 genomic RNA by Host APOBEC deaminases and Its Potential Impacts on the Viral Replication and Emergence of New Strains in COVID-19 Pandemic
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22
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Cai D, Sun C, Zhang G, Que X, Fujise K, Weintraub NL, Chen SY. A Novel Mechanism Underlying Inflammatory Smooth Muscle Phenotype in Abdominal Aortic Aneurysm. Circ Res 2021; 129:e202-e214. [PMID: 34551587 PMCID: PMC8575453 DOI: 10.1161/circresaha.121.319374] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Dunpeng Cai
- Departments of Surgery, University of Missouri School of Medicine, Columbia, MO
- Department of Medical Pharmacology & Physiology, University of Missouri School of Medicine, Columbia, MO
| | - Chenming Sun
- Department of Physiology & Pharmacology, University of Georgia, Athens, GA
| | - Gui Zhang
- Department of Physiology & Pharmacology, University of Georgia, Athens, GA
| | - Xingyi Que
- Departments of Surgery, University of Missouri School of Medicine, Columbia, MO
| | - Ken Fujise
- Harborview Medical Center, Department of Medicine, University of Washington, Seattle, WA
| | - Neal L Weintraub
- Department of Medicine, Medical College of Georgia at Augusta University, Augusta, GA
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, GA
| | - Shi-You Chen
- Departments of Surgery, University of Missouri School of Medicine, Columbia, MO
- Department of Medical Pharmacology & Physiology, University of Missouri School of Medicine, Columbia, MO
- Department of Physiology & Pharmacology, University of Georgia, Athens, GA
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23
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Bhakta S, Tsukahara T. Artificial RNA Editing with ADAR for Gene Therapy. Curr Gene Ther 2021; 20:44-54. [PMID: 32416688 DOI: 10.2174/1566523220666200516170137] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 04/28/2020] [Accepted: 04/29/2020] [Indexed: 12/14/2022]
Abstract
Editing mutated genes is a potential way for the treatment of genetic diseases. G-to-A mutations are common in mammals and can be treated by adenosine-to-inosine (A-to-I) editing, a type of substitutional RNA editing. The molecular mechanism of A-to-I editing involves the hydrolytic deamination of adenosine to an inosine base; this reaction is mediated by RNA-specific deaminases, adenosine deaminases acting on RNA (ADARs), family protein. Here, we review recent findings regarding the application of ADARs to restoring the genetic code along with different approaches involved in the process of artificial RNA editing by ADAR. We have also addressed comparative studies of various isoforms of ADARs. Therefore, we will try to provide a detailed overview of the artificial RNA editing and the role of ADAR with a focus on the enzymatic site directed A-to-I editing.
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Affiliation(s)
- Sonali Bhakta
- Area of Bioscience and Biotechnology, School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomicity, Ishikawa, 923-1292, Japan
| | - Toshifumi Tsukahara
- Area of Bioscience and Biotechnology, School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomicity, Ishikawa, 923-1292, Japan
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Abstract
C6 deamination of adenosine (A) to inosine (I) in double-stranded RNA (dsRNA) is catalyzed by a family of enzymes known as ADARs (adenosine deaminases acting on RNA) encoded by three genes in mammals. Alternative promoters and splicing produce two ADAR1 proteins, an interferon-inducible cytoplasmic p150 and a constitutively expressed p110 that like ADAR2 is a nuclear enzyme. ADAR3 lacks deaminase activity. A-to-I editing occurs with both viral and cellular RNAs. Deamination activity is dependent on dsRNA substrate structure and regulatory RNA-binding proteins and ranges from highly site selective with hepatitis D RNA and glutamate receptor precursor messenger RNA (pre-mRNA) to hyperediting of measles virus and polyomavirus transcripts and cellular inverted Alu elements. Because I base-pairs as guanosine instead of A, editing can alter mRNA decoding, pre-mRNA splicing, and microRNA silencing. Editing also alters dsRNA structure, thereby suppressing innate immune responses including interferon production and action. Expected final online publication date for the Annual Review of Virology, Volume 8 is September 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Christian K Pfaller
- Division of Veterinary Medicine, Paul-Ehrlich-Institute, Langen 63225, Germany
| | - Cyril X George
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, California 93106, USA;
| | - Charles E Samuel
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, California 93106, USA;
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The involvement of ADAR1 in antidepressant action by regulating BDNF via miR-432. Behav Brain Res 2021; 402:113087. [PMID: 33412228 DOI: 10.1016/j.bbr.2020.113087] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 11/16/2020] [Accepted: 12/16/2020] [Indexed: 12/26/2022]
Abstract
Brain-derived neurotrophic factor (BDNF) is a biomarker of depression. Recent studies have found adenosine deaminase acting on RNA1 (ADAR1) is a novel target being sensitive to stress at epigenetic level. The epigenetic regulation mechanism of stress-related depression is still unclear so far. To explore the potential regulating mechanism of ADAR1 on BDNF, over and low expression of ADAR1 in PC12 and SH-SY5Y cell lines are prepared. In the meanwhile, chronic unpredictable stress (CUS) mice are treated with ADAR1 inducer (interferon-γ, IFN-γ). ADAR1 regulates BDNF expression, which is proven by that over and low expressions of ADAR1 increase and decrease BDNF mRNA and protein respectively in vitro. Additionally, ADAR1 inducer alleviates the depressive-like behavior of CUS mice by recovering the decreased BDNF protein in brain and serum. Moreover, over and low expressions of ADAR1 reduce and enhance microRNA-432 (miR-432) expression respectively in vitro. Furtherly, over and low miR-432 expressions lead to decreased and increased BDNF and ADAR1 mRNA, protein and immunoreactivity respectively in vitro. The above results demonstrate that ADAR1 is involved in antidepressant action by regulating BDNF via miR-432. Those novel findings can provide a new idea for the study of epigenetic regulation mechanism, early diagnosis, and effective treatment of stress-related depression.
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Abstract
Population genetic diversity plays a prominent role in viral evolution, pathogenesis, immune escape, and drug resistance. Different mechanisms are responsible for creating and maintaining genetic diversity in viruses, including error-prone replication, repair avoidance, and genome editing, among others. This diversity is subsequently modulated by natural selection and random genetic drift, whose action in turn depends on multiple factors including viral genetic architecture, viral demography, and ecology. Understanding these processes should contribute to the development of more efficient control and treatment strategies against viral pathogens.
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Abstract
The type I interferonopathies comprise a heterogenous group of monogenic diseases associated with a constitutive activation of type I interferon signaling.The elucidation of the genetic causes of this group of diseases revealed an alteration of nucleic acid processing and signaling.ADAR1 is among the genes found mutated in patients with this type of disorders.This enzyme catalyzes the hydrolytic deamination of adenosines in inosines within a double-stranded RNA target (RNA editing of A to I). This RNA modification is widespread in human cells and deregulated in a variety of human diseases, ranging from cancers to neurological abnormalities.In this review, we briefly summarize the knowledge about the RNA editing alterations occurring in patients with mutations in ADAR1 gene and how these alterations might cause the inappropriate IFN activation.
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Affiliation(s)
- Loredana Frassinelli
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Silvia Galardi
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Silvia Anna Ciafrè
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Alessandro Michienzi
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy.
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Li T, Yang X, Li W, Song J, Li Z, Zhu X, Wu X, Liu Y. ADAR1 Stimulation by IFN-α Downregulates the Expression of MAVS via RNA Editing to Regulate the Anti-HBV Response. Mol Ther 2020; 29:1335-1348. [PMID: 33279720 DOI: 10.1016/j.ymthe.2020.11.031] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 10/27/2020] [Accepted: 11/25/2020] [Indexed: 02/07/2023] Open
Abstract
The partial response of chronic hepatitis B virus (CHB) patients to interferon-α (IFN-α) therapy remains elusive, which requires a better understanding of the involved molecular mechanism. In our study, bioinformatics analysis was applied to relate IFN-α regulated candidate genes and RNA editing sites by RNA sequencing. Mitochondrial antiviral signaling protein (MAVS) antiviral effect was confirmed in HepG2.2.15 cells and in two mouse models. The associations between polymorphisms in MAVS gene and response to IFN-α therapy were confirmed in CHB patients. We found that IFN-α downregulates MAVS via RNA editing that was mediated by adenosine deaminase acting on RNA (ADAR1). ADAR1 inhibited MAVS expression via a human antigen R (HuR)-mediated post-transcriptional regulation. MAVS exerted an antiviral activity and reduced the level of hepatitis B virus (HBV) markers in vitro and in vivo. IFN-α antiviral effects were significantly enhanced by MAVS co-transfection. Hepatitis B core protein (HBc) interacted with SP1 to inhibit the promoter activity of MAVS that regulates its expression. CHB patients with a rs3746662A allele had higher MAVS expression and thus were more responsive to IFN-α treatment. In this work, we demonstrated that the decrease of MAVS expression is mediated by the IFN-α-ADAR1 axis. This study also highlighted the potential for the clinical application of MAVS in combination with IFN-α for the treatment of HBV infection.
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Affiliation(s)
- Tao Li
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing 100005, P.R. China
| | - Xiaoshuang Yang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing 100005, P.R. China
| | - Wei Li
- Department of Interventional Radiology, the Affiliated Hospital of Qingdao University, Shandong 266003, P.R. China
| | - Jiaru Song
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing 100005, P.R. China
| | - Zhuo Li
- Department of Infectious Disease, Affiliated You'an Hospital, Capital University of Medical Science, Beijing 100069, P.R. China
| | - Xilin Zhu
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing 100005, P.R. China
| | - Xiaopan Wu
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing 100005, P.R. China.
| | - Ying Liu
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing 100005, P.R. China.
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Zhou S, Yang C, Zhao F, Huang Y, Lin Y, Huang C, Ma X, Du J, Wang Y, Long G, He J, Liu C, Zhang P. Double-stranded RNA deaminase ADAR1 promotes the Zika virus replication by inhibiting the activation of protein kinase PKR. J Biol Chem 2019; 294:18168-18180. [PMID: 31636123 DOI: 10.1074/jbc.ra119.009113] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 10/03/2019] [Indexed: 12/14/2022] Open
Abstract
Zika virus (ZIKV) is a mosquito-borne flavivirus that has emerged as a threat to global health. The family of adenosine deaminases acting on dsRNA (ADARs) are human host factors important for the genetic diversity and evolution of ZIKV. Here, we further investigated the role of ADAR1 in ZIKV replication by utilizing CRISPR/Cas9-based gene editing and RNAi-based gene knockdown techniques. Both ADAR1 knockout and knockdown significantly reduced ZIKV RNA synthesis, protein levels, and viral titers in several human cell lines. Trans-complementation with the full-length ADAR1 form p150 or the shorter form p110 lacking the Zα domain restored viral replication levels suppressed by the ADAR1 knockout. Moreover, we observed that the nuclear p110 form was redistributed to the cytoplasm in response to ZIKV infection. ADAR1 was not involved in viral entry but promoted viral protein translation by impairing ZIKV-induced activation of protein kinase regulated by dsRNA (PKR). Of note, the RNA-editing activity of ADAR1 was not required to promote ZIKV replication. We also found that the proviral role of ADAR1 was partially mediated through its ability to suppress IFN production and PKR activation. Our work identifies ADAR1 as a proviral factor involved in ZIKV replication, suggesting that ADAR1 could be a potential antiviral target.
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Affiliation(s)
- Shili Zhou
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou 510080, China
| | - Chao Yang
- Department of Neurosurgery, First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China
| | - Fanfan Zhao
- Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yanxia Huang
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou 510080, China
| | - Yuxia Lin
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou 510080, China
| | - Changbai Huang
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou 510080, China
| | - Xiaocao Ma
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou 510080, China
| | - Jingjie Du
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou 510080, China
| | - Yi Wang
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou 510080, China
| | - Gang Long
- Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Junfang He
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou 510080, China
| | - Chao Liu
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou 510080, China.
| | - Ping Zhang
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou 510080, China.
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Lamers MM, van den Hoogen BG, Haagmans BL. ADAR1: "Editor-in-Chief" of Cytoplasmic Innate Immunity. Front Immunol 2019; 10:1763. [PMID: 31404141 PMCID: PMC6669771 DOI: 10.3389/fimmu.2019.01763] [Citation(s) in RCA: 123] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 07/11/2019] [Indexed: 12/12/2022] Open
Abstract
Specialized receptors that recognize molecular patterns such as double stranded RNA duplexes-indicative of viral replication-are potent triggers of the innate immune system. Although their activation is beneficial during viral infection, RNA transcribed from endogenous mobile genetic elements may also act as ligands potentially causing autoimmunity. Recent advances indicate that the adenosine deaminase ADAR1 through RNA editing is involved in dampening the canonical antiviral RIG-I-like receptor-, PKR-, and OAS-RNAse L pathways to prevent autoimmunity. However, this inhibitory effect must be overcome during viral infections. In this review we discuss ADAR1's critical role in balancing immune activation and self-tolerance.
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Adenosine Deaminase Acting on RNA 1 Associates with Orf Virus OV20.0 and Enhances Viral Replication. J Virol 2019; 93:JVI.01912-18. [PMID: 30651363 DOI: 10.1128/jvi.01912-18] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 12/21/2018] [Indexed: 01/08/2023] Open
Abstract
Orf virus (ORFV) infects sheep and goats and is also an important zoonotic pathogen. The viral protein OV20.0 has been shown to suppress innate immunity by targeting the double-stranded RNA (dsRNA)-activated protein kinase (PKR) by multiple mechanisms. These mechanisms include a direct interaction with PKR and binding with two PKR activators, dsRNA and the cellular PKR activator (PACT), which ultimately leads to the inhibition of PKR activation. In the present study, we identified a novel association between OV20.0 and adenosine deaminase acting on RNA 1 (ADAR1). OV20.0 bound directly to the dsRNA binding domains (RBDs) of ADAR1 in the absence of dsRNA. Additionally, OV20.0 preferentially interacted with RBD1 of ADAR1, which was essential for its dsRNA binding ability and for the homodimerization that is critical for intact adenosine-to-inosine (A-to-I)-editing activity. Finally, the association with OV20.0 suppressed the A-to-I-editing ability of ADAR1, while ADAR1 played a proviral role during ORFV infection by inhibiting PKR phosphorylation. These observations revealed a new strategy used by OV20.0 to evade antiviral responses via PKR.IMPORTANCE Viruses evolve specific strategies to counteract host innate immunity. ORFV, an important zoonotic pathogen, encodes OV20.0 to suppress PKR activation via multiple mechanisms, including interactions with PKR and two PKR activators. In this study, we demonstrated that OV20.0 interacts with ADAR1, a cellular enzyme responsible for converting adenosine (A) to inosine (I) in RNA. The RNA binding domains, but not the catalytic domain, of ADAR1 are required for this interaction. The OV20.0-ADAR1 association affects the functions of both proteins; OV20.0 suppressed the A-to-I editing of ADAR1, while ADAR1 elevated OV20.0 expression. The proviral role of ADAR1 is likely due to the inhibition of PKR phosphorylation. As RNA editing by ADAR1 contributes to the stability of the genetic code and the structure of RNA, these observations suggest that in addition to serving as a PKR inhibitor, OV20.0 might modulate ADAR1-dependent gene expression to combat antiviral responses or achieve efficient viral infection.
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Samuel CE. Adenosine deaminase acting on RNA (ADAR1), a suppressor of double-stranded RNA-triggered innate immune responses. J Biol Chem 2019; 294:1710-1720. [PMID: 30710018 PMCID: PMC6364763 DOI: 10.1074/jbc.tm118.004166] [Citation(s) in RCA: 111] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Herbert "Herb" Tabor, who celebrated his 100th birthday this past year, served the Journal of Biological Chemistry as a member of the Editorial Board beginning in 1961, as an Associate Editor, and as Editor-in-Chief for 40 years, from 1971 until 2010. Among the many discoveries in biological chemistry during this period was the identification of RNA modification by C6 deamination of adenosine (A) to produce inosine (I) in double-stranded (ds) RNA. This posttranscriptional RNA modification by adenosine deamination, known as A-to-I RNA editing, diversifies the transcriptome and modulates the innate immune interferon response. A-to-I editing is catalyzed by a family of enzymes, adenosine deaminases acting on dsRNA (ADARs). The roles of A-to-I editing are varied and include effects on mRNA translation, pre-mRNA splicing, and micro-RNA silencing. Suppression of dsRNA-triggered induction and action of interferon, the cornerstone of innate immunity, has emerged as a key function of ADAR1 editing of self (cellular) and nonself (viral) dsRNAs. A-to-I modification of RNA is essential for the normal regulation of cellular processes. Dysregulation of A-to-I editing by ADAR1 can have profound consequences, ranging from effects on cell growth and development to autoimmune disorders.
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Affiliation(s)
- Charles E Samuel
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, California 93106.
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Zhang X, Gao X, Hu J, Xie Y, Zuo Y, Xu H, Zhu S. ADAR1p150 Forms a Complex with Dicer to Promote miRNA-222 Activity and Regulate PTEN Expression in CVB3-Induced Viral Myocarditis. Int J Mol Sci 2019; 20:ijms20020407. [PMID: 30669342 PMCID: PMC6359435 DOI: 10.3390/ijms20020407] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Revised: 01/02/2019] [Accepted: 01/04/2019] [Indexed: 02/06/2023] Open
Abstract
Adenosine deaminases acting on RNA (ADAR) are enzymes that regulate RNA metabolism through post-transcriptional mechanisms. ADAR1 is involved in a variety of pathological conditions including inflammation, cancer, and the host defense against viral infections. However, the role of ADAR1p150 in vascular disease remains unclear. In this study, we examined the expression of ADAR1p150 and its role in viral myocarditis (VMC) in a mouse model. VMC mouse cardiomyocytes showed significantly higher expression of ADAR1p150 compared to the control samples. Coimmunoprecipitation verified that ADAR1p150 forms a complex with Dicer in VMC. miRNA-222, which is involved in many cardiac diseases, is highly expressed in cardiomyocytes in VMC. In addition, the expression of miRNA-222 was promoted by ADAR1p150/Dicer. Among the target genes of miRNA-222, the expression of phosphatase-and-tensin (PTEN) protein was significantly reduced in VMC. By using a bioinformatics tool, we found a potential binding site of miRNA-222 on the PTEN gene’s 3′-UTR, suggesting that miRNA-222 might play a regulatory role. In cultured cells, miR-222 suppressed PTEN expression. Our findings suggest that ADAR1p150 plays a key role in complexing with Dicer and promoting the expression of miRNA-222, the latter of which suppresses the expression of the target gene PTEN during VMC. Our work reveals a previously unknown role of ADAR1p150 in gene expression in VMC.
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Affiliation(s)
- Xincai Zhang
- Institute of Forensic Medicine, Soochow University, Suzhou 215021, China.
| | - Xiangting Gao
- Department of Pathology, School of Medicine, Shihezi University, Shihezi 215021, China.
| | - Jun Hu
- Institute of Forensic Medicine, Soochow University, Suzhou 215021, China.
| | - Yuxin Xie
- Institute of Forensic Medicine, Soochow University, Suzhou 215021, China.
| | - Yuanyi Zuo
- Institute of Forensic Medicine, Soochow University, Suzhou 215021, China.
| | - Hongfei Xu
- Institute of Forensic Medicine, Soochow University, Suzhou 215021, China.
| | - Shaohua Zhu
- Institute of Forensic Medicine, Soochow University, Suzhou 215021, China.
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Abstract
Left-handed Z-DNA/Z-RNA is bound with high affinity by the Zα domain protein family that includes ADAR (a double-stranded RNA editing enzyme), ZBP1 and viral orthologs regulating innate immunity. Loss-of-function mutations in ADAR p150 allow persistent activation of the interferon system by Alu dsRNAs and are causal for Aicardi-Goutières Syndrome. Heterodimers of ADAR and DICER1 regulate the switch from RNA- to protein-centric immunity. Loss of DICER1 function produces age-related macular degeneration, a different type of Alu-mediated disease. The overlap of Z-forming sites with those for the signal recognition particle likely limits invasion of primate genomes by Alu retrotransposons.
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Affiliation(s)
- Alan Herbert
- Discovery, InsideOutBio, 42, 8th Street, Unit 3412, Charlestown, MA 02129 USA
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Falkenhagen A, Joshi S. Genetic Strategies for HIV Treatment and Prevention. MOLECULAR THERAPY. NUCLEIC ACIDS 2018; 13:514-533. [PMID: 30388625 PMCID: PMC6205348 DOI: 10.1016/j.omtn.2018.09.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 08/28/2018] [Accepted: 09/02/2018] [Indexed: 01/02/2023]
Abstract
Conventional HIV gene therapy approaches are based on engineering HIV target cells that are non-permissive to viral replication. However, expansion of gene-modified HIV target cells has been limited in patients. Alternative genetic strategies focus on generating gene-modified producer cells that secrete antiviral proteins (AVPs). The secreted AVPs interfere with HIV entry, and, therefore, they extend the protection against infection to unmodified HIV target cells. Since any cell type can potentially secrete AVPs, hematopoietic and non-hematopoietic cell lineages can function as producer cells. Secretion of AVPs from non-hematopoietic cells opens the possibility of using a genetic approach for HIV prevention. Another strategy aims at modifying cytotoxic T cells to selectively target and eliminate infected cells. This review provides an overview of the different genetic approaches for HIV treatment and prevention.
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Affiliation(s)
- Alexander Falkenhagen
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada; Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Sadhna Joshi
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada; Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON, Canada.
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Abstract
One of the most prevalent forms of post-transcritpional RNA modification is the conversion of adenosine nucleosides to inosine (A-to-I), mediated by the ADAR family of enzymes. The functional requirement and regulatory landscape for the majority of A-to-I editing events are, at present, uncertain. Recent studies have identified key in vivo functions of ADAR enzymes, informing our understanding of the biological importance of A-to-I editing. Large-scale studies have revealed how editing is regulated both in cis and in trans. This review will explore these recent studies and how they broaden our understanding of the functions and regulation of ADAR-mediated RNA editing.
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Affiliation(s)
- Carl R Walkley
- St Vincent's Institute of Medical Research, Fitzroy, Victoria, 3065, Australia. .,Department of Medicine, St Vincent's Hospital, University of Melbourne, Fitzroy, Victoria, 3065, Australia.
| | - Jin Billy Li
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA.
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Abstract
Inosine is one of the most common modifications found in human RNAs and the Adenosine Deaminases that act on RNA (ADARs) are the main enzymes responsible for its production. ADARs were first discovered in the 1980s and since then our understanding of ADARs has advanced tremendously. For instance, it is now known that defective ADAR function can cause human diseases. Furthermore, recently solved crystal structures of the human ADAR2 deaminase bound to RNA have provided insights regarding the catalytic and substrate recognition mechanisms. In this chapter, we describe the occurrence of inosine in human RNAs and the newest perspective on the ADAR family of enzymes, including their substrate recognition, catalytic mechanism, regulation as well as the consequences of A-to-I editing, and their relation to human diseases.
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ADAR1 and PACT contribute to efficient translation of transcripts containing HIV-1 trans-activating response (TAR) element. Biochem J 2017; 474:1241-1257. [PMID: 28167698 PMCID: PMC5363390 DOI: 10.1042/bcj20160964] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 01/30/2017] [Accepted: 02/06/2017] [Indexed: 12/15/2022]
Abstract
Human immunodeficiency virus type 1 (HIV-1) has evolved various measures to counter the host cell's innate antiviral response during the course of infection. Interferon (IFN)-stimulated gene products are produced following HIV-1 infection to limit viral replication, but viral proteins and RNAs counteract their effect. One such mechanism is specifically directed against the IFN-induced Protein Kinase PKR, which is centrally important to the cellular antiviral response. In the presence of viral RNAs, PKR is activated and phosphorylates the translation initiation factor eIF2α. This shuts down the synthesis of both host and viral proteins, allowing the cell to mount an effective antiviral response. PACT (protein activator of PKR) is a cellular protein activator of PKR, primarily functioning to activate PKR in response to cellular stress. Recent studies have indicated that during HIV-1 infection, PACT's normal cellular function is compromised and that PACT is unable to activate PKR. Using various reporter systems and in vitro kinase assays, we establish in this report that interactions between PACT, ADAR1 and HIV-1-encoded Tat protein diminish the activation of PKR in response to HIV-1 infection. Our results highlight an important pathway by which HIV-1 transcripts subvert the host cell's antiviral activities to enhance their translation.
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Janus effects of ADAR1 on CVB3-induced viral myocarditis at different infection stages. Int J Cardiol 2016; 223:898-905. [DOI: 10.1016/j.ijcard.2016.08.315] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 08/18/2016] [Accepted: 08/19/2016] [Indexed: 01/05/2023]
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Cuevas JM, Combe M, Torres-Puente M, Garijo R, Guix S, Buesa J, Rodríguez-Díaz J, Sanjuán R. Human norovirus hyper-mutation revealed by ultra-deep sequencing. INFECTION GENETICS AND EVOLUTION 2016; 41:233-239. [PMID: 27094861 PMCID: PMC7172324 DOI: 10.1016/j.meegid.2016.04.017] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 04/11/2016] [Accepted: 04/15/2016] [Indexed: 02/02/2023]
Abstract
Human noroviruses (NoVs) are a major cause of gastroenteritis worldwide. It is thought that, similar to other RNA viruses, high mutation rates allow NoVs to evolve fast and to undergo rapid immune escape at the population level. However, the rate and spectrum of spontaneous mutations of human NoVs have not been quantified previously. Here, we analyzed the intra-patient diversity of the NoV capsid by carrying out RT-PCR and ultra-deep sequencing with 100,000-fold coverage of 16 stool samples from symptomatic patients. This revealed the presence of low-frequency sequences carrying large numbers of U-to-C or A-to-G base transitions, suggesting a role for hyper-mutation in NoV diversity. To more directly test for hyper-mutation, we performed transfection assays in which the production of mutations was restricted to a single cell infection cycle. This confirmed the presence of sequences with multiple U-to-C/A-to-G transitions, and suggested that hyper-mutation contributed a large fraction of the total NoV spontaneous mutation rate. The type of changes produced and their sequence context are compatible with ADAR-mediated editing of the viral RNA. Norovirus U-to-C hyper-mutants are present in patient samples. Analysis of hyper-mutants in cell culture suggests ADAR-mediated RNA edition. Hyper-mutation may contribute to norovirus diversity and evolution.
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Affiliation(s)
- José M Cuevas
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universitat de València, Valencia, Spain
| | - Marine Combe
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universitat de València, Valencia, Spain
| | - Manoli Torres-Puente
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana, Valencia, Spain
| | - Raquel Garijo
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universitat de València, Valencia, Spain
| | - Susana Guix
- Departament de Microbiologia, Universitat de Barcelona, Barcelona, Spain
| | - Javier Buesa
- Departament de Microbiologia, Universitat de València, Valencia, Spain
| | | | - Rafael Sanjuán
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universitat de València, Valencia, Spain; Departament de Genètica, Universitat de València, Valencia, Spain.
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George CX, Ramaswami G, Li JB, Samuel CE. Editing of Cellular Self-RNAs by Adenosine Deaminase ADAR1 Suppresses Innate Immune Stress Responses. J Biol Chem 2016; 291:6158-68. [PMID: 26817845 PMCID: PMC4813567 DOI: 10.1074/jbc.m115.709014] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 01/15/2016] [Indexed: 12/24/2022] Open
Abstract
Adenosine deaminases acting on double-stranded RNA (ADARs) catalyze the deamination of adenosine (A) to produce inosine (I) in double-stranded (ds) RNA structures, a process known as A-to-I RNA editing. dsRNA is an important trigger of innate immune responses, including interferon (IFN) production and action. We examined the role of A-to-I RNA editing by two ADARs, ADAR1 and ADAR2, in the sensing of self-RNA in the absence of pathogen infection, leading to activation of IFN-induced, RNA-mediated responses in mouse embryo fibroblasts. IFN treatment of Adar1(-/-) cells lacking both the p110 constitutive and p150 IFN-inducible ADAR1 proteins induced formation of stress granules, whereas neither wild-type (WT) nor Adar2(-/-) cells displayed a comparable stress granule response following IFN treatment. Phosphorylation of protein synthesis initiation factor eIF2α at serine 51 was increased in IFN-treated Adar1(-/-) cells but not in either WT or Adar2(-/-) cells following IFN treatment. Analysis by deep sequencing of mouse exonic loci containing A-to-I-editing sites revealed that the majority of editing in mouse embryo fibroblasts was carried out by ADAR1. IFN treatment increased editing in both WT and Adar2(-/-) cells but not in either Adar1(-/-) or Adar1(-/-) (p150) cells or Stat1(-/-) or Stat2(-/-) cells. Hyper-edited sites found in predicted duplex structures showed strand bias of editing for some RNAs. These results implicate ADAR1 p150 as the major A-to-I editor in mouse embryo fibroblasts, acting as a feedback suppressor of innate immune responses otherwise triggered by self-RNAs possessing regions of double-stranded character.
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Affiliation(s)
- Cyril X George
- From the Department of Molecular, Cellular and Developmental Biology and
| | - Gokul Ramaswami
- the Department of Genetics, Stanford University, Stanford, California 94305
| | - Jin Billy Li
- the Department of Genetics, Stanford University, Stanford, California 94305
| | - Charles E Samuel
- From the Department of Molecular, Cellular and Developmental Biology and the Biomolecular Sciences and Engineering Program, University of California, Santa Barbara, California 93106 and
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Tsareva E, Kulakova O, Boyko A, Favorova O. Pharmacogenetics of multiple sclerosis. Pharmacogenet Genomics 2016; 26:103-15. [DOI: 10.1097/fpc.0000000000000194] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Hu Y, Fan L, Wu C, Wang B, Sun Z, Hu C. Identification and function analysis of the three dsRBMs in the N terminal dsRBD of grass carp (Ctenopharyngodon idella) PKR. FISH & SHELLFISH IMMUNOLOGY 2016; 50:91-100. [PMID: 26806165 DOI: 10.1016/j.fsi.2016.01.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 01/10/2016] [Accepted: 01/10/2016] [Indexed: 06/05/2023]
Abstract
The protein kinase R (PKR) can inhibit protein translation and lead to apoptosis under the circumstances of virus invasion and multiple other stress conditions. PKR is a dsRNA binding protein with a dsRBD and a kinase domain (KD). dsRBD is mostly composed of two (in mammal PKR) or three (in some fish PKR) dsRNA binding motifs (dsRBMs). Multiple sequences alignment and Phylogenetic analysis indicate that the three dsRBMs of fish PKR share analogous structure but show to be divergence origination. In this study, we have identified and analyzed the three dsRBMs from grass carp (Ctenopharyngodon idellus) PKR (CiPKR), which was cloned previously in our laboratory. dsRBMs of CiPKR have two or three conserved regions involved in dsRNA binding. Among the three dsRBMs, dsRBM1 was peculiar to some fish PKRs, while dsRBM2 and dsRBM3 were closely related to the dsRBM1 and dsRBM2 of mammal PKRs respectively. Dimerization assay indicated that dsRBM1 and dsRBM2 formed not only homo-dimer but also homo-multimer; whereas dsRBM3 formed merely homo-dimer. Meanwhile, dsRBM1-2, dsRBM2-3 and dsRBM1-2-3 could homo-dimerize and homo-multimerize also. Poly I:C pull-down assay showed that the binding of dsRBM to Poly I:C needed two or three dsRBMs to cooperate in vitro, meaning one dsRBM from CiPKR could not bind to dsRNA efficiently. To further investigate the effect of dsRBM on the function of CiPKR, we constructed pcDNA3.1/CiPKR-wt and a series of CiPKR mutants recombined plasmids including pcDNA3.1/CiPKR-ΔdsRBM2-3, pcDNA3.1/CiPKR-ΔdsRBM1,3, pcDNA3.1/CiPKR-ΔdsRBM1-2, pcDNA3.1/CiPKR-ΔdsRBM3, pcDNA3.1/CiPKR-ΔdsRBM1. The recombined plasmids respectively were co-transfected with plasmid PGL3 promoter into CIK cells. In comparison with the control group, the luciferase translation inhibitions were 78.7%, 15%, 0, 0.5%, 61.8%, 67.3% respectively. The results indicated that the protein translation inhibition caused by CiPKR mutants with only one dsRBM were very weak, while those with two or three dsRBMs inhibited the protein translation powerfully. Cell viability were 34.2%, 98.2%, 112%, 108%, 50.3%, 47.5% respectively after transfected with pcDNA3.1/CiPKR-wt, pcDNA3.1/CiPKR-ΔdsRBM2-3, pcDNA3.1/CiPKR-ΔdsRBM1,3, pcDNA3.1/CiPKR-ΔdsRBM1-2, pcDNA3.1/CiPKR-ΔdsRBM3, pcDNA3.1/CiPKR-ΔdsRBM1 in order into CIK cells for 48 h. The results from cell counting also indicated that transfection of CiPKR-wt and the mutants CiPKR-ΔdsRBM3, CiPKR-ΔdsRBM1 could inhibit the protein translation and facilitated the decrease of CIK cells number. In conclusion, our observations suggested that two dsRBMs ranking in tandem at N terminal were essential for the function of CiPKR, and the presence of the extra dsRBM1 enhanced its function.
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Affiliation(s)
- Yousheng Hu
- Department of Bioscience, College of Life Science, Nanchang University, Nanchang, 330031, China; Medical College, Jinggangshan University, Ji'an, 343009, China
| | - Lihua Fan
- Department of Bioscience, College of Life Science, Nanchang University, Nanchang, 330031, China
| | - Chuxin Wu
- Nanchang Teachers College, Nanchang, 330103, China
| | - Binhua Wang
- Department of Bioscience, College of Life Science, Nanchang University, Nanchang, 330031, China
| | - Zhicheng Sun
- Department of Bioscience, College of Life Science, Nanchang University, Nanchang, 330031, China
| | - Chengyu Hu
- Department of Bioscience, College of Life Science, Nanchang University, Nanchang, 330031, China.
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Huntley MA, Lou M, Goldstein LD, Lawrence M, Dijkgraaf GJP, Kaminker JS, Gentleman R. Complex regulation of ADAR-mediated RNA-editing across tissues. BMC Genomics 2016; 17:61. [PMID: 26768488 PMCID: PMC4714477 DOI: 10.1186/s12864-015-2291-9] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 12/11/2015] [Indexed: 01/28/2023] Open
Abstract
Background RNA-editing is a tightly regulated, and essential cellular process for a properly functioning brain. Dysfunction of A-to-I RNA editing can have catastrophic effects, particularly in the central nervous system. Thus, understanding how the process of RNA-editing is regulated has important implications for human health. However, at present, very little is known about the regulation of editing across tissues, and individuals. Results Here we present an analysis of RNA-editing patterns from 9 different tissues harvested from a single mouse. For comparison, we also analyzed data for 5 of these tissues harvested from 15 additional animals. We find that tissue specificity of editing largely reflects differential expression of substrate transcripts across tissues. We identified a surprising enrichment of editing in intronic regions of brain transcripts, that could account for previously reported higher levels of editing in brain. There exists a small but remarkable amount of editing which is tissue-specific, despite comparable expression levels of the edit site across multiple tissues. Expression levels of editing enzymes and their isoforms can explain some, but not all of this variation. Conclusions Together, these data suggest a complex regulation of the RNA-editing process beyond transcript expression levels. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2291-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Melanie A Huntley
- Department of Bioinformatics and Computational Biology, Genentech Inc., 1 DNA Way, South San Francisco, USA.
| | - Melanie Lou
- Department of Bioinformatics and Computational Biology, Genentech Inc., 1 DNA Way, South San Francisco, USA.
| | - Leonard D Goldstein
- Department of Bioinformatics and Computational Biology, Genentech Inc., 1 DNA Way, South San Francisco, USA.
| | - Michael Lawrence
- Department of Bioinformatics and Computational Biology, Genentech Inc., 1 DNA Way, South San Francisco, USA.
| | - Gerrit J P Dijkgraaf
- Department of Molecular Oncology, Genentech Inc., 1 DNA Way, South San Francisco, USA.
| | - Joshua S Kaminker
- Department of Bioinformatics and Computational Biology, Genentech Inc., 1 DNA Way, South San Francisco, USA.
| | - Robert Gentleman
- Department of Bioinformatics and Computational Biology, Genentech Inc., 1 DNA Way, South San Francisco, USA.
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Controlling the Editor: The Many Roles of RNA-Binding Proteins in Regulating A-to-I RNA Editing. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 907:189-213. [PMID: 27256387 DOI: 10.1007/978-3-319-29073-7_8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
RNA editing is a cellular process used to expand and diversify the RNA transcripts produced from a generally immutable genome. In animals, the most prevalent type of RNA editing is adenosine (A) to inosine (I) deamination catalyzed by the ADAR family. Throughout development, A-to-I editing levels increase while ADAR expression is constant, suggesting cellular mechanisms to regulate A-to-I editing exist. Furthermore, in several disease states, ADAR expression levels are similar to the normal state, but A-to-I editing levels are altered. Therefore, understanding how these enzymes are regulated in normal tissues and misregulated in disease states is of profound importance. This chapter will both discuss how to identify A-to-I editing sites across the transcriptome and explore the mechanisms that regulate ADAR editing activity, with particular focus on the diverse types of RNA-binding proteins implicated in regulating A-to-I editing in vivo.
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STAT2-dependent induction of RNA adenosine deaminase ADAR1 by type I interferon differs between mouse and human cells in the requirement for STAT1. Virology 2015; 485:363-70. [PMID: 26335850 DOI: 10.1016/j.virol.2015.08.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 08/01/2015] [Accepted: 08/04/2015] [Indexed: 12/24/2022]
Abstract
Expression of adenosine deaminase acting on RNA1 (ADAR1) is driven by alternative promoters. Promoter PA, activated by interferon (IFN), produces transcripts that encode the inducible p150 ADAR1 protein, whereas PB specifies the constitutively expressed p110 protein. We show using Stat1(-/-), Stat2(-/-) and IRF9(-/-) MEFs that induction of ADAR1 p150 occurs by STAT2- and IRF9-dependent signaling that is enhanced by, but not obligatorily dependent upon, STAT1. Chromatin immunoprecipitation analysis demonstrated STAT2 at the PA promoter in IFN-treated Stat1(-/-) cells, whereas IFN-treated wild-type cells showed both STAT1 and STAT2 bound at PA. By contrast, with human 2fTGH cells and mutants U3A or U6A, ADAR1 induction by IFN was dependent upon both STAT1 and STAT2. These results suggest that transcriptional activation of Adar1 by IFN occurs in the absence of STAT1 by a non-canonical STAT2-dependent pathway in mouse but not human cells.
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Genome-wide Analysis of Host-Plasmodium yoelii Interactions Reveals Regulators of the Type I Interferon Response. Cell Rep 2015; 12:661-72. [PMID: 26190101 DOI: 10.1016/j.celrep.2015.06.058] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 03/02/2015] [Accepted: 06/16/2015] [Indexed: 11/22/2022] Open
Abstract
Invading pathogens trigger specific host responses, an understanding of which might identify genes that function in pathogen recognition and elimination. In this study, we performed trans-species expression quantitative trait locus (ts-eQTL) analysis using genotypes of the Plasmodium yoelii malaria parasite and phenotypes of mouse gene expression. We significantly linked 1,054 host genes to parasite genetic loci (LOD score ≥ 3.0). Using LOD score patterns, which produced results that differed from direct expression-level clustering, we grouped host genes that function in related pathways, allowing functional prediction of unknown genes. As a proof of principle, 14 of 15 randomly selected genes predicted to function in type I interferon (IFN-I) responses were experimentally validated using overexpression, small hairpin RNA knockdown, viral infection, and/or infection of knockout mice. This study demonstrates an effective strategy for studying gene function, establishes a functional gene database, and identifies regulators in IFN-I pathways.
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48
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Tajaddod M, Jantsch MF, Licht K. The dynamic epitranscriptome: A to I editing modulates genetic information. Chromosoma 2015; 125:51-63. [PMID: 26148686 PMCID: PMC4761006 DOI: 10.1007/s00412-015-0526-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Revised: 06/22/2015] [Accepted: 06/24/2015] [Indexed: 02/03/2023]
Abstract
Adenosine to inosine editing (A to I editing) is a cotranscriptional process that contributes to transcriptome complexity by deamination of adenosines to inosines. Initially, the impact of A to I editing has been described for coding targets in the nervous system. Here, A to I editing leads to recoding and changes of single amino acids since inosine is normally interpreted as guanosine by cellular machines. However, more recently, new roles for A to I editing have emerged: Editing was shown to influence splicing and is found massively in Alu elements. Moreover, A to I editing is required to modulate innate immunity. We summarize the multiple ways in which A to I editing generates transcriptome variability and highlight recent findings in the field.
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Affiliation(s)
- Mansoureh Tajaddod
- Department of Chromosome Biology, Max F. Perutz Laboratories, University of Vienna, Dr. Bohr Gasse 9/5, A-1030, Vienna, Austria
| | - Michael F Jantsch
- Department of Chromosome Biology, Max F. Perutz Laboratories, University of Vienna, Dr. Bohr Gasse 9/5, A-1030, Vienna, Austria. .,Department of Cell Biology, Center of Cell Biology and Anatomy, Medical University of Vienna, Schwarzspanierstrasse 17, A-1090, Vienna, Austria.
| | - Konstantin Licht
- Department of Chromosome Biology, Max F. Perutz Laboratories, University of Vienna, Dr. Bohr Gasse 9/5, A-1030, Vienna, Austria.
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Okamura K, Abe Y, Fukai K, Tsuruta D, Suga Y, Nakamura M, Funasaka Y, Oka M, Suzuki N, Wataya-Kaneda M, Seishima M, Hozumi Y, Kawaguchi M, Suzuki T. Mutation analyses of patients with dyschromatosis symmetrica hereditaria: Ten novel mutations of the ADAR1 gene. J Dermatol Sci 2015; 79:88-90. [DOI: 10.1016/j.jdermsci.2015.04.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Revised: 03/08/2015] [Accepted: 04/16/2015] [Indexed: 11/27/2022]
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50
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Refaat B, Ashshi AM, El-Shemi AG, Azhar E. Activins and Follistatin in Chronic Hepatitis C and Its Treatment with Pegylated-Interferon-α Based Therapy. Mediators Inflamm 2015; 2015:287640. [PMID: 25969625 PMCID: PMC4417604 DOI: 10.1155/2015/287640] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2015] [Revised: 02/27/2015] [Accepted: 02/27/2015] [Indexed: 12/12/2022] Open
Abstract
Pegylated-interferon-α based therapy for the treatment of chronic hepatitis C (CHC) is considered suboptimal as not all patients respond to the treatment and it is associated with several side effects that could lead to dose reduction and/or termination of therapy. The currently used markers to monitor the response to treatment are based on viral kinetics and their performance in the prediction of treatment outcome is moderate and does not combine accuracy and their values have several limitations. Hence, the development of new sensitive and specific predictor markers could provide a useful tool for the clinicians and healthcare providers, especially in the new era of interferon-free therapy, for the classification of patients according to their response to the standard therapy and only subscribing the novel directly acting antiviral drugs to those who are anticipated not to respond to the conventional therapy and/or have absolute contraindications for its use. The importance of activins and follistatin in the regulation of immune system, liver biology, and pathology has recently emerged. This review appraises the up-to-date knowledge regarding the role of activins and follistatin in liver biology and immune system and their role in the pathophysiology of CHC.
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Affiliation(s)
- Bassem Refaat
- Laboratory Medicine Department, Faculty of Applied Medical Sciences, Umm Al-Qura University, Al-'Abdiyah Campus, P. O. Box 7607, Makkah, Saudi Arabia
| | - Ahmed Mohamed Ashshi
- Laboratory Medicine Department, Faculty of Applied Medical Sciences, Umm Al-Qura University, Al-'Abdiyah Campus, P. O. Box 7607, Makkah, Saudi Arabia
| | - Adel Galal El-Shemi
- Laboratory Medicine Department, Faculty of Applied Medical Sciences, Umm Al-Qura University, Al-'Abdiyah Campus, P. O. Box 7607, Makkah, Saudi Arabia
- Department of Pharmacology, Faculty of Medicine, Assiut University, Assiut 6515, Egypt
| | - Esam Azhar
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, P.O. Box 80216, Jeddah 21589, Saudi Arabia
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, P.O. Box 80216, Jeddah 21589, Saudi Arabia
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