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1
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Verstraten R, Cetraro P, Fitzpatrick AH, Alwie Y, Frommeyer YN, Loliashvili E, Stein SC, Häussler S, Ouwendijk WJ, Depledge DP. Defining expansions and perturbations to the RNA polymerase III transcriptome and epitranscriptome by modified direct RNA nanopore sequencing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.03.07.641986. [PMID: 40161704 PMCID: PMC11952314 DOI: 10.1101/2025.03.07.641986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 04/02/2025]
Abstract
RNA polymerase III (Pol III) transcribes cytosolic transfer RNAs (tRNAs) and other non-coding RNAs (ncRNAs) essential to cellular function. However, many aspects of Pol III transcription and processing, including RNA modifications, remain poorly understood, mainly due to a lack of available sensitive and systematic methods for their analysis. Here, we present DRAP3R (Direct Read and Analysis of Polymerase III transcribed RNAs), a modified nanopore direct RNA sequencing approach and analysis framework that enables the specific and sensitive capture of nascent Pol III transcribed RNAs. Applying DRAP3R to distinct cell types, we identify previously unconfirmed tRNA genes and other novel Pol III transcribed RNAs, thus expanding the known Pol III transcriptome. Critically, DRAP3R also enables discrimination between co- and post-transcriptional RNA modifications such as pseudouridine (Ψ) and N 6-methyladenosine (m6A) at single-nucleotide resolution across all examined transcript types and reveals differential Ψ installation patterns across tRNA isodecoders and other ncRNAs. Finally, applying DRAP3R to epithelial cells infected with Herpes Simplex Virus Type 1 reveals an extensive remodelling of both the Pol III transcriptome and epitranscriptome. Our findings thus establish DRAP3R as a powerful tool for systematically studying Pol III transcribed RNAs and their modifications in diverse cellular contexts.
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Affiliation(s)
- Ruth Verstraten
- Institute of Virology, Hannover Medical School, Hannover, Germany
- German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, Hannover, Germany
| | - Pierina Cetraro
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | | | - Yasmine Alwie
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Yannick Noah Frommeyer
- Institute for Molecular Bacteriology, TWINCORE GmbH, Center of Clinical and Experimental Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Center for Infection Research, Hannover, Germany
| | | | - Saskia C. Stein
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Susanne Häussler
- Institute for Molecular Bacteriology, TWINCORE GmbH, Center of Clinical and Experimental Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Center for Infection Research, Hannover, Germany
- Department of Molecular Bacteriology, Helmholtz Center for Infection Research, Braunschweig, Germany
- Department of Clinical Microbiology, Copenhagen University Hospital – Rigshospitalet, 2100 Copenhagen, Denmark
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany
| | | | - Daniel P. Depledge
- Institute of Virology, Hannover Medical School, Hannover, Germany
- German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, Hannover, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany
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2
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Borghol AH, Bitar ER, Hanna A, Naim G, Rahal EA. The role of Epstein-Barr virus in autoimmune and autoinflammatory diseases. Crit Rev Microbiol 2025; 51:296-316. [PMID: 38634723 DOI: 10.1080/1040841x.2024.2344114] [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: 01/16/2024] [Revised: 03/15/2024] [Accepted: 04/11/2024] [Indexed: 04/19/2024]
Abstract
Epstein-Barr Virus (EBV), a dsDNA herpesvirus, is believed to play a significant role in exacerbating and potentially triggering autoimmune and autoinflammatory maladies. Around 90% of the world is infected with the virus, which establishes latency within lymphocytes. EBV is also known to cause infectious mononucleosis, a self-limited flu-like illness, in adolescents. EBV is often reactivated and it employs several mechanisms of evading the host immune system. It has also been implicated in inducing host immune dysfunction potentially resulting in exacerbation or triggering of inflammatory processes. EBV has therefore been linked to a number of autoimmune diseases, including systemic lupus erythematosus, multiple sclerosis, rheumatoid arthritis, and Sjögren's syndrome. The review examines the molecular mechanisms through which the virus alters host immune system components thus possibly resulting in autoimmune processes. Understanding the mechanisms underpinning EBV-associated autoimmunity is pivotal; however, the precise causal pathways remain elusive. Research on therapeutic agents and vaccines for EBV has been stagnant for a long number of years until recent advances shed light on potential therapeutic targets. The implications of EBV in autoimmunity underscore the importance of developing targeted therapeutic strategies and, potentially, vaccines to mitigate the autoimmune burden associated with this ubiquitous virus.
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Affiliation(s)
- Abdul Hamid Borghol
- Department of Experimental Pathology, Immunology and Microbiology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
- Center for Infectious Diseases Research (CIDR), American University of Beirut, Beirut, Lebanon
| | - Elio R Bitar
- Department of Experimental Pathology, Immunology and Microbiology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
- Center for Infectious Diseases Research (CIDR), American University of Beirut, Beirut, Lebanon
| | - Aya Hanna
- Department of Experimental Pathology, Immunology and Microbiology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
- Center for Infectious Diseases Research (CIDR), American University of Beirut, Beirut, Lebanon
| | - Georges Naim
- Department of Experimental Pathology, Immunology and Microbiology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
- Center for Infectious Diseases Research (CIDR), American University of Beirut, Beirut, Lebanon
| | - Elias A Rahal
- Department of Experimental Pathology, Immunology and Microbiology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
- Center for Infectious Diseases Research (CIDR), American University of Beirut, Beirut, Lebanon
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3
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Quan L, Dai J, Luo Y, Wang L, Liu Y, Meng J, Yang F, You X. The 100 top-cited studies in systemic lupus erythematosus: A bibliometric analysis. Hum Vaccin Immunother 2024; 20:2387461. [PMID: 39149877 PMCID: PMC11328883 DOI: 10.1080/21645515.2024.2387461] [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: 04/28/2024] [Revised: 07/12/2024] [Accepted: 07/30/2024] [Indexed: 08/17/2024] Open
Abstract
Systemic lupus erythematosus (SLE) is an autoimmune inflammatory tissue disease. In view of the explosive growth in research on SLE, bibliometrics was performed to evaluate the 100 top-cited papers in this realm. We performed the search with terms "systemic lupus erythematosus" the Web of Science Core Collection database on May 3, 2023. Relevant literatures were screened. Data were extracted and analyzed by SPSS. The citations of 100 top-cited SLE studies spanned from 472 to 13,557. Most studies (60 out of 100) were conducted in the United States. Total citation times were positively associated with ACY, which was negatively correlated with the length of time since publication. Approximately half of the studies focused on the underlying mechanisms of SLE. New biologic therapies garnered attention and development. Our findings provide valuable insights into the developments in crucial areas of SLE and shed contributions to future studies.
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Affiliation(s)
- Liuliu Quan
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Jiawen Dai
- Tianjin Institutes of Health Science, Tianjin, China
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Tianjin Key Laboratory of Gene Therapy for Blood Diseases, CAMS Key Laboratory of Gene Therapy for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Yuan Luo
- West China School of Medicine, Sichuan University, Chengdu, China
| | - Lin Wang
- School of Clinical Medicine, Southwest Medical University, Luzhou, China
| | - Yue Liu
- West China School of Medicine, Sichuan University, Chengdu, China
| | - Jiaqi Meng
- West China School of Medicine, Sichuan University, Chengdu, China
| | - Fan Yang
- West China School of Medicine, Sichuan University, Chengdu, China
| | - Xin You
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Key Laboratory of Rheumatology & Clinical Immunology, Ministry of Education, Beijing, China
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4
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Solares S, León J, García-Gutiérrez L. The Functional Interaction Between Epstein-Barr Virus and MYC in the Pathogenesis of Burkitt Lymphoma. Cancers (Basel) 2024; 16:4212. [PMID: 39766110 PMCID: PMC11674381 DOI: 10.3390/cancers16244212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2024] [Revised: 12/13/2024] [Accepted: 12/14/2024] [Indexed: 01/11/2025] Open
Abstract
The Epstein-Barr virus (EBV) is associated with a wide range of diseases, malignant and non-malignant. EBV was, in fact, the first virus described with cell transformation capacity, discovered by Epstein in 1964 in lymphoma samples from African children. Since then, EBV has been associated with several human tumors including nasopharyngeal carcinoma, gastric carcinoma, T-cell lymphoma, Hodgkin lymphoma, diffuse large B cell lymphoma, and Burkitt lymphoma among others. The molecular hallmark of Burkitt lymphoma (BL) is a chromosomal translocation that involves the MYC gene and immunoglobulin loci, resulting in the deregulated expression of MYC, an oncogenic transcription factor that appears deregulated in about half of human tumors. The role of MYC in lymphoma is well established, as MYC overexpression drives B cell proliferation through multiple mechanisms, foremost, the stimulation of the cell cycle. Indeed, MYC is found overexpressed or deregulated in several non-Hodgkin lymphomas. Most endemic and many sporadic BLs are associated with EBV infection. While some mechanisms by which EBV can contribute to BL have been reported, the mechanism that links MYC translocation and EBV infection in BL is still under debate. Here, we review the main EBV-associated diseases, with a special focus on BL, and we discuss the interaction of EBV and MYC translocation during B cell malignant transformation in BL.
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Affiliation(s)
| | | | - Lucía García-Gutiérrez
- Instituto de Biomedicina y Biotecnología de Cantabria, Departamento de Biología Molecular, Universidad de Cantabria-CSIC, Albert Einstein 22, 39011 Cantabria, Spain; (S.S.); (J.L.)
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Chiu YF, Ponlachantra K, Sugden B. How Epstein Barr Virus Causes Lymphomas. Viruses 2024; 16:1744. [PMID: 39599857 PMCID: PMC11599019 DOI: 10.3390/v16111744] [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: 10/16/2024] [Revised: 10/30/2024] [Accepted: 11/04/2024] [Indexed: 11/29/2024] Open
Abstract
Since Epstein-Barr Virus (EBV) was isolated 60 years ago, it has been studied clinically, epidemiologically, immunologically, and molecularly in the ensuing years. These combined studies allow a broad mechanistic understanding of how this ubiquitous human pathogen which infects more than 90% of adults can rarely cause multiple types of lymphomas. We survey these findings to provide a coherent description of its oncogenesis.
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Affiliation(s)
- Ya-Fang Chiu
- Department of Microbiology and Immunology, Chang Gung University, Taoyuan 33302, Taiwan;
- Graduate Institute of Biomedical Sciences, Chang Gung University, Taoyuan 33302, Taiwan
- Research Center for Emerging Viral Infections, Chang Gung University, Taoyuan 33302, Taiwan
- Division of Infectious Diseases, Department of Medicine, New Taipei Municipal Tucheng Hospital, New Taipei City 236017, Taiwan
- Department of Laboratory Medicine, Chang Gung Memorial Hospital, Linkou 33305, Taiwan
| | - Khongpon Ponlachantra
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology, Rayong 21210, Thailand;
| | - Bill Sugden
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI 53705, USA
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6
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Hudson E, Yang L, Chu EK, Zhuang H, Arja RD, Betancourt BY, Bhattacharyya I, Han S, Cha S, Chan EKL, Sebastian M, Stalvey C, Fritzler MJ, Reeves WH. Evidence that autoantibody production may be driven by acute Epstein-Barr virus infection in Sjögren's disease. Ann Rheum Dis 2024; 84:ard-2024-226226. [PMID: 39472059 PMCID: PMC12037870 DOI: 10.1136/ard-2024-226226] [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: 06/06/2024] [Accepted: 10/15/2024] [Indexed: 01/01/2025]
Abstract
OBJECTIVES Sjögren's disease (SD) is an autoimmune disease affecting the exocrine glands that is associated with autoantibodies against Ro60/SS-A, anti-Ro52/TRIM21, La/SS-B and others. We examined the role of acute Epstein-Barr virus (EBV) infection in the pathogenesis of these autoantibodies in a previously healthy patient (patient 1) with primary EBV infection who developed SD with anti-Ro/La and anti-Smith/U1 ribonucleoprotein (Sm/U1RNP) autoantibodies and had lymphoplasmacytic foci on labial salivary gland biopsy. METHODS Immune responses to Epstein-Barr nuclear antigen-1 (EBNA1) and the Ro52/Ro60/La and Sm/U1RNP autoantigens and peptides were examined by immunoassay in patient 1, healthy and disease controls. RESULTS Anti-Ro52 and anti-Ro60 autoantibodies were present 7 days after primary infection and underwent IgM to IgG switching, suggesting that EBV infection promoted their production. More than 7 months after primary infection, new and increasing levels of antibodies against EBNA1 and the U1RNP autoantigen appeared concomitantly. These antibodies bound homologous peptide sequences shared by EBNA1, SmB' and the U1-C (U1RNP) protein, consistent with induction by molecular mimicry. Although Ro60 and EBNA1 crossreact immunologically, we found that anti-Ro60/anti-Ro52 antibody production was stimulated by acute EBV infection long before the onset of anti-EBNA1. Unexpectedly, a subset of healthy control sera had anti-SmB' peptide antibodies that were not correlated with anti-EBNA1 peptide antibodies. In contrast, anti-SmB' and EBNA1 peptide antibody levels correlated in anti-Sm/U1RNP+ lupus sera. CONCLUSIONS Primary EBV infection can promote anti-Ro60/anti-Ro52 and anti-U1RNP responses, though by different mechanisms. Some healthy individuals produce anti-SmB' peptide autoantibodies independently of a response to EBNA1.
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Affiliation(s)
- Erin Hudson
- Division of Rheumatology and Clinical Immunology, University of Florida Health Science Center, Gainesville, Florida, USA
| | - Lijun Yang
- Pathology, University of Florida Health Science Center, Gainesville, Florida, USA
| | - Elizabeth K Chu
- Division of Rheumatology and Clinical Immunology, University of Florida Health Science Center, Gainesville, Florida, USA
| | - Haoyang Zhuang
- Division of Rheumatology and Clinical Immunology, University of Florida Health Science Center, Gainesville, Florida, USA
| | - Rawad Daniel Arja
- Division of Rheumatology and Clinical Immunology, University of Florida Health Science Center, Gainesville, Florida, USA
| | - Blas Y Betancourt
- Division of Rheumatology and Clinical Immunology, University of Florida Health Science Center, Gainesville, Florida, USA
| | | | - Shuhong Han
- Division of Rheumatology and Clinical Immunology, University of Florida Health Science Center, Gainesville, Florida, USA
| | - Seunghee Cha
- Oral Medicine, University of Florida, Gainesville, Florida, USA
| | - Edward K L Chan
- Oral Biology, Anatomy and Cell Biology, University of Florida Health Science Center, Gainesville, Florida, USA
| | - Mathew Sebastian
- Department of Medicine, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
| | | | - Marvin J Fritzler
- Department of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Westley H Reeves
- Division of Rheumatology and Clinical Immunology, University of Florida Health Science Center, Gainesville, Florida, USA
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7
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Paudel S, Lee N. Epstein-Barr virus noncoding RNA EBER1 promotes the expression of a ribosomal protein paralog to boost oxidative phosphorylation. J Med Virol 2024; 96:e29869. [PMID: 39165093 PMCID: PMC11361555 DOI: 10.1002/jmv.29869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2024] [Accepted: 08/08/2024] [Indexed: 08/22/2024]
Abstract
Epstein-Barr virus (EBV) is a highly successful pathogen that infects ~95% of the adult population and is associated with diverse cancers and autoimmune diseases. The most abundant viral factor in latently infected cells is not a protein but a noncoding RNA called EBV-encoded RNA 1 (EBER1). Even though EBER1 is highly abundant and was discovered over forty years ago, the function of EBER1 has remained elusive. EBER1 interacts with the ribosomal protein L22, which normally suppresses the expression of its paralog L22-like 1 (L22L1). Here we show that when L22 binds EBER1, it cannot suppress L22L1, resulting in L22L1 being expressed and incorporated into ribosomes. We further show that L22L1-containing ribosomes preferentially translate mRNAs involved in the oxidative phosphorylation pathway. Moreover, upregulation of L22L1 is indispensable for growth transformation and immortalization of resting B cells upon EBV infection. Taken together, our results suggest that the function of EBER1 is to modulate host gene expression at the translational level, thus bypassing the need for dysregulating host gene transcription.
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Affiliation(s)
- Sita Paudel
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Nara Lee
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
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8
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Mustelin T, Andrade F. Autoimmunity: the neoantigen hypothesis. Front Immunol 2024; 15:1432985. [PMID: 38994353 PMCID: PMC11236689 DOI: 10.3389/fimmu.2024.1432985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Accepted: 06/17/2024] [Indexed: 07/13/2024] Open
Affiliation(s)
- Tomas Mustelin
- Division of Rheumatology, Department of Medicine, University of Washington, Seattle, WA, United States
| | - Felipe Andrade
- Division of Rheumatology, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
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9
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Paudel S, Lee N. Epstein-Barr virus noncoding RNA EBER1 promotes the expression of a ribosomal protein paralog to boost oxidative phosphorylation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.15.599158. [PMID: 38915488 PMCID: PMC11195164 DOI: 10.1101/2024.06.15.599158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Epstein-Barr virus (EBV) is a highly successful pathogen that infects ~95% of the adult population and is associated with diverse cancers and autoimmune diseases. The most abundant viral factor in latently infected cells is not a protein but a noncoding RNA called EBV-encoded RNA 1 (EBER1). Even though EBER1 is highly abundant and was discovered over forty years ago, the function of EBER1 has remained elusive. EBER1 interacts with the ribosomal protein L22, which normally suppresses the expression of its paralog L22-like 1 (L22L1). Here we show that when L22 binds EBER1, it cannot suppress L22L1, resulting in L22L1 being expressed and incorporated into ribosomes. We further show that L22L1-containing ribosomes preferentially translate mRNAs involved in the oxidative phosphorylation pathway. Moreover, upregulation of L22L1 is indispensable for growth transformation and immortalization of resting B cells upon EBV infection. Taken together, our results suggest that the function of EBER1 is to modulate host gene expression at the translational level, thus bypassing the need for dysregulating host gene transcription.
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Affiliation(s)
- Sita Paudel
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Nara Lee
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
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10
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Sun Y, Shi D, Sun J, Zhang Y, Liu W, Luo B. Regulation mechanism of EBV-encoded EBER1 and LMP2A on YAP1 and the impact of YAP1 on the EBV infection status in EBV-associated gastric carcinoma. Virus Res 2024; 343:199352. [PMID: 38462175 PMCID: PMC10982081 DOI: 10.1016/j.virusres.2024.199352] [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: 01/25/2024] [Revised: 03/07/2024] [Accepted: 03/07/2024] [Indexed: 03/12/2024]
Abstract
This study aims to explore the role and regulatory mechanism of Yes-associated protein 1 (YAP1) in the development of Epstein-Barr virus-associated gastric cancer (EBVaGC). Here we showed that EBV can upregulate the expression and activity of YAP1 protein through its encoded latent products EBV-encoded small RNA 1 (EBER1) and latent membrane protein 2A (LMP2A), enhancing the malignant characteristics of EBVaGC cells. In addition, we also showed that overexpression of YAP1 induced the expression of EBV encoding latent and lytic phase genes and proteins in the epithelial cell line AGS-EBV infected with EBV, and increased the copy number of the EBV genome, while loss of YAP1 expression reduced the aforementioned indicators. Moreover, we found that YAP1 enhanced EBV lytic reactivation induced by two known activators, 12-O-tetradecanoylhorbol-13-acetate (TPA) and sodium butyrate (NaB). These results indicated a bidirectional regulatory mechanism between EBV and YAP1 proteins, providing new experimental evidence for further understanding the regulation of EBV infection patterns and carcinogenic mechanisms in gastric cancer.
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Affiliation(s)
- Yujie Sun
- Department of Pathogenic Biology, School of Basic Medicine, Qingdao University, Qingdao 266071, China
| | - Duo Shi
- Department of Pathogenic Biology, School of Basic Medicine, Qingdao University, Qingdao 266071, China
| | - Jiting Sun
- Department of Pathogenic Biology, School of Basic Medicine, Qingdao University, Qingdao 266071, China
| | - Yan Zhang
- Department of Pathogenic Biology, School of Basic Medicine, Qingdao University, Qingdao 266071, China; Department of Clinical Laboratory, Zibo Central Hospital, ZiBo 255036, China
| | - Wen Liu
- Department of Pathogenic Biology, School of Basic Medicine, Qingdao University, Qingdao 266071, China.
| | - Bing Luo
- Department of Pathogenic Biology, School of Basic Medicine, Qingdao University, Qingdao 266071, China.
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11
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Salnikov MY, MacNeil KM, Mymryk JS. The viral etiology of EBV-associated gastric cancers contributes to their unique pathology, clinical outcomes, treatment responses and immune landscape. Front Immunol 2024; 15:1358511. [PMID: 38596668 PMCID: PMC11002251 DOI: 10.3389/fimmu.2024.1358511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 03/14/2024] [Indexed: 04/11/2024] Open
Abstract
Epstein-Barr virus (EBV) is a pathogen known to cause a number of malignancies, often taking years for them to develop after primary infection. EBV-associated gastric cancer (EBVaGC) is one such malignancy, and is an immunologically, molecularly and pathologically distinct entity from EBV-negative gastric cancer (EBVnGC). In comparison with EBVnGCs, EBVaGCs overexpress a number of immune regulatory genes to help form an immunosuppressive tumor microenvironment (TME), have improved prognosis, and overall have an "immune-hot" phenotype. This review provides an overview of the histopathology, clinical features and clinical outcomes of EBVaGCs. We also summarize the differences between the TMEs of EBVaGCs and EBVnGCs, which includes significant differences in cell composition and immune infiltration. A list of available EBVaGC and EBVnGC gene expression datasets and computational tools are also provided within this review. Finally, an overview is provided of the various chemo- and immuno-therapeutics available in treating gastric cancers (GCs), with a focus on EBVaGCs.
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Affiliation(s)
- Mikhail Y. Salnikov
- Department of Microbiology and Immunology, Western University, London, ON, Canada
| | - Katelyn M. MacNeil
- Department of Microbiology and Immunology, Western University, London, ON, Canada
| | - Joe S. Mymryk
- Department of Microbiology and Immunology, Western University, London, ON, Canada
- Department of Oncology, Western University, London, ON, Canada
- Department of Otolaryngology, Western University, London, ON, Canada
- Lawson Health Research Institute, London, ON, Canada
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12
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Silva JDM, Alves CEDC, Pontes GS. Epstein-Barr virus: the mastermind of immune chaos. Front Immunol 2024; 15:1297994. [PMID: 38384471 PMCID: PMC10879370 DOI: 10.3389/fimmu.2024.1297994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 01/23/2024] [Indexed: 02/23/2024] Open
Abstract
The Epstein-Barr virus (EBV) is a ubiquitous human pathogen linked to various diseases, including infectious mononucleosis and multiple types of cancer. To control and eliminate EBV, the host's immune system deploys its most potent defenses, including pattern recognition receptors, Natural Killer cells, CD8+ and CD4+ T cells, among others. The interaction between EBV and the human immune system is complex and multifaceted. EBV employs a variety of strategies to evade detection and elimination by both the innate and adaptive immune systems. This demonstrates EBV's mastery of navigating the complexities of the immunological landscape. Further investigation into these complex mechanisms is imperative to advance the development of enhanced therapeutic approaches with heightened efficacy. This review provides a comprehensive overview of various mechanisms known to date, employed by the EBV to elude the immune response, while establishing enduring latent infections or instigate its lytic replication.
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Affiliation(s)
- Jean de Melo Silva
- Laboratory of Virology and Immunology, National Institute of Amazonian Research (INPA), Manaus, AM, Brazil
- Post-Graduate Program in Basic and Applied Immunology, Institute of Biological Science, Federal University of Amazonas, Manaus, AM, Brazil
| | | | - Gemilson Soares Pontes
- Laboratory of Virology and Immunology, National Institute of Amazonian Research (INPA), Manaus, AM, Brazil
- Post-Graduate Program in Basic and Applied Immunology, Institute of Biological Science, Federal University of Amazonas, Manaus, AM, Brazil
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13
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Rambold U, Sperling S, Chew Z, Wang Y, Steer B, Zeller K, Strobl LJ, Zimber-Strobl U, Adler H. A Mouse Model to Study the Pathogenesis of γ-herpesviral Infections in Germinal Center B Cells. Cells 2023; 12:2780. [PMID: 38132100 PMCID: PMC10741729 DOI: 10.3390/cells12242780] [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: 10/27/2023] [Revised: 11/27/2023] [Accepted: 12/01/2023] [Indexed: 12/23/2023] Open
Abstract
CD30-positive germinal center (GC)-derived B cell lymphomas are frequently linked to Epstein-Barr Virus (EBV) infection. However, a suitable animal model for the investigation of the interplay between γ-herpesvirus and host cells in B cell pathogenesis is currently lacking. Here, we present a novel in vivo model enabling the analysis of genetically modified viruses in combination with genetically modified GC B cells. As a murine γ-herpesvirus, we used MHV-68 closely mirroring the biology of EBV. Our key finding was that Cre-mediated recombination can be successfully induced by an MHV-68 infection in GC B cells from Cγ1-Cre mice allowing for deletion or activation of loxP-flanked cellular genes. The implementation of PrimeFlow RNA assay for MHV-68 demonstrated the enrichment of MHV-68 in GC and isotype-switched B cells. As illustrations of virus and cellular modifications, we inserted the EBV gene LMP2A into the MHV-68 genome and induced constitutively active CD30-signaling in GC B cells through MHV-68 infections, respectively. While the LMP2A-expressing MHV-68 behaved similarly to wildtype MHV-68, virally induced constitutively active CD30-signaling in GC B cells led to the expansion of a pre-plasmablastic population. The findings underscore the potential of our novel tools to address crucial questions about the interaction between herpesviral infections and deregulated cellular gene-expression in future studies.
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Affiliation(s)
- Ursula Rambold
- Institute of Asthma and Allergy Prevention, Helmholtz Center Munich, German Research Center for Environmental Health, Member of the German Center of Lung Research (DZL), 85764 Neuherberg, Germany; (U.R.); (B.S.)
| | - Stefanie Sperling
- Research Unit Gene Vectors, Research Group B Cell Development and Activation, Helmholtz Center Munich, German Research Center for Environmental Health GmbH, 81377 Munich, Germany (Y.W.); (K.Z.); (L.J.S.)
| | - Zakir Chew
- Research Unit Gene Vectors, Research Group B Cell Development and Activation, Helmholtz Center Munich, German Research Center for Environmental Health GmbH, 81377 Munich, Germany (Y.W.); (K.Z.); (L.J.S.)
| | - Yan Wang
- Research Unit Gene Vectors, Research Group B Cell Development and Activation, Helmholtz Center Munich, German Research Center for Environmental Health GmbH, 81377 Munich, Germany (Y.W.); (K.Z.); (L.J.S.)
| | - Beatrix Steer
- Institute of Asthma and Allergy Prevention, Helmholtz Center Munich, German Research Center for Environmental Health, Member of the German Center of Lung Research (DZL), 85764 Neuherberg, Germany; (U.R.); (B.S.)
| | - Krisztina Zeller
- Research Unit Gene Vectors, Research Group B Cell Development and Activation, Helmholtz Center Munich, German Research Center for Environmental Health GmbH, 81377 Munich, Germany (Y.W.); (K.Z.); (L.J.S.)
| | - Lothar J. Strobl
- Research Unit Gene Vectors, Research Group B Cell Development and Activation, Helmholtz Center Munich, German Research Center for Environmental Health GmbH, 81377 Munich, Germany (Y.W.); (K.Z.); (L.J.S.)
- Institute of Lung Health and Immunity, Helmholtz Center Munich, German Research Center for Environmental Health, Member of the German Center of Lung Research (DZL), 85764 Neuherberg, Germany
| | - Ursula Zimber-Strobl
- Research Unit Gene Vectors, Research Group B Cell Development and Activation, Helmholtz Center Munich, German Research Center for Environmental Health GmbH, 81377 Munich, Germany (Y.W.); (K.Z.); (L.J.S.)
- Institute of Lung Health and Immunity, Helmholtz Center Munich, German Research Center for Environmental Health, Member of the German Center of Lung Research (DZL), 85764 Neuherberg, Germany
| | - Heiko Adler
- Institute of Asthma and Allergy Prevention, Helmholtz Center Munich, German Research Center for Environmental Health, Member of the German Center of Lung Research (DZL), 85764 Neuherberg, Germany; (U.R.); (B.S.)
- Walther-Straub-Institute of Pharmacology and Toxicology, Ludwig-Maximilians-University Munich, Member of the German Center of Lung Research (DZL), 80336 Munich, Germany
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14
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Kawada JI, Ito Y, Ohshima K, Yamada M, Kataoka S, Muramatsu H, Sawada A, Wada T, Imadome KI, Arai A, Iwatsuki K, Ohga S, Kimura H. Updated guidelines for chronic active Epstein-Barr virus disease. Int J Hematol 2023; 118:568-576. [PMID: 37728704 PMCID: PMC10615970 DOI: 10.1007/s12185-023-03660-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 08/31/2023] [Accepted: 09/06/2023] [Indexed: 09/21/2023]
Abstract
Chronic active Epstein-Barr virus disease (CAEBV), formerly named chronic active Epstein-Barr virus infection, is characterized by systemic inflammation and clonal proliferation of Epstein-Barr virus (EBV)-infected T or NK cells. As CAEBV is a potentially life-threatening illness, appropriate diagnosis and therapeutic interventions are necessary for favorable clinical outcomes. Substantial evidence regarding the pathogenesis and treatment of CAEBV has been accumulated since previous guidelines for the diagnosis of CAEBV were proposed. To reflect this evidence, we updated the guidelines for the diagnosis and treatment of CAEBV to improve clinical management of the disease. The details of the updated guidelines are presented in this report. Diagnosis of CAEBV now requires confirmation of a high copy number of EBV genome and EBV-infected T or NK cells. An EBV DNA load ≥ 10,000 IU/mL in whole blood is proposed as the diagnostic cutoff value for CAEBV in this updated guideline. A standard treatment approach for CAEBV has not been established, and hematopoietic stem cell transplantation (HSCT) is considered the only curative treatment. Chemotherapy can be administered to control disease activity before HSCT.
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Affiliation(s)
- Jun-Ichi Kawada
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan.
| | - Yoshinori Ito
- Department of Pediatrics and Child Health, Nihon University School of Medicine, Tokyo, Japan
| | - Koichi Ohshima
- Department of Pathology, School of Medicine, Kurume University, Kurume, Japan
| | - Masaki Yamada
- Department of Advanced Medicine for Viral Infections, National Center for Child Health and Development, Tokyo, Japan
| | - Shinsuke Kataoka
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hideki Muramatsu
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Akihisa Sawada
- Department of Hematology/Oncology, Osaka Women's and Children's Hospital, Izumi, Japan
| | - Taizo Wada
- Department of Pediatrics, Kanazawa University, Kanazawa, Japan
| | - Ken-Ichi Imadome
- Department of Advanced Medicine for Viral Infections, National Center for Child Health and Development, Tokyo, Japan
| | - Ayako Arai
- Division of Hematology and Oncology, Department of Internal Medicine, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Keiji Iwatsuki
- Department of Dermatology, Dentistry, and Pharmaceutical Sciences, Okayama University Graduate School of Medicine, Okayama, Japan
| | - Shouichi Ohga
- Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Hiroshi Kimura
- Department of Virology, Nagoya University Graduate School of Medicine, Nagoya, Japan.
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15
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AlDaif BA, Mercer AA, Fleming SB. The parapoxvirus Orf virus inhibits dsDNA-mediated type I IFN expression via STING-dependent and STING-independent signalling pathways. J Gen Virol 2023; 104. [PMID: 37882657 DOI: 10.1099/jgv.0.001912] [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] [Indexed: 10/27/2023] Open
Abstract
Type I interferons (IFNs) are critical in the host defence against viruses. They induce hundreds of interferon-stimulated genes (ISGs) many of which have an antiviral role. Poxviruses induce IFNs via their pathogen-associated molecular patterns, in particular, their genomic DNA. In a majority of cell types, dsDNA is detected by a range of cytoplasmic DNA sensors that mediate type I IFN expression via stimulator of interferon genes (STING). Orf virus (ORFV) induces cutaneous pustular skin lesions and is the type species of the Parapoxvirus genus within the Poxviridae family. The aim of this study was to investigate whether ORFV modulates dsDNA-induced type I IFN expression via STING-dependent signalling pathways in human dermal fibroblasts (hNDF) and THP-1 cells. We showed that ORFV infection of these cell types treated with poly(dA:dT) resulted in strong inhibition of expression of IFN-β. In hNDFs, we showed using siRNA knock-down that STING was essential for type I IFN induction. IFN-β expression was further reduced when both STING and RIG-I were knocked down. In addition, HEK293 cells that do not express STING or Toll-like receptors also produce IFN-β following stimulation with poly(dA:dT). The 5' triphosphate dsRNA produced by RNA polymerase III specifically results in the induction of type I IFNs through the RIG-I receptor. We showed that ORFV infection resulted in strong inhibition of IFN-β expression in HEK293 cells stimulated with poly(dA:dT). Overall, this study shows that ORFV potently counteracts the STING-dependent and STING-independent IFN response by antagonizing dsDNA-activated IFN signalling pathways.
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Affiliation(s)
- Basheer A AlDaif
- Virus Research Unit, Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Andrew A Mercer
- Virus Research Unit, Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Stephen B Fleming
- Virus Research Unit, Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
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16
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Gorbea C, Elhakiem A, Cazalla D. Shaping the host cell environment with viral noncoding RNAs. Semin Cell Dev Biol 2023; 146:20-30. [PMID: 36581481 PMCID: PMC10101873 DOI: 10.1016/j.semcdb.2022.12.008] [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: 08/29/2022] [Revised: 12/24/2022] [Accepted: 12/24/2022] [Indexed: 12/29/2022]
Abstract
Just like the cells they infect viruses express different classes of noncoding RNAs (ncRNAs). Viral ncRNAs come in all shapes and forms, and they usually associate with cellular proteins that are important for their functions. Viral ncRNAs have diverse functions, but they all contribute to the viral control of the cellular environment. Viruses utilize ncRNAs to regulate viral replication, to decide whether they should remain latent or reactivate, to evade the host immune responses, or to promote cellular transformation. In this review we describe the diverse functions played by different classes of ncRNAs expressed by adenoviruses and herpesviruses, how they contribute to the viral infection, and how their study led to insights into RNA-based mechanisms at play in host cells.
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Affiliation(s)
- Carlos Gorbea
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Abdalla Elhakiem
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Demián Cazalla
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
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17
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Gouzouasis V, Tastsoglou S, Giannakakis A, Hatzigeorgiou AG. Virus-Derived Small RNAs and microRNAs in Health and Disease. Annu Rev Biomed Data Sci 2023; 6:275-298. [PMID: 37159873 DOI: 10.1146/annurev-biodatasci-122220-111429] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
MicroRNAs (miRNAs) are short noncoding RNAs that can regulate all steps of gene expression (induction, transcription, and translation). Several virus families, primarily double-stranded DNA viruses, encode small RNAs (sRNAs), including miRNAs. These virus-derived miRNAs (v-miRNAs) help the virus evade the host's innate and adaptive immune system and maintain an environment of chronic latent infection. In this review, the functions of the sRNA-mediated virus-host interactions are highlighted, delineating their implication in chronic stress, inflammation, immunopathology, and disease. We provide insights into the latest viral RNA-based research-in silico approaches for functional characterization of v-miRNAs and other RNA types. The latest research can assist toward the identification of therapeutic targets to combat viral infections.
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Affiliation(s)
- Vasileios Gouzouasis
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
- Laboratory of Molecular Genetics, Department of Immunology, Hellenic Pasteur Institute, Athens, Greece
- DIANA-Lab, Department of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece;
- DIANA-Lab, Hellenic Pasteur Institute, Athens, Greece
| | - Spyros Tastsoglou
- DIANA-Lab, Department of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece;
- DIANA-Lab, Hellenic Pasteur Institute, Athens, Greece
| | - Antonis Giannakakis
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
- University Research Institute of Maternal and Child Health and Precision Medicine, UNESCO Chair on Adolescent Health Care, National and Kapodistrian University of Athens, Athens, Greece
| | - Artemis G Hatzigeorgiou
- DIANA-Lab, Department of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece;
- DIANA-Lab, Hellenic Pasteur Institute, Athens, Greece
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18
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Yura Y, Hamada M. Outline of Salivary Gland Pathogenesis of Sjögren's Syndrome and Current Therapeutic Approaches. Int J Mol Sci 2023; 24:11179. [PMID: 37446355 DOI: 10.3390/ijms241311179] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 06/30/2023] [Accepted: 07/03/2023] [Indexed: 07/15/2023] Open
Abstract
Sjögren's syndrome (SS) is an autoimmune disease characterized by the involvement of exocrine glands such as the salivary and lacrimal glands. The minor salivary glands, from which tissue samples may be obtained, are important for the diagnosis, evaluation of therapeutic efficacy, and genetic analyses of SS. In the onset of SS, autoantigens derived from the salivary glands are recognized by antigen-presenting dendritic cells, leading to the activation of T and B cells, cytokine production, autoantibody production by plasma cells, the formation of ectopic germinal centers, and the destruction of salivary gland epithelial cells. A recent therapeutic approach with immune checkpoint inhibitors for malignant tumors enhances the anti-tumor activity of cytotoxic effector T cells, but also induces SS-like autoimmune disease as an adverse event. In the treatment of xerostomia, muscarinic agonists and salivary gland duct cleansing procedure, as well as sialendoscopy, are expected to ameliorate symptoms. Clinical trials on biological therapy to attenuate the hyperresponsiveness of B cells in SS patients with systemic organ involvement have progressed. The efficacy of treatment with mesenchymal stem cells and chimeric antigen receptor T cells for SS has also been investigated. In this review, we will provide an overview of the pathogenesis of salivary gland lesions and recent trends in therapeutic approaches for SS.
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Affiliation(s)
- Yoshiaki Yura
- Department of Oral & Maxillofacial Oncology and Surgery, Osaka University Graduate School of Dentistry, Osaka 565-0871, Japan
| | - Masakazu Hamada
- Department of Oral & Maxillofacial Oncology and Surgery, Osaka University Graduate School of Dentistry, Osaka 565-0871, Japan
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19
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Pearce DR, Akarca AU, De Maeyer RPH, Kostina E, Huebner A, Sivakumar M, Karasaki T, Shah K, Janes SM, McGranahan N, Reddy V, Akbar AN, Moore DA, Marafioti T, Swanton C, Hynds RE. Phenotyping of lymphoproliferative tumours generated in xenografts of non-small cell lung cancer. Front Oncol 2023; 13:1156743. [PMID: 37342197 PMCID: PMC10277614 DOI: 10.3389/fonc.2023.1156743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 05/11/2023] [Indexed: 06/22/2023] Open
Abstract
Background Patient-derived xenograft (PDX) models involve the engraftment of tumour tissue in immunocompromised mice and represent an important pre-clinical oncology research method. A limitation of non-small cell lung cancer (NSCLC) PDX model derivation in NOD-scid IL2Rgammanull (NSG) mice is that a subset of initial engraftments are of lymphocytic, rather than tumour origin. Methods The immunophenotype of lymphoproliferations arising in the lung TRACERx PDX pipeline were characterised. To present the histology data herein, we developed a Python-based tool for generating patient-level pathology overview figures from whole-slide image files; PATHOverview is available on GitHub (https://github.com/EpiCENTR-Lab/PATHOverview). Results Lymphoproliferations occurred in 17.8% of lung adenocarcinoma and 10% of lung squamous cell carcinoma transplantations, despite none of these patients having a prior or subsequent clinical history of lymphoproliferative disease. Lymphoproliferations were predominantly human CD20+ B cells and had the immunophenotype expected for post-transplantation diffuse large B cell lymphoma with plasma cell features. All lymphoproliferations expressed Epstein-Barr-encoded RNAs (EBER). Analysis of immunoglobulin light chain gene rearrangements in three tumours where multiple tumour regions had resulted in lymphoproliferations suggested that each had independent clonal origins. Discussion Overall, these data suggest that B cell clones with lymphoproliferative potential are present within primary NSCLC tumours, and that these are under continuous immune surveillance. Since these cells can be expanded following transplantation into NSG mice, our data highlight the value of quality control measures to identify lymphoproliferations within xenograft pipelines and support the incorporation of strategies to minimise lymphoproliferations during the early stages of xenograft establishment pipelines.
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Affiliation(s)
- David R. Pearce
- Cancer Research UK (CRUK) Lung Cancer Centre of Excellence, UCL Cancer Institute, University College London, London, United Kingdom
- Cancer Evolution and Genome Stability Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Ayse U. Akarca
- Department of Cellular Pathology, University College London Hospitals, London, United Kingdom
| | | | - Emily Kostina
- Epithelial Cell Biology in ENT Research (EpiCENTR) Group, Developmental Biology and Cancer Department, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Ariana Huebner
- Cancer Research UK (CRUK) Lung Cancer Centre of Excellence, UCL Cancer Institute, University College London, London, United Kingdom
- Cancer Evolution and Genome Stability Laboratory, The Francis Crick Institute, London, United Kingdom
- Cancer Genome Evolution Research Group, UCL Cancer Institute, University College London, London, United Kingdom
| | - Monica Sivakumar
- Cancer Research UK (CRUK) Lung Cancer Centre of Excellence, UCL Cancer Institute, University College London, London, United Kingdom
- Department of Cellular Pathology, University College London Hospitals, London, United Kingdom
| | - Takahiro Karasaki
- Cancer Evolution and Genome Stability Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Kavina Shah
- Division of Medicine, University College London, London, United Kingdom
| | - Sam M. Janes
- Lungs for Living Research Centre, UCL Respiratory, Division of Medicine, University College London, London, United Kingdom
| | - Nicholas McGranahan
- Cancer Research UK (CRUK) Lung Cancer Centre of Excellence, UCL Cancer Institute, University College London, London, United Kingdom
- Cancer Genome Evolution Research Group, UCL Cancer Institute, University College London, London, United Kingdom
| | - Venkat Reddy
- Division of Medicine, University College London, London, United Kingdom
| | - Arne N. Akbar
- Division of Medicine, University College London, London, United Kingdom
| | - David A. Moore
- Cancer Research UK (CRUK) Lung Cancer Centre of Excellence, UCL Cancer Institute, University College London, London, United Kingdom
- Department of Cellular Pathology, University College London Hospitals, London, United Kingdom
| | - Teresa Marafioti
- Department of Cellular Pathology, University College London Hospitals, London, United Kingdom
| | - Charles Swanton
- Cancer Research UK (CRUK) Lung Cancer Centre of Excellence, UCL Cancer Institute, University College London, London, United Kingdom
- Cancer Evolution and Genome Stability Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Robert E. Hynds
- Cancer Research UK (CRUK) Lung Cancer Centre of Excellence, UCL Cancer Institute, University College London, London, United Kingdom
- Cancer Evolution and Genome Stability Laboratory, The Francis Crick Institute, London, United Kingdom
- Epithelial Cell Biology in ENT Research (EpiCENTR) Group, Developmental Biology and Cancer Department, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
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20
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Li T, Zhang W, Xie M. Fluorescent In Situ Detection of RNA-Protein Interactions in Intact Cells by RNA-PLA. Methods Mol Biol 2023; 2666:165-175. [PMID: 37166665 PMCID: PMC11106780 DOI: 10.1007/978-1-0716-3191-1_13] [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] [Indexed: 05/12/2023]
Abstract
RNA-protein proximity ligation assay (RNA-PLA) enables the detection of specific RNA-protein interactions in fixed cells. In RNA-PLA, bridging and ligation of a circular DNA template occurs if the target RNA and protein are within 40 nanometers of each other. The resulting circular template is amplified by rolling circle amplification and abundantly recognized by fluorescent antisense DNA oligonucleotides. This strategy therefore enables localization of RNA-protein interactions in situ with high specificity and sensitivity. Here, we describe the use of RNA-PLA to detect interactions between a nuclear viral RNA and a host RNA-binding protein in Epstein-Barr virus (EBV)-infected B cells.
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Affiliation(s)
- Tianqi Li
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL, USA
| | - Wei Zhang
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Mingyi Xie
- UF Health Cancer Center, University of Florida, Gainesville, FL, USA.
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21
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Wen KW, Wang L, Menke JR, Damania B. Cancers associated with human gammaherpesviruses. FEBS J 2022; 289:7631-7669. [PMID: 34536980 PMCID: PMC9019786 DOI: 10.1111/febs.16206] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 08/10/2021] [Accepted: 09/16/2021] [Indexed: 01/14/2023]
Abstract
Epstein-Barr virus (EBV; human herpesvirus 4; HHV-4) and Kaposi sarcoma-associated herpesvirus (KSHV; human herpesvirus 8; HHV-8) are human gammaherpesviruses that have oncogenic properties. EBV is a lymphocryptovirus, whereas HHV-8/KSHV is a rhadinovirus. As lymphotropic viruses, EBV and KSHV are associated with several lymphoproliferative diseases or plasmacytic/plasmablastic neoplasms. Interestingly, these viruses can also infect epithelial cells causing carcinomas and, in the case of KSHV, endothelial cells, causing sarcoma. EBV is associated with Burkitt lymphoma, classic Hodgkin lymphoma, nasopharyngeal carcinoma, plasmablastic lymphoma, lymphomatoid granulomatosis, leiomyosarcoma, and subsets of diffuse large B-cell lymphoma, post-transplant lymphoproliferative disorder, and gastric carcinoma. KSHV is implicated in Kaposi sarcoma, primary effusion lymphoma, multicentric Castleman disease, and KSHV-positive diffuse large B-cell lymphoma. Pathogenesis by these two herpesviruses is intrinsically linked to viral proteins expressed during the lytic and latent lifecycles. This comprehensive review intends to provide an overview of the EBV and KSHV viral cycles, viral proteins that contribute to oncogenesis, and the current understanding of the pathogenesis and clinicopathology of their related neoplastic entities.
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Affiliation(s)
- Kwun Wah Wen
- Department of Pathology and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA 94158
| | - Linlin Wang
- Department of Laboratory Medicine, University of California, San Francisco, CA 94158
| | - Joshua R. Menke
- Department of Pathology, Stanford University, Palo Alto, CA 94304
| | - Blossom Damania
- Department of Microbiology & Immunology & Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599
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22
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The Impact of Deleting Stem-Loop 1 of Epstein-Barr Virus-Encoded RNA 1 on Cell Proliferation. Viruses 2022; 14:v14112538. [PMID: 36423146 PMCID: PMC9696203 DOI: 10.3390/v14112538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/10/2022] [Accepted: 11/14/2022] [Indexed: 11/18/2022] Open
Abstract
Epstein-Barr virus-encoded RNAs (EBERs) are two small, noncoding, structurally conserved transcripts, constitutively expressed at >106 copies per EBV-infected cell. They have been shown to drive cell growth. However, the mechanism(s) involved in EBER-induced proliferation is not clear. In this study, we investigated the molecular mechanisms and structural impact of EBER1. Sequences of EBER1 stem-loops (SL) 1, 3, and 4 were deleted, creating three mutants: ∆SL1, ∆SL3, and ∆SL4. These mutants were cloned into pHebo plasmids and expressed in Jurkat cell lines. Cells transfected with wildtype EBER1 and pHebo were used as controls. Cell proliferation was monitored by microscopy and flow cytometry. Microarray, qPCR, and Western blotting were used to investigate the cell cycle markers. We found significantly higher cell proliferation in wildtype EBER1 cells compared to pHebo, ∆SL1, and ∆SL3, but not ∆SL4 mutants. There was also significant upregulation of S-phase and G2/M phase markers in wildtype EBER1 and ∆SL4 mutant. Furthermore, CDT1, a factor for DNA replication, was upregulated in wildtype EBER1 and ∆SL4 mutant. However, in ∆SL1 mutant, CDT1 was significantly downregulated and translocated to the cytoplasm. These data indicate that the structure of EBER1 is important in cell proliferation.
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23
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Henry BA, Marchand V, Schlegel BT, Helm M, Motorin Y, Lee N. Pseudouridylation of Epstein-Barr virus noncoding RNA EBER2 facilitates lytic replication. RNA (NEW YORK, N.Y.) 2022; 28:1542-1552. [PMID: 36100352 PMCID: PMC9745832 DOI: 10.1261/rna.079219.122] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 09/06/2022] [Indexed: 06/15/2023]
Abstract
Epstein-Barr virus (EBV) expresses two highly abundant noncoding RNAs called EBV-encoded RNA 1 (EBER1) and EBER2, which are preserved in all clinical isolates of EBV, thus underscoring their essential function in the viral life cycle. Recent epitranscriptomics studies have uncovered a vast array of distinct RNA modifications within cellular as well as viral noncoding RNAs that are instrumental in executing their function. Here we show that EBER2 is marked by pseudouridylation, and by using HydraPsiSeq the modification site was mapped to a single nucleotide within the 3' region of EBER2. The writer enzyme was identified to be the snoRNA-dependent pseudouridine synthase Dyskerin, which is the catalytic subunit of H/ACA small nucleolar ribonucleoprotein complexes, and is guided to EBER2 by SNORA22. Similar to other noncoding RNAs for which pseudouridylation has a positive effect on RNA stability, loss of EBER2 pseudouridylation results in a decrease in RNA levels. Furthermore, pseudouridylation of EBER2 is required for the prolific accumulation of progeny viral genomes, suggesting that this single modification in EBER2 is important for efficient viral lytic replication. Taken together, our findings add to the list of RNA modifications that are essential for noncoding RNAs to implement their physiological roles.
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Affiliation(s)
- Belle A Henry
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15219, USA
| | - Virginie Marchand
- Université de Lorraine, CNRS, INSERM, UAR2008/US40 IBSLor, F-54000 Nancy, France
| | - Brent T Schlegel
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15219, USA
| | - Mark Helm
- Johannes Gutenberg University Mainz, Institute of Pharmacy and Biochemistry, 55128 Mainz, Germany
| | - Yuri Motorin
- Université de Lorraine, CNRS, INSERM, UAR2008/US40 IBSLor, F-54000 Nancy, France
- Université de Lorraine, CNRS, UMR7365 IMoPA, F-54000 Nancy, France
| | - Nara Lee
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15219, USA
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CD4+ Cytotoxic T Cells Involved in the Development of EBV-Associated Diseases. Pathogens 2022; 11:pathogens11080831. [PMID: 35894054 PMCID: PMC9330826 DOI: 10.3390/pathogens11080831] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 07/17/2022] [Accepted: 07/22/2022] [Indexed: 11/17/2022] Open
Abstract
Activated cytotoxic CD4 T cells (HLA-DR+) play an important role in the control of EBV infection, especially in cells with latency I (EBNA-1). One of the evasion mechanisms of these latency cells is generated by gp42, which, via peripherally binding to the β1 domain of the β chain of MHC class II (HLA-DQ, -DR, and -DP) of the infected B lymphocyte, can block/alter the HLA class II/T-cell receptor (TCR) interaction, and confer an increased level of susceptibility towards the development of EBV-associated autoimmune diseases or cancer in genetically predisposed individuals (HLA-DRB1* and DQB1* alleles). The main developments predisposing the factors of these diseases are: EBV infection; HLA class II risk alleles; sex; and tissue that is infiltrated with EBV-latent cells, forming ectopic lymphoid structures. Therefore, there is a need to identify treatments for eliminating cells with EBV latency, because the current treatments (e.g., antivirals and rituximab) are ineffective.
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25
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Virus Infections Play Crucial Roles in the Pathogenesis of Sjögren’s Syndrome. Viruses 2022; 14:v14071474. [PMID: 35891453 PMCID: PMC9320594 DOI: 10.3390/v14071474] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 06/29/2022] [Accepted: 07/02/2022] [Indexed: 12/13/2022] Open
Abstract
Sjögren’s syndrome (SS) is an autoimmune disease especially targeting exocrine glands, such as the salivary and lacrimal glands. A radical therapy for SS based on its etiology has not been established because of the complex pathogenesis of the disease. Several studies have demonstrated a relationship between virus infection and SS pathogenesis. In particular, infection with the Epstein-Barr (EB) virus among others is a potent factor associated with the onset or development of SS. Specifically, virus infection in the target organs of SS triggers or promotes autoreactive responses involving the process of autoantigen formation, antigen-presenting function, or T-cell response. Our review of recent research highlights the crucial roles of virus infection in the pathogenesis of SS and discusses the critical association between virus infection and the etiology of autoimmunity in SS.
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26
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Wang Y, Ungerleider N, Hoffman BA, Kara M, Farrell PJ, Flemington EK, Lee N, Tibbetts SA. A Polymorphism in the Epstein-Barr Virus EBER2 Noncoding RNA Drives In Vivo Expansion of Latently Infected B Cells. mBio 2022; 13:e0083622. [PMID: 35642944 PMCID: PMC9239156 DOI: 10.1128/mbio.00836-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 05/10/2022] [Indexed: 01/31/2023] Open
Abstract
The oncogenic gammaherpesviruses, including human Epstein-Barr virus (EBV), human Kaposi's sarcoma-associated herpesvirus (KSHV), and murine gammaherpesvirus 68 (MHV68, γHV68, MuHV-4), are associated with numerous malignancies, including B cell lymphomas and nasopharyngeal carcinoma. These viruses employ numerous molecular strategies to colonize the host, including the expression of noncoding RNAs (ncRNAs). As the first viral ncRNAs identified, EBV-encoded RNA 1 and 2 (EBER1 and EBER2, respectively) have been investigated extensively for decades; however, their specific in vivo functions remain largely unknown. In work here, we used chimeric MHV68 viruses in an in vivo complementation system to test whether EBV EBER2 contributes to acute and/or chronic phases of infection. Expression of EBER2 derived from EBV strain B95-8 resulted in a significant expansion of latently infected B cells in vivo, which was accompanied by a decrease in virus-infected plasma cells. EBV strains typically carry one of two variants of EBER2, which differ primarily by a 5-nucleotide core polymorphism identified initially in the EBV strain M81. Strikingly, mutation of the 5 nucleotides that define this core polymorphism resulted in the loss of the infected B cell expansion and restored plasma cell infection. This work reveals that the B95-8 variant of EBER2 promotes the expansion of the latently infected B cell pool in vivo and may do so in part through inhibition of terminal differentiation. These findings provide new insight into mechanisms by which viral ncRNAs promote in vivo colonization and further and provide further evidence of the inherent tumorigenic risks associated with gammaherpesvirus manipulation of B cell differentiation. IMPORTANCE The oncogenic gammaherpesviruses, including human Epstein-Barr virus (EBV), human Kaposi's sarcoma-associated herpesvirus (KSHV), and murine gammaherpesvirus 68, employ numerous strategies to colonize the host, including expression of noncoding RNAs (ncRNAs). As the first viral ncRNAs ever identified, EBV-encoded RNA 1 and 2 (EBER1 and EBER2) have been investigated extensively for decades; however, their specific in vivo functions remain largely unknown. Work here reveals that an EBV EBER2 variant highly associated with B cell lymphoma promoted a significantly increased expansion of the infected B cell pool in vivo, which coincided with altered B cell differentiation. Mutation of the 5 nucleotides that define this EBER2 variant resulted in the loss of B cell expansion and normal B cell differentiation. These findings provide new insight into the mechanisms by which EBV manipulates B cells in vivo to retain infected cells in the high-risk B cell differentiation pathway where they are poised for tumorigenesis.
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Affiliation(s)
- Yiping Wang
- Department of Molecular Genetics and Microbiology, UF Health Cancer Center, UF Genetics Institute, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Nathan Ungerleider
- Department of Pathology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, Louisiana, USA
| | - Brett A. Hoffman
- Department of Molecular Genetics and Microbiology, UF Health Cancer Center, UF Genetics Institute, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Mehmet Kara
- Department of Molecular Genetics and Microbiology, UF Health Cancer Center, UF Genetics Institute, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Paul J. Farrell
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Erik K. Flemington
- Department of Pathology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, Louisiana, USA
| | - Nara Lee
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Scott A. Tibbetts
- Department of Molecular Genetics and Microbiology, UF Health Cancer Center, UF Genetics Institute, College of Medicine, University of Florida, Gainesville, Florida, USA
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27
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Nishikawa H, Christiany P, Hayashi T, Iizasa H, Yoshiyama H, Hatakeyama M. Kinase Activity of PAR1b, Which Mediates Nuclear Translocation of the BRCA1 Tumor Suppressor, Is Potentiated by Nucleic Acid-Mediated PAR1b Multimerization. Int J Mol Sci 2022; 23:6634. [PMID: 35743080 PMCID: PMC9223676 DOI: 10.3390/ijms23126634] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/09/2022] [Accepted: 06/12/2022] [Indexed: 02/07/2023] Open
Abstract
PAR1b is a cytoplasmic serine/threonine kinase that controls cell polarity and cell-cell interaction by regulating microtubule stability while mediating cytoplasmic-to-nuclear translocation of BRCA1. PAR1b is also a cellular target of the CagA protein of Helicobacter pylori, which leads to chronic infection causatively associated with the development of gastric cancer. The CagA-PAR1b interaction inactivates the kinase activity of PAR1b and thereby dampens PAR1b-mediated BRCA1 phosphorylation, which reduces the level of nuclear BRCA1 and thereby leads to BRCAness and BRCAness-associated genome instability underlying gastric carcinogenesis. While PAR1b can multimerize within the cells, little is known about the mechanism and functional role of PAR1b multimerization. We found in the present study that PAR1b was multimerized in vitro by binding with nucleic acids (both single- and double-stranded DNA/RNA) via the spacer region in a manner independent of nucleic-acid sequences, which markedly potentiated the kinase activity of PAR1b. Consistent with these in vitro observations, cytoplasmic introduction of double-stranded DNA or expression of single-stranded RNA increased the PAR1b kinase activity in the cells. These findings indicate that the cytoplasmic DNA/RNA contribute to nuclear accumulation of BRCA1 by constitutively activating/potentiating cytoplasmic PAR1b kinase activity, which is subverted in gastric epithelial cells upon delivery of H. pylori CagA oncoprotein.
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Affiliation(s)
- Hiroko Nishikawa
- Division of Microbiology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan; (H.N.); (P.C.); (T.H.)
| | - Priscillia Christiany
- Division of Microbiology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan; (H.N.); (P.C.); (T.H.)
| | - Takeru Hayashi
- Division of Microbiology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan; (H.N.); (P.C.); (T.H.)
| | - Hisashi Iizasa
- Department of Microbiology, Faculty of Medicine, Shimane University, Izumo 693-8501, Japan; (H.I.); (H.Y.)
| | - Hironori Yoshiyama
- Department of Microbiology, Faculty of Medicine, Shimane University, Izumo 693-8501, Japan; (H.I.); (H.Y.)
| | - Masanori Hatakeyama
- Division of Microbiology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan; (H.N.); (P.C.); (T.H.)
- Laboratory of Virology, Institute of Microbial Chemistry, Microbial Chemistry Research Foundation, Shinagawa-ku, Tokyo 141-0021, Japan
- Center for Infectious Cancers, Institute for Genetic Medicine, Hokkaido University, Kita-ku, Sapporo 060-0815, Japan
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28
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The Epstein-Barr virus noncoding RNA EBER2 transactivates the UCHL1 deubiquitinase to accelerate cell growth. Proc Natl Acad Sci U S A 2021; 118:2115508118. [PMID: 34686609 DOI: 10.1073/pnas.2115508118] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/08/2021] [Indexed: 12/23/2022] Open
Abstract
The Epstein-Barr virus (EBV) transforms resting B cells and is involved in the development of B cell lymphomas. We report here that the viral noncoding RNA EBER2 accelerates B cell growth by potentiating expression of the UCHL1 deubiquitinase that itself increased expression of the Aurora kinases and of cyclin B1. Importantly, this effect was also visible in Burkitt's lymphoma cells that express none of the virus's known oncogenes. Mechanistically, EBER2 bound the UCHL1 messenger RNA (mRNA), thereby bringing a protein complex that includes PU.1, a UCHL1 transactivator, to the vicinity of its promoter. Although the EBV oncogene LMP1 has been suggested to induce UCHL1, we show here that EBER2 plays a much more important role to reach significant levels of the deubiquitinase in infected cells. However, some viruses that carried a polymorphic LMP1 had an increased ability to achieve full UCHL1 expression. This work identifies a direct cellular target of a viral noncoding RNA that is likely to be central to EBV's oncogenic properties.
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29
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Ahmed W, Hassan Z, Abdelmowla YAA, Philip PS, Shmygol A, Khan G. Epstein-Barr virus noncoding small RNA (EBER1) induces cell proliferation by up-regulating cellular mitochondrial activity and calcium influx. Virus Res 2021; 305:198550. [PMID: 34454973 DOI: 10.1016/j.virusres.2021.198550] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 08/11/2021] [Accepted: 08/17/2021] [Indexed: 11/19/2022]
Abstract
Epstein-Barr virus encoded RNAs (EBER1 and EBER2) are two non-polyadenylated, non-protein coding small RNAs expressed at high levels in all forms of EBV latent infections. Although not directly involved in cell transformation, a number of studies have reported that these RNAs may be involved in cell proliferation. However, which of the two EBERs play a major role in this process and the mechanisms involved remains unknown. The aim of this study was to investigate the role and mechanism of EBER1-induced cell proliferation. Using stably transfected EBER1 cell lines, and multiple methodologies, we show that EBER1 transfected epithelial, B and T cell lines proliferate at a higher rate, have higher metabolic activity and increased DNA synthesis. The mitochondrial number and activity was also observed to be higher in the EBER1 transfected cells. Moreover, cytochrome c activity and store operated calcium entry (SOCE) were potentiated in the EBER1 expressing cells. Finally, the genes associated with cell proliferation were also observed to be up-regulated in the EBER1 transfected cells. Taken together, our data has unravelled the role of mitochondria and cellular calcium pathway that appear to be involved in EBER1 induced cell proliferation of EBV infected cells.
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Affiliation(s)
- Waqar Ahmed
- Departments of Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Zubaida Hassan
- Departments of Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Yasmeen A A Abdelmowla
- Departments of Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Pretty S Philip
- Departments of Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Anatoliy Shmygol
- Departments of Physiology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Gulfaraz Khan
- Departments of Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates; Zayed Center for Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates.
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30
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MicroRNA and Other Non-Coding RNAs in Epstein-Barr Virus-Associated Cancers. Cancers (Basel) 2021; 13:cancers13153909. [PMID: 34359809 PMCID: PMC8345394 DOI: 10.3390/cancers13153909] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/27/2021] [Accepted: 08/01/2021] [Indexed: 12/12/2022] Open
Abstract
EBV is a direct causative agent in around 1.5% of all cancers. The oncogenic properties of EBV are related to its ability to activate processes needed for cellular proliferation, survival, migration, and immune evasion. The EBV latency program is required for the immortalization of infected B cells and involves the expression of non-coding RNAs (ncRNAs), including viral microRNAs. These ncRNAs have different functions that contribute to virus persistence in the asymptomatic host and to the development of EBV-associated cancers. In this review, we discuss the function and potential clinical utility of EBV microRNAs and other ncRNAs in EBV-associated malignancies. This review is not intended to be comprehensive, but rather to provide examples of the importance of ncRNAs.
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31
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Lytic Infection with Murine Gammaherpesvirus 68 Activates Host and Viral RNA Polymerase III Promoters and Enhances Noncoding RNA Expression. J Virol 2021; 95:e0007921. [PMID: 33910955 PMCID: PMC8223928 DOI: 10.1128/jvi.00079-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
RNA polymerase III (pol III) transcribes multiple noncoding RNAs (ncRNAs) that are essential for cellular function. Pol III-dependent transcription is also engaged during certain viral infections, including those of the gammaherpesviruses (γHVs), where pol III-dependent viral ncRNAs promote pathogenesis. Additionally, several host ncRNAs are upregulated during γHV infection and play integral roles in pathogenesis by facilitating viral establishment and gene expression. Here, we sought to investigate how pol III promoters and transcripts are regulated during gammaherpesvirus infection using the murine gammaherpesvirus 68 (γHV68) system. To compare the transcription of host and viral pol III-dependent ncRNAs, we analyzed a series of pol III promoters for host and viral ncRNAs using a luciferase reporter optimized to measure pol III activity. We measured promoter activity from the reporter gene at the translation level via luciferase activity and at the transcription level via reverse transcription-quantitative PCR (RT-qPCR). We further measured endogenous ncRNA expression at single-cell resolution by flow cytometry. These studies demonstrated that lytic infection with γHV68 increased the transcription from multiple host and viral pol III promoters and further identified the ability of accessory sequences to influence both baseline and inducible promoter activity after infection. RNA flow cytometry revealed the induction of endogenous pol III-derived ncRNAs that tightly correlated with viral gene expression. These studies highlight how lytic gammaherpesvirus infection alters the transcriptional landscape of host cells to increase pol III-derived RNAs, a process that may further modify cellular function and enhance viral gene expression and pathogenesis. IMPORTANCE Gammaherpesviruses are a prime example of how viruses can alter the host transcriptional landscape to establish infection. Despite major insights into how these viruses modify RNA polymerase II-dependent generation of messenger RNAs, how these viruses influence the activity of host RNA polymerase III remains much less clear. Small noncoding RNAs produced by RNA polymerase III are increasingly recognized to play critical regulatory roles in cell biology and virus infection. Studies of RNA polymerase III-dependent transcription are complicated by multiple promoter types and diverse RNAs with variable stability and processing requirements. Here, we characterized a reporter system to directly study RNA polymerase III-dependent responses during gammaherpesvirus infection and utilized single-cell flow cytometry-based methods to reveal that gammaherpesvirus lytic replication broadly induces pol III activity to enhance host and viral noncoding RNA expression within the infected cell.
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32
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Münz C. Immune Escape by Non-coding RNAs of the Epstein Barr Virus. Front Microbiol 2021; 12:657387. [PMID: 34234755 PMCID: PMC8257079 DOI: 10.3389/fmicb.2021.657387] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 05/28/2021] [Indexed: 01/20/2023] Open
Abstract
Epstein Barr virus (EBV) is one of the most successful pathogens of humans, persistently colonizing more than 95% of the adult human population. At the same time EBV encodes oncogenes that can readily transform human B cells in culture and threaten healthy virus carriers with lymphomagenesis. Cytotoxic lymphocytes have been identified in experimental models and by primary immunodeficiencies as the main protective immune compartments controlling EBV. EBV has reached a stalemate with these cytotoxic T and innate lymphocytes to ensure persistence in most infected humans. Recent evidence suggests that the non-coding RNAs of the virus contribute to viral immune escape to prevent immune eradication. This knowledge might be used in the future to attenuate EBV for vaccine development against this human tumor virus that was discovered more than 55 years ago.
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Affiliation(s)
- Christian Münz
- Viral Immunobiology, Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
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33
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Hatano Y, Ideta T, Hirata A, Hatano K, Tomita H, Okada H, Shimizu M, Tanaka T, Hara A. Virus-Driven Carcinogenesis. Cancers (Basel) 2021; 13:2625. [PMID: 34071792 PMCID: PMC8198641 DOI: 10.3390/cancers13112625] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/22/2021] [Accepted: 05/25/2021] [Indexed: 12/13/2022] Open
Abstract
Cancer arises from the accumulation of genetic and epigenetic alterations. Even in the era of precision oncology, carcinogens contributing to neoplastic process are still an important focus of research. Comprehensive genomic analyses have revealed various combinations of base substitutions, referred to as the mutational signatures, in cancer. Each mutational signature is believed to arise from specific DNA damage and repair processes, including carcinogens. However, as a type of carcinogen, tumor viruses increase the cancer risk by alternative mechanisms, including insertional mutagenesis, viral oncogenes, and immunosuppression. In this review, we summarize virus-driven carcinogenesis to provide a framework for the control of malignant cell proliferation. We first provide a brief overview of oncogenic viruses and describe their implication in virus-related tumors. Next, we describe tumor viruses (HPV, Human papilloma virus; HBV, Hepatitis B virus; HCV, Hepatitis C virus; EBV, Epstein-Barr virus; Kaposi sarcoma herpesvirus; MCV, Merkel cell polyoma virus; HTLV-1, Human T-cell lymphotropic virus, type-1) and tumor virus-related cancers. Lastly, we introduce emerging tumor virus candidates, human cytomegalovirus (CMV), human herpesvirus-6 (HHV-6) and adeno-associated virus-2 (AAV-2). We expect this review to be a hub in a complex network of data for virus-associated carcinogenesis.
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Affiliation(s)
- Yuichiro Hatano
- Department of Tumor Pathology, Gifu University Graduate School of Medicine, Gifu 501-1194, Japan; (H.T.); (A.H.)
| | - Takayasu Ideta
- Department of Gastroenterology, Gifu University Graduate School of Medicine, Gifu 501-1194, Japan; (T.I.); (M.S.)
- Department of Laboratory Medicine, Gifu University Graduate School of Medicine, Gifu 501-1194, Japan
| | - Akihiro Hirata
- Laboratory of Veterinary Pathology, Joint Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1194, Japan;
| | - Kayoko Hatano
- Department of Obstetrics and Gynecology, Gifu University Hospital, Gifu 501-1194, Japan;
| | - Hiroyuki Tomita
- Department of Tumor Pathology, Gifu University Graduate School of Medicine, Gifu 501-1194, Japan; (H.T.); (A.H.)
| | - Hideshi Okada
- Department of Emergency and Disaster Medicine, Gifu University Graduate School of Medicine, Gifu 501-1194, Japan;
| | - Masahito Shimizu
- Department of Gastroenterology, Gifu University Graduate School of Medicine, Gifu 501-1194, Japan; (T.I.); (M.S.)
| | - Takuji Tanaka
- Department of Diagnostic Pathology (DDP) and Research Center of Diagnostic Pathology (RC-DiP), Gifu Municipal Hospital, Gifu 500-8513, Japan;
| | - Akira Hara
- Department of Tumor Pathology, Gifu University Graduate School of Medicine, Gifu 501-1194, Japan; (H.T.); (A.H.)
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34
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Fournier B, Boutboul D, Bruneau J, Miot C, Boulanger C, Malphettes M, Pellier I, Dunogué B, Terrier B, Suarez F, Blanche S, Castelle M, Winter S, Delecluse HJ, Molina T, Picard C, Ehl S, Moshous D, Galicier L, Barlogis V, Fischer A, Neven B, Latour S. Rapid identification and characterization of infected cells in blood during chronic active Epstein-Barr virus infection. J Exp Med 2021; 217:152032. [PMID: 32812031 PMCID: PMC7596820 DOI: 10.1084/jem.20192262] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 05/29/2020] [Accepted: 07/09/2020] [Indexed: 12/13/2022] Open
Abstract
Epstein-Barr virus (EBV) preferentially infects epithelial cells and B lymphocytes and sometimes T and NK lymphocytes. Persistence of EBV-infected cells results in severe lymphoproliferative disorders (LPDs). Diagnosis of EBV-driven T or NK cell LPD and chronic active EBV diseases (CAEBV) is difficult, often requiring biopsies. Herein, we report a flow-FISH cytometry assay that detects cells expressing EBV-encoded small RNAs (EBERs), allowing rapid identification of EBV-infected cells among PBMCs. EBV-infected B, T, and/or NK cells were detectable in various LPD conditions. Diagnosis of CAEBV in 22 patients of Caucasian and African origins was established. All exhibited circulating EBV-infected T and/or NK cells, highlighting that CAEBV is not restricted to native American and Asian populations. Proportions of EBV-infected cells correlated with blood EBV loads. We showed that EBV-infected T cells had an effector memory activated phenotype, whereas EBV-infected B cells expressed plasma cell differentiation markers. Thus, this method achieves accurate and unambiguous diagnoses of different forms of EBV-driven LPD and represents a powerful tool to study their pathophysiological mechanisms.
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Affiliation(s)
- Benjamin Fournier
- Laboratory of Lymphocyte Activation and Susceptibility to EBV Infection, Institut National de la Santé et de la Recherche Médicale UMR 1163, Imagine Institute, Paris, France.,Université de Paris, Paris, France
| | - David Boutboul
- Department of Clinical Immunology, Saint-Louis Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Julie Bruneau
- Université de Paris, Paris, France.,Department of Pathology, Necker-Enfants Malades Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Charline Miot
- Department of Pediatric Immunology Hematology and Oncology, University Hospital, Angers, France
| | - Cécile Boulanger
- Institut Roi Albert II, Cancerology and Hematology Departments, University Clinics Saint-Luc Hospital, Brussels, Belgium
| | - Marion Malphettes
- Department of Clinical Immunology, Saint-Louis Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Isabelle Pellier
- Department of Pediatric Immunology Hematology and Oncology, University Hospital, Angers, France
| | - Bertrand Dunogué
- Department of Internal Medicine, Cochin Hospital, National Referral Centre for Systemic and Autoimmune Diseases, Cochin Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Benjamin Terrier
- Department of Internal Medicine, Cochin Hospital, National Referral Centre for Systemic and Autoimmune Diseases, Cochin Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Felipe Suarez
- Department of Adult Hematology, Necker-Enfants Malades Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Stéphane Blanche
- Department of Pediatric Immunology, Hematology and Rheumatology, Necker-Enfants Malades Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Martin Castelle
- Department of Pediatric Immunology, Hematology and Rheumatology, Necker-Enfants Malades Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Sarah Winter
- Department of Pediatric Immunology, Hematology and Rheumatology, Necker-Enfants Malades Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Henri-Jacques Delecluse
- Unit F100, Institut National de la Santé et de la Recherche Médicale U1074, Deutsches Krebsforschungszentrum, German Cancer Research Center, Heidelberg, Germany
| | - Thierry Molina
- Université de Paris, Paris, France.,Department of Pathology, Necker-Enfants Malades Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Capucine Picard
- Laboratory of Lymphocyte Activation and Susceptibility to EBV Infection, Institut National de la Santé et de la Recherche Médicale UMR 1163, Imagine Institute, Paris, France.,Université de Paris, Paris, France.,Study Center for Primary Immunodeficiencies, Necker-Enfants Malades Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Stephan Ehl
- Institute for Immunodeficiency-Center for Chronic Immunodeficiency, Department of Pediatrics and Adolescent Medicine, Medical Center - Faculty of Medicine, University of Freiburg, Germany
| | - Despina Moshous
- Université de Paris, Paris, France.,Department of Pediatric Immunology, Hematology and Rheumatology, Necker-Enfants Malades Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Lionel Galicier
- Department of Clinical Immunology, Saint-Louis Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Vincent Barlogis
- Department of Pediatric Hematology-Oncology, La Timone Hospital, Marseille, France
| | - Alain Fischer
- Université de Paris, Paris, France.,Department of Pediatric Immunology, Hematology and Rheumatology, Necker-Enfants Malades Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France.,Collège de France, Paris, France.,Institut National de la Santé et de la Recherche Médicale UMR 1163, Paris, France
| | - Bénédicte Neven
- Université de Paris, Paris, France.,Department of Pediatric Immunology, Hematology and Rheumatology, Necker-Enfants Malades Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Sylvain Latour
- Laboratory of Lymphocyte Activation and Susceptibility to EBV Infection, Institut National de la Santé et de la Recherche Médicale UMR 1163, Imagine Institute, Paris, France.,Université de Paris, Paris, France
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35
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Abstract
Epstein-Barr virus (EBV) was the first human cancer-causing virus to be discovered over fifty years ago. Given its relatively large genome size for a virus and hence the capacity to store more than mere protein-coding information, EBV also harbours genetic material for producing an array of distinct noncoding (nc)RNAs. The double-stranded nature of its DNA genome allows the utilization of the whole gamut of ncRNA types, including both RNA polymerase II and III transcripts, in devising a sophisticated strategy to ensure its replication upon infection in host cells and evasion of host immune responses. Owing to the development of sensitive technologies in recent years, mostly entailing next-generation sequencing, the list of ncRNA types generated by EBV has expanded now to include two RNAs (EBER1 and EBER2) best categorized as long ncRNAs, dozens of microRNAs, one small nucleolar RNA, stable intronic sequence RNAs, and the most recently discovered circular RNAs. With the application of cutting-edge technology, the molecular mechanisms of some of these noncoding transcripts are beginning to emerge, while others remain yet to be elucidated. As viruses often take advantage of existing molecular pathways established by the host, it is likely that further novel concepts of the greatly unexplored noncoding world can be learned from studying the many EBV ncRNAs.
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Affiliation(s)
- Nara Lee
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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36
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Andrews RJ, O’Leary CA, Moss WN. A survey of RNA secondary structural propensity encoded within human herpesvirus genomes: global comparisons and local motifs. PeerJ 2020; 8:e9882. [PMID: 32974099 PMCID: PMC7487152 DOI: 10.7717/peerj.9882] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 08/16/2020] [Indexed: 12/13/2022] Open
Abstract
There are nine herpesviruses known to infect humans, of which Epstein-Barr virus (EBV) is the most widely distributed (>90% of adults infected). This ubiquitous virus is implicated in a variety of cancers and autoimmune diseases. Previous analyses of the EBV genome revealed numerous regions with evidence of generating unusually stable and conserved RNA secondary structures and led to the discovery of a novel class of EBV non-coding (nc)RNAs: the stable intronic sequence (sis)RNAs. To gain a better understanding of the roles of RNA structure in EBV biology and pathogenicity, we revisit EBV using recently developed tools for genome-wide motif discovery and RNA structural characterization. This corroborated previous results and revealed novel motifs with potential functionality; one of which has been experimentally validated. Additionally, since many herpesviruses increasingly rival the seroprevalence of EBV (VZV, HHV-6 and HHV-7 being the most notable), analyses were expanded to include all sequenced human Herpesvirus RefSeq genomes, allowing for genomic comparisons. In total 10 genomes were analyzed, for EBV (types 1 and 2), HCMV, HHV-6A, HHV-6B, HHV-7, HSV-1, HSV-2, KSHV, and VZV. All resulting data were archived in the RNAStructuromeDB (https://structurome.bb.iastate.edu/herpesvirus) to make them available to a wide array of researchers.
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Affiliation(s)
- Ryan J. Andrews
- The Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, United States of America
| | - Collin A. O’Leary
- The Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, United States of America
| | - Walter N. Moss
- The Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, United States of America
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37
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Henry BA, Kanarek JP, Kotter A, Helm M, Lee N. 5-methylcytosine modification of an Epstein-Barr virus noncoding RNA decreases its stability. RNA (NEW YORK, N.Y.) 2020; 26:1038-1048. [PMID: 32354721 PMCID: PMC7373997 DOI: 10.1261/rna.075275.120] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 04/27/2020] [Indexed: 05/06/2023]
Abstract
Many cellular noncoding RNAs contain chemically modified nucleotides that are essential for their function. The Epstein-Barr virus expresses two highly abundant noncoding RNAs called EBV-encoded RNA 1 (EBER1) and EBER2. To examine whether these viral RNAs contain modified nucleotides, we purified native EBERs from EBV-infected cells and performed mass spectrometry analysis. While EBER2 contains no modified nucleotides at stoichiometric amounts, EBER1 was found to carry 5-methylcytosine (m5C) modification. Bisulfite sequencing indicated that a single cytosine of EBER1 is methylated in ∼95% of molecules, and the RNA methyltransferase NSUN2 was identified as the EBER1-specific writer. Intriguingly, ablation of NSUN2 and thus loss of m5C modification resulted in an increase in EBER1 levels. We further found that EBER1 is a substrate for the RNase Angiogenin and cleavage in vivo is dependent on the presence of m5C, providing an explanation as to why loss of m5C increases EBER1 levels. Taken together, our observations indicate that m5C, a modification previously shown for tRNAs to oppose Angiogenin-mediated degradation, can also adversely affect RNA stability.
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Affiliation(s)
- Belle A Henry
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15219, USA
| | - Jack P Kanarek
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15219, USA
| | - Annika Kotter
- Johannes Gutenberg University Mainz, Institute of Pharmaceutical and Biomedical Sciences, 55128 Mainz, Germany
| | - Mark Helm
- Johannes Gutenberg University Mainz, Institute of Pharmaceutical and Biomedical Sciences, 55128 Mainz, Germany
| | - Nara Lee
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15219, USA
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38
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Weidner-Glunde M, Kruminis-Kaszkiel E, Savanagouder M. Herpesviral Latency-Common Themes. Pathogens 2020; 9:E125. [PMID: 32075270 PMCID: PMC7167855 DOI: 10.3390/pathogens9020125] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 02/09/2020] [Accepted: 02/14/2020] [Indexed: 12/14/2022] Open
Abstract
Latency establishment is the hallmark feature of herpesviruses, a group of viruses, of which nine are known to infect humans. They have co-evolved alongside their hosts, and mastered manipulation of cellular pathways and tweaking various processes to their advantage. As a result, they are very well adapted to persistence. The members of the three subfamilies belonging to the family Herpesviridae differ with regard to cell tropism, target cells for the latent reservoir, and characteristics of the infection. The mechanisms governing the latent state also seem quite different. Our knowledge about latency is most complete for the gammaherpesviruses due to previously missing adequate latency models for the alpha and beta-herpesviruses. Nevertheless, with advances in cell biology and the availability of appropriate cell-culture and animal models, the common features of the latency in the different subfamilies began to emerge. Three criteria have been set forth to define latency and differentiate it from persistent or abortive infection: 1) persistence of the viral genome, 2) limited viral gene expression with no viral particle production, and 3) the ability to reactivate to a lytic cycle. This review discusses these criteria for each of the subfamilies and highlights the common strategies adopted by herpesviruses to establish latency.
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Affiliation(s)
- Magdalena Weidner-Glunde
- Department of Reproductive Immunology and Pathology, Institute of Animal Reproduction and Food Research of Polish Academy of Sciences, Tuwima Str. 10, 10-748 Olsztyn, Poland; (E.K.-K.); (M.S.)
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39
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Epstein-Barr virus EBER1 and murine gammaherpesvirus TMER4 share conserved in vivo function to promote B cell egress and dissemination. Proc Natl Acad Sci U S A 2019; 116:25392-25394. [PMID: 31796588 PMCID: PMC6926008 DOI: 10.1073/pnas.1915752116] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The oncogenic gammaherpesviruses, including human Epstein–Barr virus (EBV), human Kaposi’s sarcoma-associated herpesvirus (KSHV), and murine gammaherpesvirus 68 (MHV68, γHV68, MuHV-4) establish life-long latency in circulating B cells. The precise determinants that mediate in vivo gammaherpesvirus latency and tumorigenesis remain unclear. The EBV-encoded RNAs (EBERs) are among the first noncoding RNAs ever identified and have been the subject of decades of studies; however, their biological roles during in vivo infection remain unknown. Herein, we use a series of refined virus mutants to define the active isoform of MHV68 noncoding RNA TMER4 and demonstrate that EBV EBER1 functionally conserves this activity in vivo to promote egress of infected B cells from lymph nodes into peripheral circulation.
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40
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Withers JB, Mondol V, Pawlica P, Rosa-Mercado NA, Tycowski KT, Ghasempur S, Torabi SF, Steitz JA. Idiosyncrasies of Viral Noncoding RNAs Provide Insights into Host Cell Biology. Annu Rev Virol 2019; 6:297-317. [PMID: 31039329 PMCID: PMC6768742 DOI: 10.1146/annurev-virology-092818-015811] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Like their host cells, many viruses express noncoding RNAs (ncRNAs). Despite the technical challenge of ascribing function to ncRNAs, diverse biological roles for virally expressed ncRNAs have been described, including regulation of viral replication, modulation of host gene expression, host immune evasion, cellular survival, and cellular transformation. Insights into conserved interactions between viral ncRNAs and host cell machinery frequently lead to novel findings concerning host cell biology. In this review, we discuss the functions and biogenesis of ncRNAs produced by animal viruses. Specifically, we describe noncanonical pathways of microRNA (miRNA) biogenesis and novel mechanisms used by viruses to manipulate miRNA and messenger RNA stability. We also highlight recent advances in understanding the function of viral long ncRNAs and circular RNAs.
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Affiliation(s)
- Johanna B Withers
- Department of Molecular Biophysics and Biochemistry, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06536, USA; , , , , , , ,
- Howard Hughes Medical Institute, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06536, USA
| | - Vanessa Mondol
- Department of Molecular Biophysics and Biochemistry, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06536, USA; , , , , , , ,
| | - Paulina Pawlica
- Department of Molecular Biophysics and Biochemistry, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06536, USA; , , , , , , ,
| | - Nicolle A Rosa-Mercado
- Department of Molecular Biophysics and Biochemistry, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06536, USA; , , , , , , ,
| | - Kazimierz T Tycowski
- Department of Molecular Biophysics and Biochemistry, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06536, USA; , , , , , , ,
- Howard Hughes Medical Institute, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06536, USA
| | - Salehe Ghasempur
- Department of Molecular Biophysics and Biochemistry, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06536, USA; , , , , , , ,
| | - Seyed F Torabi
- Department of Molecular Biophysics and Biochemistry, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06536, USA; , , , , , , ,
| | - Joan A Steitz
- Department of Molecular Biophysics and Biochemistry, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06536, USA; , , , , , , ,
- Howard Hughes Medical Institute, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06536, USA
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41
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Tsang CM, Lui VWY, Bruce JP, Pugh TJ, Lo KW. Translational genomics of nasopharyngeal cancer. Semin Cancer Biol 2019; 61:84-100. [PMID: 31521748 DOI: 10.1016/j.semcancer.2019.09.006] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 09/11/2019] [Accepted: 09/11/2019] [Indexed: 12/26/2022]
Abstract
Nasopharyngeal carcinoma (NPC), also named the Cantonese cancer, is a unique cancer with strong etiological association with infection of the Epstein-Barr virus (EBV). With particularly high prevalence in Southeast Asia, the involvement of EBV and genetic aberrations contributive to NPC tumorigenesis have remained unclear for decades. Recently, genomic analysis of NPC has defined it as a genetically homogeneous cancer, driven largely by NF-κB signaling caused by either somatic aberrations of NF-κB negative regulators or by overexpression of the latent membrane protein 1 (LMP1), an EBV viral oncoprotein. This represents a landmark finding of the NPC genome. Exome and RNA sequencing data from new EBV-positive NPC models also highlight the importance of PI3K pathway aberrations in NPC. We also realize for the first time that NPC mutational burden, mutational signatures, MAPK/PI3K aberrations, and MHC Class I gene aberrations, are prognostic for patient outcome. Together, these multiple genomic discoveries begin to shape the focus of NPC therapy development. Given the challenge of NF-κB targeting in human cancers, more innovative drug discovery approaches should be explored to target the unique atypical NF-κB activation feature of NPC. Our next decade of NPC research should focus on further identification of the -omic landscapes of recurrent and metastatic NPC, development of gene-based precision medicines, as well as large-scale drug screening with the newly developed and well-characterized EBV-positive NPC models. Focused preclinical and clinical investigations on these major directions may identify new and effective targeting strategies to further improve survival of NPC patients.
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Affiliation(s)
- Chi Man Tsang
- Department of Anatomical and cellular Pathology and State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Hong Kong Special Administrative Region
| | - Vivian Wai Yan Lui
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region
| | - Jeffrey P Bruce
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada
| | - Trevor J Pugh
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 1L7, Canada; Ontario Institute for Cancer Research, Toronto, ON, M5G 1L7, Canada
| | - Kwok Wai Lo
- Department of Anatomical and cellular Pathology and State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Hong Kong Special Administrative Region.
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42
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Epstein–Barr virus ncRNA from a nasopharyngeal carcinoma induces an inflammatory response that promotes virus production. Nat Microbiol 2019; 4:2475-2486. [DOI: 10.1038/s41564-019-0546-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 07/25/2019] [Indexed: 01/01/2023]
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43
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Münz C. Latency and lytic replication in Epstein-Barr virus-associated oncogenesis. Nat Rev Microbiol 2019; 17:691-700. [PMID: 31477887 DOI: 10.1038/s41579-019-0249-7] [Citation(s) in RCA: 285] [Impact Index Per Article: 47.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/18/2019] [Indexed: 12/19/2022]
Abstract
Epstein-Barr virus (EBV) was the first tumour virus identified in humans. The virus is primarily associated with lymphomas and epithelial cell cancers. These tumours express latent EBV antigens and the oncogenic potential of individual latent EBV proteins has been extensively explored. Nevertheless, it was presumed that the pro-proliferative and anti-apoptotic functions of these oncogenes allow the virus to persist in humans; however, recent evidence suggests that cellular transformation is not required for virus maintenance. Vice versa, lytic EBV replication was assumed to destroy latently infected cells and thereby inhibit tumorigenesis, but at least the initiation of the lytic cycle has now been shown to support EBV-driven malignancies. In addition to these changes in the roles of latent and lytic EBV proteins during tumorigenesis, the function of non-coding RNAs has become clearer, suggesting that they might mainly mediate immune escape rather than cellular transformation. In this Review, these recent findings will be discussed with respect to the role of EBV-encoded oncogenes in viral persistence and the contributions of lytic replication as well as non-coding RNAs in virus-driven tumour formation. Accordingly, early lytic EBV antigens and attenuated viruses without oncogenes and microRNAs could be harnessed for immunotherapies and vaccination.
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Affiliation(s)
- Christian Münz
- Viral Immunobiology, Institute of Experimental Immunology, University of Zürich, Zürich, Switzerland.
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44
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Abstract
PURPOSE OF REVIEW The purpose of this article is to draw attention to the role of Epstein-Barr virus (EBV) virus in the pathogenesis of the primary Sjögren's syndrome. The article introduces the problem of consequences of EBV acute infection, and its reactivation, in association with the immune response modulation by the virus and with an increased risk of developing systemic autoimmune diseases and EBV-associated cancers. RECENT FINDINGS The knowledge about the mechanisms by which the virus may stay for years in a latent phase, unrecognized by the host response immune cells is constantly expanding. There are several mechanisms and theories about EBV influence on the autoimmune process in Sjogren's syndrome (pSS), including the similarity (molecular mimicry) between viral EBNA-2 protein and Ro-60 antigen or EBER-1 and EBER-2 viral proteins and La antigen. SUMMARY The influence of EBV infection on the development and course of pSS has been proven. It has also been established that both EBV and pSS result in the increased risk of tumor (especially lymphoma) development. In the light of these findings, new ways to manage EBV infections are being sought. Optimal methods for assessing EBV infection status are being devised. Research also aims at finding therapies, which target EBV through the inhibition of the autoimmune process and of viral activity. The present article is an attempt to discuss the most important phenomena and elements linking EBV infection to the primary Sjögren's syndrome.
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Affiliation(s)
- Maria Maślińska
- National Institute of Geriatrics, Rheumatology and Rehabilitation, Early Arthritis Clinic, Spartanska1, Warsaw, Poland
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45
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Vinayak J, Marrella SA, Hussain RH, Rozenfeld L, Solomon K, Bayfield MA. Human La binds mRNAs through contacts to the poly(A) tail. Nucleic Acids Res 2019; 46:4228-4240. [PMID: 29447394 PMCID: PMC5934636 DOI: 10.1093/nar/gky090] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 01/31/2018] [Indexed: 12/31/2022] Open
Abstract
In addition to a role in the processing of nascent RNA polymerase III transcripts, La proteins are also associated with promoting cap-independent translation from the internal ribosome entry sites of numerous cellular and viral coding RNAs. La binding to RNA polymerase III transcripts via their common UUU-3’OH motif is well characterized, but the mechanism of La binding to coding RNAs is poorly understood. Using electromobility shift assays and cross-linking immunoprecipitation, we show that in addition to a sequence specific UUU-3’OH binding mode, human La exhibits a sequence specific and length dependent poly(A) binding mode. We demonstrate that this poly(A) binding mode uses the canonical nucleic acid interaction winged helix face of the eponymous La motif, previously shown to be vacant during uridylate binding. We also show that cytoplasmic, but not nuclear La, engages poly(A) RNA in human cells, that La entry into polysomes utilizes the poly(A) binding mode, and that La promotion of translation from the cyclin D1 internal ribosome entry site occurs in competition with cytoplasmic poly(A) binding protein (PABP). Our data are consistent with human La functioning in translation through contacts to the poly(A) tail.
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Affiliation(s)
- Jyotsna Vinayak
- Department of Biology, York University, 4700 Keele St., Life Science Building #327E, Toronto, ON M3J 1P3, Canada
| | - Stefano A Marrella
- Department of Biology, York University, 4700 Keele St., Life Science Building #327E, Toronto, ON M3J 1P3, Canada
| | - Rawaa H Hussain
- Department of Biology, York University, 4700 Keele St., Life Science Building #327E, Toronto, ON M3J 1P3, Canada
| | - Leonid Rozenfeld
- Department of Biology, York University, 4700 Keele St., Life Science Building #327E, Toronto, ON M3J 1P3, Canada
| | - Karine Solomon
- Department of Biology, York University, 4700 Keele St., Life Science Building #327E, Toronto, ON M3J 1P3, Canada
| | - Mark A Bayfield
- Department of Biology, York University, 4700 Keele St., Life Science Building #327E, Toronto, ON M3J 1P3, Canada
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46
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Roy Chattopadhyay N, Chakrabarti S, Chatterjee K, Deb Roy S, Kumar Sahu S, Reddy RR, Das P, Bijay Kanrar B, Kumar Das A, Tsering S, Puii Z, Zomawia E, Singh YI, Suryawanshi A, Choudhuri T. Histocompatibility locus antigens regions contribute to the ethnicity bias of Epstein-Barr virus-associated nasopharyngeal carcinoma in higher-incidence populations. Scand J Immunol 2019; 90:e12796. [PMID: 31145476 DOI: 10.1111/sji.12796] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 05/28/2019] [Indexed: 02/04/2023]
Abstract
Nasopharyngeal carcinoma (NPC) is one the most confusing and rare malignancy in most part of the world with significantly high occurrence in some populations of Southeast Asia, North Africa and Alaska. Apart from the dietary and environmental factors, NPC is well-associated with Epstein-Barr virus (EBV) infection in these ethnic groups. However, the internal molecular mechanism(s) for such association in specific populations is not known till date. Polymorphisms in the genes of histocompatibility locus antigens (HLA) are reported in NPC, but association of any particular polymorphism with ethnicity is not established yet. Here, we report a set of HLA polymorphisms in EBV-infected NPC samples from Northeast Indian population. These polymorphisms might play an important role for the lack of proper immune function against EBV infection and thus, eventually, for NPC generation in endemic populations like those of Northeast India.
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Affiliation(s)
| | | | - Koustav Chatterjee
- Department of Biotechnology, Visva Bharati University, Santiniketan, Bolpur, West Bengal, India
| | - Sankar Deb Roy
- Department of Radiation Oncology, Civil Hospital, Dimapur, Nagaland, India
| | - Sushil Kumar Sahu
- Depatrment of Pharmacology & Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - R Rajendra Reddy
- Division of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, India
| | - Piyanki Das
- Department of Biotechnology, Visva Bharati University, Santiniketan, Bolpur, West Bengal, India
| | - Basab Bijay Kanrar
- Department of Biotechnology, Visva Bharati University, Santiniketan, Bolpur, West Bengal, India
| | - Ashok Kumar Das
- ENT Department, Dr B. Borooah Cancer Institute, Guwahati, Assam, India
| | - Sam Tsering
- Tertiary Cancer Center, Tomo Riba Institute of Health And Medical Sciences, Arunachal Pradesh, India
| | | | | | - Y Indibor Singh
- Department of Radiotherapy, Regional Institute of Medical Sciences, Imphal, Manipur, India
| | - Amol Suryawanshi
- Division of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, India
| | - Tathagata Choudhuri
- Department of Biotechnology, Visva Bharati University, Santiniketan, Bolpur, West Bengal, India
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47
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Hancock MH, Skalsky RL. Roles of Non-coding RNAs During Herpesvirus Infection. Curr Top Microbiol Immunol 2019; 419:243-280. [PMID: 28674945 DOI: 10.1007/82_2017_31] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Non-coding RNAs (ncRNAs) play essential roles in multiple aspects of the life cycles of herpesviruses and contribute to lifelong persistence of herpesviruses within their respective hosts. In this chapter, we discuss the types of ncRNAs produced by the different herpesvirus families during infection, some of the cellular ncRNAs manipulated by these viruses, and the overall contributions of ncRNAs to the viral life cycle, influence on the host environment, and pathogenesis.
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Affiliation(s)
- Meaghan H Hancock
- Vaccine and Gene Therapy Institute at Oregon Health and Science University, Beaverton, OR, USA
| | - Rebecca L Skalsky
- Vaccine and Gene Therapy Institute at Oregon Health and Science University, Beaverton, OR, USA.
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48
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Cheng S, Li Z, He J, Fu S, Duan Y, Zhou Q, Yan Y, Liu X, Liu L, Feng C, Zhang L, He J, Deng Y, Sun LQ. Epstein-Barr virus noncoding RNAs from the extracellular vesicles of nasopharyngeal carcinoma (NPC) cells promote angiogenesis via TLR3/RIG-I-mediated VCAM-1 expression. Biochim Biophys Acta Mol Basis Dis 2019; 1865:1201-1213. [PMID: 30659926 DOI: 10.1016/j.bbadis.2019.01.015] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Revised: 12/30/2018] [Accepted: 01/13/2019] [Indexed: 02/07/2023]
Abstract
Viral noncoding RNAs (Epstein-Barr virus-encoded RNAs, EBERs) are believed to play a critical role in the progression of lymphoma and nasopharyngeal carcinoma (NPC). However, the accurate mechanisms accounting for their oncogenic function have not been elucidated, especially in terms of interaction between tumor cells and mesenchymal cells. Here, we report that, in addition to NPC cells, EBERs are also found in endothelial cells in Epstein-Barr virus (EBV)-infected NPC parenchymal tissues, which implicates NPC-derived extracellular vesicles (EVs) in transmitting EBERs to endothelial cells. In support of this hypothesis, we first ascertained if EBERs could be transferred to endothelial cells via EVs isolated from NPC culture supernatant. Then, we clarified that EVs-derived EBERs could promote angiogenesis through stimulation of VCAM-1 expression. Finally, we explored the involvement of EBER recognition by TLR3 and RIG-I in NPC angiogenesis. Our observations collectively illustrate the significance and mechanism of EVs-derived EBERs in angiogenesis and underlie the interaction mechanisms between EBV-infected NPC cells and the tumor microenvironment.
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Affiliation(s)
- Shiyue Cheng
- Center for Molecular Medicine, Xiangya Hospital and Collaboration Innovation Center for Cancer Medicine, Central South University, China; Key Laboratory of Molecular Radiation Oncology of Hunan Province, China
| | - Zhi Li
- Center for Molecular Medicine, Xiangya Hospital and Collaboration Innovation Center for Cancer Medicine, Central South University, China; Key Laboratory of Molecular Radiation Oncology of Hunan Province, China.
| | - Junju He
- Center for Molecular Medicine, Xiangya Hospital and Collaboration Innovation Center for Cancer Medicine, Central South University, China; Key Laboratory of Molecular Radiation Oncology of Hunan Province, China
| | - Shujun Fu
- Center for Molecular Medicine, Xiangya Hospital and Collaboration Innovation Center for Cancer Medicine, Central South University, China; Key Laboratory of Molecular Radiation Oncology of Hunan Province, China
| | - Yumei Duan
- Department of Pathology, Xiangya Hospital, Central South University, China
| | - Qin Zhou
- Department of Oncology, Xiangya Hospital, Central South University, China
| | - Yuanliang Yan
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Xiaoyu Liu
- Shanghai Institute of Medical Image, Fudan University, Shanghai 200032, China
| | - Liyu Liu
- Center for Molecular Medicine, Xiangya Hospital and Collaboration Innovation Center for Cancer Medicine, Central South University, China; Key Laboratory of Molecular Radiation Oncology of Hunan Province, China
| | - Chang Feng
- Center for Molecular Medicine, Xiangya Hospital and Collaboration Innovation Center for Cancer Medicine, Central South University, China; Key Laboratory of Molecular Radiation Oncology of Hunan Province, China
| | - Lu Zhang
- Center for Molecular Medicine, Xiangya Hospital and Collaboration Innovation Center for Cancer Medicine, Central South University, China; Key Laboratory of Molecular Radiation Oncology of Hunan Province, China
| | - Jiang He
- Center for Molecular Medicine, Xiangya Hospital and Collaboration Innovation Center for Cancer Medicine, Central South University, China; Key Laboratory of Molecular Radiation Oncology of Hunan Province, China
| | - Yuezhen Deng
- Center for Molecular Medicine, Xiangya Hospital and Collaboration Innovation Center for Cancer Medicine, Central South University, China; Key Laboratory of Molecular Radiation Oncology of Hunan Province, China
| | - Lun-Quan Sun
- Center for Molecular Medicine, Xiangya Hospital and Collaboration Innovation Center for Cancer Medicine, Central South University, China; Key Laboratory of Molecular Radiation Oncology of Hunan Province, China.
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49
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Detection of Epstein-Barr Virus Infection in Non-Small Cell Lung Cancer. Cancers (Basel) 2019; 11:cancers11060759. [PMID: 31159203 PMCID: PMC6627930 DOI: 10.3390/cancers11060759] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 05/27/2019] [Accepted: 05/28/2019] [Indexed: 12/12/2022] Open
Abstract
Previous investigations proposed a link between the Epstein-Barr virus (EBV) and lung cancer (LC), but the results are highly controversial largely due to the insufficient sample size and the inherent limitation of the traditional viral screening methods such as PCR. Unlike PCR, current next-generation sequencing (NGS) utilizes an unbiased method for the global assessment of all exogenous agents within a cancer sample with high sensitivity and specificity. In our current study, we aim to resolve this long-standing controversy by utilizing our unbiased NGS-based informatics approaches in conjunction with traditional molecular methods to investigate the role of EBV in a total of 1127 LC. In situ hybridization analysis of 110 LC and 10 normal lung samples detected EBV transcripts in 3 LC samples. Comprehensive virome analyses of RNA sequencing (RNA-seq) data sets from 1017 LC and 110 paired adjacent normal lung specimens revealed EBV transcripts in three lung squamous cell carcinoma and one lung adenocarcinoma samples. In the sample with the highest EBV coverage, transcripts from the BamHI A region accounted for the majority of EBV reads. Expression of EBNA-1, LMP-1 and LMP-2 was observed. A number of viral circular RNA candidates were also detected. Thus, we for the first time revealed a type II latency-like viral transcriptome in the setting of LC in vivo. The high-level expression of viral BamHI A transcripts in LC suggests a functional role of these transcripts, likely as long non-coding RNA. Analyses of cellular gene expression and stained tissue sections indicated an increased immune cell infiltration in the sample expressing high levels of EBV transcripts compared to samples expressing low EBV transcripts. Increased level of immune checkpoint blockade factors was also detected in the sample with higher levels of EBV transcripts, indicating an induced immune tolerance. Lastly, inhibition of immune pathways and activation of oncogenic pathways were detected in the sample with high EBV transcripts compared to the EBV-low LC indicating the direct regulation of cancer pathways by EBV. Taken together, our data support the notion that EBV likely plays a pathological role in a subset of LC.
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50
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Ungerleider NA, Jain V, Wang Y, Maness NJ, Blair RV, Alvarez X, Midkiff C, Kolson D, Bai S, Roberts C, Moss WN, Wang X, Serfecz J, Seddon M, Lehman T, Ma T, Dong Y, Renne R, Tibbetts SA, Flemington EK. Comparative Analysis of Gammaherpesvirus Circular RNA Repertoires: Conserved and Unique Viral Circular RNAs. J Virol 2019; 93:e01952-18. [PMID: 30567979 PMCID: PMC6401440 DOI: 10.1128/jvi.01952-18] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 12/11/2018] [Indexed: 01/02/2023] Open
Abstract
Recent studies have identified circular RNAs (circRNAs) expressed from the Epstein-Barr virus (EBV) and Kaposi's sarcoma herpesvirus (KSHV) human DNA tumor viruses. To gain initial insights into the potential relevance of EBV circRNAs in virus biology and disease, we assessed the circRNAome of the interspecies homologue rhesus macaque lymphocryptovirus (rLCV) in a naturally occurring lymphoma from a simian immunodeficiency virus (SIV)-infected rhesus macaque. This analysis revealed rLCV orthologues of the latency-associated EBV circular RNAs circRPMS1_E4_E3a and circEBNA_U. Also identified in two samples displaying unusually high lytic gene expression was a novel rLCV circRNA that contains both conserved and rLCV-specific RPMS1 exons and whose backsplice junctions flank an rLCV lytic origin of replication (OriLyt). Analysis of a lytic infection model for the murid herpesvirus 68 (MHV68) rhadinovirus identified a cluster of circRNAs near an MHV68 lytic origin of replication, with the most abundant of these, circM11_ORF69, spanning the OriLyt. Lastly, analysis of KSHV latency and reactivation models revealed the latency associated circRNA originating from the vIRF4 gene as the predominant viral circRNA. Together, the results of this study broaden our appreciation for circRNA repertoires in the Lymphocryptovirus and Rhadinovirus genera of gammaherpesviruses and provide evolutionary support for viral circRNA functions in latency and viral replication.IMPORTANCE Infection with oncogenic gammaherpesviruses leads to long-term viral persistence through a dynamic interplay between the virus and the host immune system. Critical for remodeling of the host cell environment after the immune responses are viral noncoding RNAs that modulate host signaling pathways without attracting adaptive immune recognition. Despite the importance of noncoding RNAs in persistent infection, the circRNA class of noncoding RNAs has only recently been identified in gammaherpesviruses. Accordingly, their roles in virus infection and associated oncogenesis are unknown. Here we report evolutionary conservation of EBV-encoded circRNAs determined by assessing the circRNAome in rLCV-infected lymphomas from an SIV-infected rhesus macaque, and we report latent and lytic circRNAs from KSHV and MHV68. These experiments demonstrate utilization of the circular RNA class of RNAs across 4 members of the gammaherpesvirus subfamily, and they identify orthologues and potential homoplastic circRNAs, implying conserved circRNA functions in virus biology and associated malignancies.
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Affiliation(s)
- Nathan A Ungerleider
- Department of Pathology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, Louisiana, USA
| | - Vaibhav Jain
- Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, Gainesville, Florida, USA
| | - Yiping Wang
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida, USA
| | - Nicholas J Maness
- Department of Microbiology and Immunology, Tulane Regional Primate Center, Covington, Louisiana, USA
| | - Robert V Blair
- Division of Comparative Pathology, Tulane Regional Primate Center, Covington, Louisiana, USA
| | - Xavier Alvarez
- Division of Comparative Pathology, Tulane Regional Primate Center, Covington, Louisiana, USA
| | - Cecily Midkiff
- Division of Comparative Pathology, Tulane Regional Primate Center, Covington, Louisiana, USA
| | - Dennis Kolson
- Division of Comparative Pathology, Tulane Regional Primate Center, Covington, Louisiana, USA
| | - Shanshan Bai
- Department of Neurology, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Claire Roberts
- Department of Pathology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, Louisiana, USA
| | - Walter N Moss
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, USA
| | - Xia Wang
- Department of Pathology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, Louisiana, USA
| | - Jacqueline Serfecz
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida, USA
| | | | | | - Tianfang Ma
- Department of Structural and Cellular Biology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, Louisiana, USA
| | - Yan Dong
- Department of Structural and Cellular Biology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, Louisiana, USA
| | - Rolf Renne
- Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, Gainesville, Florida, USA
| | - Scott A Tibbetts
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida, USA
| | - Erik K Flemington
- Department of Pathology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, Louisiana, USA
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