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Majerciak V, Yang W, Zheng J, Zhu J, Zheng ZM. A Genome-Wide Epstein-Barr Virus Polyadenylation Map and Its Antisense RNA to EBNA. J Virol 2019; 93:e01593-18. [PMID: 30355690 PMCID: PMC6321932 DOI: 10.1128/jvi.01593-18] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 10/17/2018] [Indexed: 12/14/2022] Open
Abstract
Epstein-Barr virus (EBV) is a ubiquitous human pathogen associated with Burkitt's lymphoma and nasopharyngeal carcinoma. Although the EBV genome harbors more than a hundred genes, a full transcription map with EBV polyadenylation profiles remains unknown. To elucidate the 3' ends of all EBV transcripts genome-wide, we performed the first comprehensive analysis of viral polyadenylation sites (pA sites) using our previously reported polyadenylation sequencing (PA-seq) technology. We identified that EBV utilizes a total of 62 pA sites in JSC-1, 60 in Raji, and 53 in Akata cells for the expression of EBV genes from both plus and minus DNA strands; 42 of these pA sites are commonly used in all three cell lines. The majority of identified pA sites were mapped to the intergenic regions downstream of previously annotated EBV open reading frames (ORFs) and viral promoters. pA sites lacking an association with any known EBV genes were also identified, mostly for the minus DNA strand within the EBNA locus, a major locus responsible for maintenance of viral latency and cell transformation. The expression of these novel antisense transcripts to EBNA were verified by 3' rapid amplification of cDNA ends (RACE) and Northern blot analyses in several EBV-positive (EBV+) cell lines. In contrast to EBNA RNA expressed during latency, expression of EBNA-antisense transcripts, which is restricted in latent cells, can be significantly induced by viral lytic infection, suggesting potential regulation of viral gene expression by EBNA-antisense transcription during lytic EBV infection. Our data provide the first evidence that EBV has an unrecognized mechanism that regulates EBV reactivation from latency.IMPORTANCE Epstein-Barr virus represents an important human pathogen with an etiological role in the development of several cancers. By elucidation of a genome-wide polyadenylation landscape of EBV in JSC-1, Raji, and Akata cells, we have redefined the EBV transcriptome and mapped individual polymerase II (Pol II) transcripts of viral genes to each one of the mapped pA sites at single-nucleotide resolution as well as the depth of expression. By unveiling a new class of viral lytic RNA transcripts antisense to latent EBNAs, we provide a novel mechanism of how EBV might control the expression of viral latent genes and lytic infection. Thus, this report takes another step closer to understanding EBV gene structure and expression and paves a new path for antiviral approaches.
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Affiliation(s)
- Vladimir Majerciak
- Tumor Virus RNA Biology Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA
| | - Wenjing Yang
- Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Jing Zheng
- Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Jun Zhu
- Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Zhi-Ming Zheng
- Tumor Virus RNA Biology Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA
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Chen Y, Fachko D, Ivanov NS, Skinner CM, Skalsky RL. Epstein-Barr virus microRNAs regulate B cell receptor signal transduction and lytic reactivation. PLoS Pathog 2019; 15:e1007535. [PMID: 30615681 PMCID: PMC6336353 DOI: 10.1371/journal.ppat.1007535] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 01/17/2019] [Accepted: 12/17/2018] [Indexed: 12/15/2022] Open
Abstract
MicroRNAs (miRNAs) are post-transcriptional regulatory RNAs that can modulate cell signaling and play key roles in cell state transitions. Epstein-Barr virus (EBV) expresses >40 viral miRNAs that manipulate both viral and cellular gene expression patterns and contribute to reprogramming of the host environment during infection. Here, we identified a subset of EBV miRNAs that desensitize cells to B cell receptor (BCR) stimuli, and attenuate the downstream activation of NF-kappaB or AP1-dependent transcription. Bioinformatics and pathway analysis of Ago PAR-CLIP datasets identified multiple EBV miRNA targets related to BCR signal transduction, including GRB2, SOS1, MALT1, RAC1, and INPP5D, which we validated in reporter assays. BCR signaling is critical for B cell activation, proliferation, and differentiation, and for EBV, is linked to reactivation. In functional assays, we demonstrate that EBV miR-BHRF1-2-5p contributes to the growth of latently infected B cells through GRB2 regulation. We further determined that activities of EBV miR-BHRF1-2-5p, EBV miR-BART2-5p, and a cellular miRNA, miR-17-5p, directly regulate virus reactivation triggered by BCR engagement. Our findings provide mechanistic insight into some of the key miRNA interactions impacting the proliferation of latently infected B cells and importantly, governing the latent to lytic switch.
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Affiliation(s)
- Yan Chen
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, Oregon, United States of America
| | - Devin Fachko
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, Oregon, United States of America
| | - Nikita S. Ivanov
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, Oregon, United States of America
| | - Camille M. Skinner
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, Oregon, United States of America
| | - Rebecca L. Skalsky
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, Oregon, United States of America
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Forrest C, Hislop AD, Rickinson AB, Zuo J. Proteome-wide analysis of CD8+ T cell responses to EBV reveals differences between primary and persistent infection. PLoS Pathog 2018; 14:e1007110. [PMID: 30248160 PMCID: PMC6171963 DOI: 10.1371/journal.ppat.1007110] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 10/04/2018] [Accepted: 08/27/2018] [Indexed: 02/07/2023] Open
Abstract
Human herpesviruses are antigenically rich agents that induce strong CD8+T cell responses in primary infection yet persist for life, continually challenging T cell memory through recurrent lytic replication and potentially influencing the spectrum of antigen-specific responses. Here we describe the first lytic proteome-wide analysis of CD8+ T cell responses to a gamma1-herpesvirus, Epstein-Barr virus (EBV), and the first such proteome-wide analysis of primary versus memory CD8+ T cell responses to any human herpesvirus. Primary effector preparations were generated directly from activated CD8+ T cells in the blood of infectious mononucleosis (IM) patients by in vitro mitogenic expansion. For memory preparations, EBV-specific cells in the blood of long-term virus carriers were first re-stimulated in vitro by autologous dendritic cells loaded with a lysate of lytically-infected cells, then expanded as for IM cells. Preparations from 7 donors of each type were screened against each of 70 EBV lytic cycle proteins in combination with the donor's individual HLA class I alleles. Multiple reactivities against immediate early (IE), early (E) and late (L) lytic cycle proteins, including many hitherto unrecognised targets, were detected in both contexts. Interestingly however, the two donor cohorts showed a different balance between IE, E and L reactivities. Primary responses targeted IE and a small group of E proteins preferentially, seemingly in line with their better presentation on the infected cell surface before later-expressed viral evasins take full hold. By contrast, target choice equilibrates in virus carriage with responses to key IE and E antigens still present but with responses to a select subset of L proteins now often prominent. We infer that, for EBV at least, long-term virus carriage with its low level virus replication and lytic antigen release is associated with a re-shaping of the virus-specific response.
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Affiliation(s)
- Calum Forrest
- Institute for Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Andrew D. Hislop
- Institute for Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Alan B. Rickinson
- Institute for Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Jianmin Zuo
- Institute for Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
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Nightingale K, Lin KM, Ravenhill BJ, Davies C, Nobre L, Fielding CA, Ruckova E, Fletcher-Etherington A, Soday L, Nichols H, Sugrue D, Wang ECY, Moreno P, Umrania Y, Huttlin EL, Antrobus R, Davison AJ, Wilkinson GWG, Stanton RJ, Tomasec P, Weekes MP. High-Definition Analysis of Host Protein Stability during Human Cytomegalovirus Infection Reveals Antiviral Factors and Viral Evasion Mechanisms. Cell Host Microbe 2018; 24:447-460.e11. [PMID: 30122656 PMCID: PMC6146656 DOI: 10.1016/j.chom.2018.07.011] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 06/01/2018] [Accepted: 06/25/2018] [Indexed: 12/03/2022]
Abstract
Human cytomegalovirus (HCMV) is an important pathogen with multiple immune evasion strategies, including virally facilitated degradation of host antiviral restriction factors. Here, we describe a multiplexed approach to discover proteins with innate immune function on the basis of active degradation by the proteasome or lysosome during early-phase HCMV infection. Using three orthogonal proteomic/transcriptomic screens to quantify protein degradation, with high confidence we identified 35 proteins enriched in antiviral restriction factors. A final screen employed a comprehensive panel of viral mutants to predict viral genes that target >250 human proteins. This approach revealed that helicase-like transcription factor (HLTF), a DNA helicase important in DNA repair, potently inhibits early viral gene expression but is rapidly degraded during infection. The functionally unknown HCMV protein UL145 facilitates HLTF degradation by recruiting the Cullin4 E3 ligase complex. Our approach and data will enable further identifications of innate pathways targeted by HCMV and other viruses. Multiplexed viral screens uncover host proteins targeted by early HCMV infection Finding host proteins targeted for degradation by HCMV reveals immune evasion strategies A screen of HCMV deletion mutants discovers viral factors that target >250 host proteins HLTF is an antiviral restriction factor that is targeted for degradation by HCMV UL145
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Affiliation(s)
- Katie Nightingale
- Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK
| | - Kai-Min Lin
- Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK
| | - Benjamin J Ravenhill
- Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK
| | - Colin Davies
- Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK
| | - Luis Nobre
- Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK
| | - Ceri A Fielding
- Cardiff University School of Medicine, Division of Infection and Immunity, Henry Wellcome Building, Heath Park, Cardiff CF14 4XN, UK
| | - Eva Ruckova
- Regional Centre for Applied Molecular Oncology (RECAMO), Masaryk Memorial Cancer Institute, Zluty Kopec 7, 65653 Brno, Czech Republic
| | | | - Lior Soday
- Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK
| | - Hester Nichols
- Cardiff University School of Medicine, Division of Infection and Immunity, Henry Wellcome Building, Heath Park, Cardiff CF14 4XN, UK
| | - Daniel Sugrue
- Cardiff University School of Medicine, Division of Infection and Immunity, Henry Wellcome Building, Heath Park, Cardiff CF14 4XN, UK
| | - Eddie C Y Wang
- Cardiff University School of Medicine, Division of Infection and Immunity, Henry Wellcome Building, Heath Park, Cardiff CF14 4XN, UK
| | - Pablo Moreno
- Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK
| | - Yagnesh Umrania
- Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK
| | - Edward L Huttlin
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Robin Antrobus
- Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK
| | - Andrew J Davison
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow G61 1QH, UK
| | - Gavin W G Wilkinson
- Cardiff University School of Medicine, Division of Infection and Immunity, Henry Wellcome Building, Heath Park, Cardiff CF14 4XN, UK
| | - Richard J Stanton
- Cardiff University School of Medicine, Division of Infection and Immunity, Henry Wellcome Building, Heath Park, Cardiff CF14 4XN, UK
| | - Peter Tomasec
- Cardiff University School of Medicine, Division of Infection and Immunity, Henry Wellcome Building, Heath Park, Cardiff CF14 4XN, UK
| | - Michael P Weekes
- Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK.
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Djavadian R, Hayes M, Johannsen E. CAGE-seq analysis of Epstein-Barr virus lytic gene transcription: 3 kinetic classes from 2 mechanisms. PLoS Pathog 2018; 14:e1007114. [PMID: 29864140 PMCID: PMC6005644 DOI: 10.1371/journal.ppat.1007114] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Revised: 06/14/2018] [Accepted: 05/21/2018] [Indexed: 01/18/2023] Open
Abstract
Epstein-Barr virus (EBV) lytic replication proceeds through an ordered cascade of gene expression that integrates lytic DNA amplification and late gene transcription. We and others previously demonstrated that 6 EBV proteins that have orthologs in β- and γ-, but not in α-herpesviruses, mediate late gene transcription in a lytic DNA replication-dependent manner. We proposed a model in which the βγ gene-encoded viral pre-initiation complex (vPIC) mediates transcription from newly replicated viral DNA. While this model explains the dependence of late gene transcription on lytic DNA replication, it does not account for this dependence in α-herpesviruses nor for recent reports that some EBV late genes are transcribed independently of vPIC. To rigorously define which transcription start sites (TSS) are dependent on viral lytic DNA replication or the βγ complex, we performed Cap Analysis of Gene Expression (CAGE)-seq on cells infected with wildtype EBV or EBV mutants defective for DNA replication, βγ function, or lacking an origin of lytic replication (OriLyt). This approach identified 16 true-late, 32 early, and 16 TSS that are active at low levels early and are further upregulated in a DNA replication-dependent manner (leaky late). Almost all late gene transcription is vPIC-dependent, with BCRF1 (vIL10), BDLF2, and BDLF3 transcripts being notable exceptions. We present evidence that leaky late transcription is not due to a distinct mechanism, but results from superimposition of the early and late transcription mechanisms at the same promoter. Our results represent the most comprehensive characterization of EBV lytic gene expression kinetics reported to date and suggest that most, but not all EBV late genes are vPIC-dependent.
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Affiliation(s)
- Reza Djavadian
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
- Department of Oncology (McArdle Laboratory for Cancer Research), University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - Mitchell Hayes
- Department of Oncology (McArdle Laboratory for Cancer Research), University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - Eric Johannsen
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
- Department of Oncology (McArdle Laboratory for Cancer Research), University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
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Williams M, Ariza ME. EBV Positive Diffuse Large B Cell Lymphoma and Chronic Lymphocytic Leukemia Patients Exhibit Increased Anti-dUTPase Antibodies. Cancers (Basel) 2018; 10:E129. [PMID: 29723986 PMCID: PMC5977102 DOI: 10.3390/cancers10050129] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 04/20/2018] [Accepted: 04/25/2018] [Indexed: 12/22/2022] Open
Abstract
The Epstein-Barr virus (EBV), which is a ubiquitous γ-herpesvirus, establishes a latent infection in more than 90% of the global adult population. EBV-associated malignancies have increased by 14.6% over the last 20 years, and account for approximately 1.5% of all cancers worldwide and 1.8% of all cancer deaths. However, the potential involvement/contribution of lytic proteins to the pathophysiology of EBV-associated cancers is not well understood. We have previously demonstrated that the EBV-deoxyuridine triphosphate nucleotidohydrolase (dUTPase) modulates innate and adaptive immune responses by engaging the Toll-Like Receptor 2 (TLR2), which leads to the modulation of downstream genes involved in oncogenesis, chronic inflammation, and in effector T-cell function. Furthermore, examination of serum samples from diffuse large B-cell lymphoma (DLBCL) and chronic lymphocytic leukemia patients revealed the presence of increased levels of anti-dUTPase antibodies in both cohorts compared to controls with the highest levels (3.67-fold increase) observed in DLBCL female cases and the lowest (2.12-fold increase) in DLBCL males. Using computer-generated algorithms, dUTPase amino acid sequence alignments, and functional studies of BLLF3 mutants, we identified a putative amino acid motif involved with TLR2 interaction. These findings suggest that the EBV-dUTPase: TLR2 interaction is a potential molecular target that could be used for developing novel therapeutics (small molecules/vaccines).
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Affiliation(s)
- Marshall Williams
- Department of Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, OH 43210, USA.
- Institute for Behavioral Medicine Research, The Ohio State University College of Medicine, Columbus, OH 43210, USA.
| | - Maria Eugenia Ariza
- Department of Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, OH 43210, USA.
- Institute for Behavioral Medicine Research, The Ohio State University College of Medicine, Columbus, OH 43210, USA.
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Lactic Acid Downregulates Viral MicroRNA To Promote Epstein-Barr Virus-Immortalized B Lymphoblastic Cell Adhesion and Growth. J Virol 2018; 92:JVI.00033-18. [PMID: 29444941 DOI: 10.1128/jvi.00033-18] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 02/06/2018] [Indexed: 01/23/2023] Open
Abstract
High plasma lactate is associated with poor prognosis of many malignancies, but its role in virally mediated cancer progression and underlying molecular mechanisms are unclear. Epstein-Barr virus (EBV), the first human oncogenic virus, causes several cancers, including B-cell lymphoma. Here, we report that lactate dehydrogenase A (LDH-A) expression and lactate production are elevated in EBV-immortalized B lymphoblastic cells, and lactic acid (LA; acidic lactate) at low concentration triggers EBV-infected B-cell adhesion, morphological changes, and proliferation in vitro and in vivo Moreover, LA-induced responses of EBV-infected B cells uniquely occurs in viral latency type III, and it is dramatically associated with the inhibition of global viral microRNAs, particularly the miR-BHRF1 cluster, and the high expression of SMAD3, JUN, and COL1A genes. The introduction of miR-BHRF1-1 blocks the LA-induced effects of EBV-infected B cells. Thus, this may be a novel mechanism to explain EBV-immortalized B lymphoblastic cell malignancy in an LA microenvironment.IMPORTANCE The tumor microenvironment is complicated, and lactate, which is created by cell metabolism, contributes to an acidic microenvironment that facilitates cancer progression. However, how LA operates in virus-associated cancers is unclear. Thus, we studied how EBV (the first tumor virus identified in humans; it is associated with many cancers) upregulates the expression of LDH-A and lactate production in B lymphoma cells. Elevated LA induces adhesion and the growth of EBV-infected B cells by inhibiting viral microRNA transcription. Thus, we offer a novel understanding of how EBV utilizes an acidic microenvironment to promote cancer development.
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CRISPR-Cas9 Genetic Analysis of Virus-Host Interactions. Viruses 2018; 10:v10020055. [PMID: 29385696 PMCID: PMC5850362 DOI: 10.3390/v10020055] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Revised: 01/28/2018] [Accepted: 01/29/2018] [Indexed: 12/12/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) has greatly expanded the ability to genetically probe virus–host interactions. CRISPR systems enable focused or systematic, genomewide studies of nearly all aspects of a virus lifecycle. Combined with its relative ease of use and high reproducibility, CRISPR is becoming an essential tool in studies of the host factors important for viral pathogenesis. Here, we review the use of CRISPR–Cas9 for the loss-of-function analysis of host dependency factors. We focus on the use of CRISPR-pooled screens for the systematic identification of host dependency factors, particularly in Epstein–Barr virus-transformed B cells. We also discuss the use of CRISPR interference (CRISPRi) and gain-of-function CRISPR activation (CRISPRa) approaches to probe virus–host interactions. Finally, we comment on the future directions enabled by combinatorial CRISPR screens.
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Lv DW, Zhang K, Li R. Interferon regulatory factor 8 regulates caspase-1 expression to facilitate Epstein-Barr virus reactivation in response to B cell receptor stimulation and chemical induction. PLoS Pathog 2018; 14:e1006868. [PMID: 29357389 PMCID: PMC5794192 DOI: 10.1371/journal.ppat.1006868] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 02/01/2018] [Accepted: 01/09/2018] [Indexed: 12/30/2022] Open
Abstract
Interferon regulatory factor 8 (IRF8), also known as interferon consensus sequence-binding protein (ICSBP), is a transcription factor of the IRF family. IRF8 plays a key role in normal B cell differentiation, a cellular process that is intrinsically associated with Epstein-Barr virus (EBV) reactivation. However, whether IRF8 regulates EBV lytic replication remains unknown. In this study, we utilized a CRISPR/Cas9 genomic editing approach to deplete IRF8 and found that IRF8 depletion dramatically inhibits the reactivation of EBV upon lytic induction. We demonstrated that IRF8 depletion suppresses the expression of a group of genes involved in apoptosis and thus inhibits apoptosis induction upon lytic induction by B cell receptor (BCR) stimulation or chemical induction. The protein levels of caspase-1, caspase-3 and caspase-8 all dramatically decreased in IRF8-depleted cells, which led to reduced caspase activation and the stabilization of KAP1, PAX5 and DNMT3A upon BCR stimulation. Interestingly, caspase inhibition blocked the degradation of KAP1, PAX5 and DNMT3A, suppressed EBV lytic gene expression and viral DNA replication upon lytic induction, suggesting that the reduced caspase expression in IRF8-depleted cells contributes to the suppression of EBV lytic replication. We further demonstrated that IRF8 directly regulates CASP1 (caspase-1) gene expression through targeting its gene promoter and knockdown of caspase-1 abrogates EBV reactivation upon lytic induction, partially through the stabilization of KAP1. Together our study suggested that, by modulating the activation of caspases and the subsequent cleavage of KAP1 upon lytic induction, IRF8 plays a critical role in EBV lytic reactivation. Infection with Epstein-Barr virus (EBV) is closely associated with human cancers of both B cell and epithelial cell origin. The EBV life cycle is tightly regulated by both viral and cellular factors. Here, we demonstrate that interferon regulatory factor 8 (IRF8) is required for EBV lytic replication. Mechanistically, IRF8 directly regulates caspase-1 expression and hence caspase activation upon B cell receptor (BCR) stimulation and chemical induction, which leads to the cleavage and de-stabilization of several host factors suppressing lytic replication, including KAP1. Caspase-1 depletion blocks EBV reactivation while KAP1 depletion facilitates reactivation in caspase-1 depleted cells. These results together establish a IRF8/caspase-1/KAP1 axis important for EBV reactivation.
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Affiliation(s)
- Dong-Wen Lv
- Department of Oral and Craniofacial Molecular Biology and Philips Institute for Oral Health Research, School of Dentistry, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Kun Zhang
- Department of Oral and Craniofacial Molecular Biology and Philips Institute for Oral Health Research, School of Dentistry, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Renfeng Li
- Department of Oral and Craniofacial Molecular Biology and Philips Institute for Oral Health Research, School of Dentistry, Virginia Commonwealth University, Richmond, Virginia, United States of America
- Department of Microbiology and Immunology, School of Medicine, Virginia Commonwealth University, Richmond, Virginia, United States of America
- Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia, United States of America
- * E-mail:
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Kim DK, Park J, Han D, Yang J, Kim A, Woo J, Kim Y, Mook-Jung I. Molecular and functional signatures in a novel Alzheimer's disease mouse model assessed by quantitative proteomics. Mol Neurodegener 2018; 13:2. [PMID: 29338754 PMCID: PMC5771139 DOI: 10.1186/s13024-017-0234-4] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 12/29/2017] [Indexed: 01/10/2023] Open
Abstract
Background Alzheimer’s disease (AD), the most common neurodegenerative disorder, is characterized by the deposition of extracellular amyloid plaques and intracellular neurofibrillary tangles. To understand the pathological mechanisms underlying AD, developing animal models that completely encompass the main features of AD pathologies is indispensable. Although mouse models that display pathological hallmarks of AD (amyloid plaques, neurofibrillary tangles, or both) have been developed and investigated, a systematic approach for understanding the molecular characteristics of AD mouse models is lacking. Methods To elucidate the mechanisms underlying the contribution of amyloid beta (Aβ) and tau in AD pathogenesis, we herein generated a novel animal model of AD, namely the AD-like pathology with amyloid and neurofibrillary tangles (ADLPAPT) mice. The ADLPAPT mice carry three human transgenes, including amyloid precursor protein, presenilin-1, and tau, with six mutations. To characterize the molecular and functional signatures of AD in ADLPAPT mice, we analyzed the hippocampal proteome and performed comparisons with individual-pathology transgenic mice (i.e., amyloid or neurofibrillary tangles) and wild-type mice using quantitative proteomics with 10-plex tandem mass tag. Results The ADLPAPT mice exhibited accelerated neurofibrillary tangle formation in addition to amyloid plaques, neuronal loss in the CA1 area, and memory deficit at an early age. In addition, our proteomic analysis identified nearly 10,000 protein groups, which enabled the identification of hundreds of differentially expressed proteins (DEPs) in ADLPAPT mice. Bioinformatics analysis of DEPs revealed that ADLPAPT mice experienced age-dependent active immune responses and synaptic dysfunctions. Conclusions Our study is the first to compare and describe the proteomic characteristics in amyloid and neurofibrillary tangle pathologies using isobaric label-based quantitative proteomics. Furthermore, we analyzed the hippocampal proteome of the newly developed ADLPAPT model mice to investigate how both Aβ and tau pathologies regulate the hippocampal proteome. Because the ADLPAPT mouse model recapitulates the main features of AD pathogenesis, the proteomic data derived from its hippocampus has significant utility as a novel resource for the research on the Aβ-tau axis and pathophysiological changes in vivo. Electronic supplementary material The online version of this article (10.1186/s13024-017-0234-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Dong Kyu Kim
- Department of Biomedical Sciences, Seoul National University, College of Medicine, 103 Daehak-ro, Seoul, 110-799, South Korea
| | - Joonho Park
- Interdisciplinary Program in Bioengineering, College of Engineering, Seoul National University, 1 Gwanak-ro, Seoul, 151-742, South Korea
| | - Dohyun Han
- Biomedical Research Institute, Seoul National University Hospital, 101 Daehak-ro, Seoul, 110-744, South Korea
| | - Jinhee Yang
- Department of Biomedical Sciences, Seoul National University, College of Medicine, 103 Daehak-ro, Seoul, 110-799, South Korea
| | - Ahbin Kim
- Department of Biomedical Sciences, Seoul National University, College of Medicine, 103 Daehak-ro, Seoul, 110-799, South Korea
| | - Jongmin Woo
- Department of Biomedical Sciences, Seoul National University, College of Medicine, 103 Daehak-ro, Seoul, 110-799, South Korea
| | - Youngsoo Kim
- Interdisciplinary Program in Bioengineering, College of Engineering, Seoul National University, 1 Gwanak-ro, Seoul, 151-742, South Korea.
| | - Inhee Mook-Jung
- Department of Biomedical Sciences, Seoul National University, College of Medicine, 103 Daehak-ro, Seoul, 110-799, South Korea. .,Neuroscience Research Institute, Seoul National University, College of Medicine, Seoul, 110-799, South Korea.
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Wang M, Wu W, Zhang Y, Yao G, Gu B. Rapamycin enhances lytic replication of Epstein-Barr virus in gastric carcinoma cells by increasing the transcriptional activities of immediate-early lytic promoters. Virus Res 2018; 244:173-180. [PMID: 29169830 DOI: 10.1016/j.virusres.2017.11.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2017] [Revised: 11/18/2017] [Accepted: 11/18/2017] [Indexed: 12/12/2022]
Abstract
Epstein-Barr virus (EBV), a human herpesvirus, is linked to both epithelial and lymphoid malignancies. Induction of EBV reactivation is a potential therapeutic strategy for EBV-associated tumors. In this study, we assessed the effects of rapamycin on EBV reactivation in gastric carcinoma cells. We found that rapamycin upregulated expression of EBV lytic proteins and increased the viral proliferation triggered by the EBV lytic inducer sodium butyrate. Reverse transcription-qPCR, luciferase activity assays, chromatin immunoprecipitation and western blotting were employed to explore the mechanism by which rapamycin promotes EBV reactivation. Our results showed that rapamycin treatment resulted in increased mRNA levels of EBV immediate-early genes. Rapamycin also enhanced the transcriptional activities of the EBV immediate-early lytic promoters Zp and Rp by strengthening Sp1 binding. Repression of the cellular ataxia telangiectasia-mutated/p53 pathway by siRNA-mediated knockdown of the ataxia telangiectasia-mutated gene significantly abrogated virus reactivation by rapamycin/sodium butyrate treatment, indicating that the ataxia telangiectasia-mutated/p53 pathway is involved in rapamycin-promoted EBV reactivation. Taken together, these findings demonstrate that rapamycin might have the potential to enhance the effectiveness of oncolytic viral therapies developed for EBV-associated malignancies.
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MESH Headings
- Ataxia Telangiectasia Mutated Proteins/antagonists & inhibitors
- Ataxia Telangiectasia Mutated Proteins/genetics
- Ataxia Telangiectasia Mutated Proteins/metabolism
- Butyric Acid/pharmacology
- Cell Line, Tumor
- Cell Survival/drug effects
- DNA, Viral/genetics
- DNA, Viral/metabolism
- Gastric Mucosa/drug effects
- Gastric Mucosa/metabolism
- Gastric Mucosa/virology
- Gene Expression Regulation
- Genes, Reporter
- Herpesvirus 4, Human/drug effects
- Herpesvirus 4, Human/genetics
- Herpesvirus 4, Human/growth & development
- Herpesvirus 4, Human/metabolism
- Humans
- Immediate-Early Proteins/agonists
- Immediate-Early Proteins/genetics
- Immediate-Early Proteins/metabolism
- Luciferases/genetics
- Luciferases/metabolism
- Oncolytic Virotherapy/methods
- Promoter Regions, Genetic/drug effects
- Protein Binding
- RNA, Small Interfering/genetics
- RNA, Small Interfering/metabolism
- Sirolimus/pharmacology
- Sp1 Transcription Factor/genetics
- Sp1 Transcription Factor/metabolism
- Transcription, Genetic
- Tumor Suppressor Protein p53/antagonists & inhibitors
- Tumor Suppressor Protein p53/genetics
- Tumor Suppressor Protein p53/metabolism
- Virus Activation/drug effects
- Virus Replication/drug effects
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Affiliation(s)
- Man Wang
- Institute for Translational Medicine, Medical College of Qingdao University, Qingdao, 266021, China.
| | - Wei Wu
- Institute for Translational Medicine, Medical College of Qingdao University, Qingdao, 266021, China
| | - Yinfeng Zhang
- Institute for Translational Medicine, Medical College of Qingdao University, Qingdao, 266021, China
| | - Guoliang Yao
- Department of General Surgery, The First Affiliated Hospital of Henan University of Science and Technology, Luoyang, 471003, China
| | - Bianli Gu
- Henan Key Laboratory of Cancer Epigenetics, Cancer Hospital, The First Affiliated Hospital, College of Clinical Medicine, Medical College of Henan University of Science and Technology, Luoyang, 471003, China
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Pei Y, Lewis AE, Robertson ES. Current Progress in EBV-Associated B-Cell Lymphomas. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1018:57-74. [PMID: 29052132 DOI: 10.1007/978-981-10-5765-6_5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Epstein-Barr virus (EBV) was the first human tumor virus discovered more than 50 years ago. EBV-associated lymphomagenesis is still a significant viral-associated disease as it involves a diverse range of pathologies, especially B-cell lymphomas. Recent development of high-throughput next-generation sequencing technologies and in vivo mouse models have significantly promoted our understanding of the fundamental molecular mechanisms which drive these cancers and allowed for the development of therapeutic intervention strategies. This review will highlight the current advances in EBV-associated B-cell lymphomas, focusing on transcriptional regulation, chromosome aberrations, in vivo studies of EBV-mediated lymphomagenesis, as well as the treatment strategies to target viral-associated lymphomas.
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Affiliation(s)
- Yonggang Pei
- Department of Otorhinolaryngology-Head and Neck Surgery, and Microbiology, Tumor Virology Program, Abramson Comprehensive Cancer Center, Perelman School of Medicine at the University of Pennsylvania, 3610 Hamilton Walk, 201E Johnson Pavilion, Philadelphia, PA, 19104, USA
| | - Alexandria E Lewis
- Department of Otorhinolaryngology-Head and Neck Surgery, and Microbiology, Tumor Virology Program, Abramson Comprehensive Cancer Center, Perelman School of Medicine at the University of Pennsylvania, 3610 Hamilton Walk, 201E Johnson Pavilion, Philadelphia, PA, 19104, USA
| | - Erle S Robertson
- Department of Otorhinolaryngology-Head and Neck Surgery, and Microbiology, Tumor Virology Program, Abramson Comprehensive Cancer Center, Perelman School of Medicine at the University of Pennsylvania, 3610 Hamilton Walk, 201E Johnson Pavilion, Philadelphia, PA, 19104, USA.
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