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Norman RX, Chen YC, Recchia EE, Loi J, Rosemarie Q, Lesko SL, Patel S, Sherer N, Takaku M, Burkard ME, Suzuki A. One step 4x and 12x 3D-ExM: robust super-resolution microscopy in cell biology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.13.607782. [PMID: 39185153 PMCID: PMC11343106 DOI: 10.1101/2024.08.13.607782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/27/2024]
Abstract
Super-resolution microscopy has become an indispensable tool across diverse research fields, offering unprecedented insights into biological architectures with nanometer scale resolution. Compared to traditional nanometer-scale imaging methods such as electron microscopy, super-resolution microscopy offers several advantages, including the simultaneous labeling of multiple target biomolecules with high specificity and simpler sample preparation, making it accessible to most researchers. In this study, we introduce two optimized methods of super-resolution imaging: 4-fold and 12-fold 3D-isotropic and preserved Expansion Microscopy (4x and 12x 3D-ExM). 3D-ExM is a straightforward expansion microscopy method featuring a single-step process, providing robust and reproducible 3D isotropic expansion for both 2D and 3D cell culture models. With standard confocal microscopy, 12x 3D-ExM achieves a lateral resolution of under 30 nm, enabling the visualization of nanoscale structures, including chromosomes, kinetochores, nuclear pore complexes, and Epstein-Barr virus particles. These results demonstrate that 3D-ExM provides cost-effective and user-friendly super-resolution microscopy, making it highly suitable for a wide range of cell biology research, including studies on cellular and chromatin architectures.
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Affiliation(s)
- Roshan X Norman
- Biophysics Graduate Program, University of Wisconsin-Madison, Madison, Wisconsin
- Department of Oncology, McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin
- Department of Medicine, Hematology/Oncology, University of Wisconsin-Madison, Madison, Wisconsin
| | - Yu-Chia Chen
- Department of Oncology, McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin
- Molecular and Cellular Pharmacology Graduate Program, University of Wisconsin-Madison, Madison, Wisconsin
| | - Emma E Recchia
- Department of Oncology, McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin
| | - Jonathan Loi
- Biophysics Graduate Program, University of Wisconsin-Madison, Madison, Wisconsin
- Department of Oncology, McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin
| | - Quincy Rosemarie
- Department of Oncology, McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin
| | - Sydney L Lesko
- Department of Oncology, McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin
| | - Smit Patel
- Department of Oncology, McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin
| | - Nathan Sherer
- Department of Oncology, McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin
- UW Carbone Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin
| | - Motoki Takaku
- Department of Biomedical Science, University of North Dakota School of Medicine and Health Science, Grand Forks, North Dakota, USA
| | - Mark E Burkard
- Biophysics Graduate Program, University of Wisconsin-Madison, Madison, Wisconsin
- Department of Oncology, McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin
- Department of Medicine, Hematology/Oncology, University of Wisconsin-Madison, Madison, Wisconsin
- UW Carbone Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin
| | - Aussie Suzuki
- Biophysics Graduate Program, University of Wisconsin-Madison, Madison, Wisconsin
- Department of Oncology, McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin
- UW Carbone Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin
- Lead Contact
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You H, Havey L, Li Z, Asara J, Guo R. Epstein-Barr-Virus-Driven Cardiolipin Synthesis Sustains Metabolic Remodeling During B-cell Lymphomagenesis. RESEARCH SQUARE 2024:rs.3.rs-4013392. [PMID: 38659762 PMCID: PMC11042403 DOI: 10.21203/rs.3.rs-4013392/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Epstein-Barr Virus (EBV) is associated with a range of B-cell malignancies, including Burkitt, Hodgkin, post-transplant, and AIDS-related lymphomas. Studies highlight EBV's transformative capability to induce oncometabolism in B-cells to support energy, biosynthetic precursors, and redox equivalents necessary for transition from quiescent to proliferation. Mitochondrial dysfunction presents an intrinsic barrier to EBV B-cell immortalization. Yet, how EBV maintains B-cell mitochondrial function and metabolic fluxes remains unclear. Here we show that EBV boosts cardiolipin(CL) biosynthesis, essential for mitochondrial cristae biogenesis, via EBNA2-induced CL enzyme transactivation. Pharmaceutical and CRISPR genetic analyses underscore the essentiality of CL biosynthesis in EBV-transformed B-cells. Metabolomic and isotopic tracing highlight CL's role in sustaining respiration, one-carbon metabolism, and aspartate synthesis, all vital for EBV-transformed B-cells. Targeting CL biosynthesis destabilizes mitochondrial one-carbon enzymes, causing synthetic lethality when coupled with a SHMT1/2 inhibitor. We demonstrate EBV-induced CL metabolism as a therapeutic target, offering new strategies against EBV-associated B-cell malignancies.
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Affiliation(s)
- Haixi You
- Department of Molecular Biology and Microbiology, Tufts University, Boston, MA, USA
| | - Larissa Havey
- Department of Molecular Biology and Microbiology, Tufts University, Boston, MA, USA
| | - Zhixuan Li
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston MA, USA
| | - John Asara
- Division of Signal Transduction, Beth Israel Deaconess Medical Center and Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Rui Guo
- Department of Molecular Biology and Microbiology, Tufts University, Boston, MA, USA
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Molina E, García-Gutiérrez L, Junco V, Perez-Olivares M, de Yébenes VG, Blanco R, Quevedo L, Acosta JC, Marín AV, Ulgiati D, Merino R, Delgado MD, Varela I, Regueiro JR, Moreno de Alborán I, Ramiro AR, León J. MYC directly transactivates CR2/CD21, the receptor of the Epstein-Barr virus, enhancing the viral infection of Burkitt lymphoma cells. Oncogene 2023; 42:3358-3370. [PMID: 37773203 DOI: 10.1038/s41388-023-02846-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 09/12/2023] [Accepted: 09/18/2023] [Indexed: 10/01/2023]
Abstract
MYC is an oncogenic transcription factor dysregulated in about half of total human tumors. While transcriptomic studies reveal more than 1000 genes regulated by MYC, a much smaller fraction of genes is directly transactivated by MYC. Virtually all Burkitt lymphoma (BL) carry chromosomal translocations involving MYC oncogene. Most endemic BL and a fraction of sporadic BL are associated with Epstein-Barr virus (EBV) infection. The currently accepted mechanism is that EBV is the BL-causing agent inducing MYC translocation. Herein we show that the EBV receptor, CR2 (also called CD21), is a direct MYC target gene. This is based on several pieces of evidence: MYC induces CR2 expression in both proliferating and arrested cells and in the absence of protein synthesis, binds the CR2 promoter and transactivates CR2 in an E-box-dependent manner. Moreover, using mice with conditional MYC ablation we show that MYC induces CR2 in primary B cells. Importantly, modulation of MYC levels directly correlates with EBV's ability of infection in BL cells. Altogether, in contrast to the widely accepted hypothesis for the correlation between EBV and BL, we propose an alternative hypothesis in which MYC dysregulation could be the first event leading to the subsequent EBV infection.
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Affiliation(s)
- Ester Molina
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, Santander, Spain
- Departamento de Biología Molecular, Universidad de Cantabria, Santander, Spain
- The Hormel Institute, University of Minnesota, Austin, MN, USA
| | - Lucía García-Gutiérrez
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, Santander, Spain
- Departamento de Biología Molecular, Universidad de Cantabria, Santander, Spain
| | - Vanessa Junco
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, Santander, Spain
- Departamento de Biología Molecular, Universidad de Cantabria, Santander, Spain
| | - Mercedes Perez-Olivares
- Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB)-CSIC, Madrid, Spain
| | - Virginia G de Yébenes
- Centro Nacional de Investigaciones Cardiovasculares-CNIC Carlos III, Madrid, Spain
- Department of Immunology, Ophthalmology and ENT, Universidad Complutense, School of Medicine and 12 de Octubre Health Research Institute (imas12), Madrid, Spain
| | - Rosa Blanco
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, Santander, Spain
- Departamento de Biología Molecular, Universidad de Cantabria, Santander, Spain
| | - Laura Quevedo
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, Santander, Spain
- Departamento de Biología Molecular, Universidad de Cantabria, Santander, Spain
| | - Juan C Acosta
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, Santander, Spain
- Departamento de Biología Molecular, Universidad de Cantabria, Santander, Spain
| | - Ana V Marín
- Department of Immunology, Ophthalmology and ENT, Universidad Complutense, School of Medicine and 12 de Octubre Health Research Institute (imas12), Madrid, Spain
| | - Daniela Ulgiati
- School of Biomedical Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Ramon Merino
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, Santander, Spain
- Departamento de Biología Molecular, Universidad de Cantabria, Santander, Spain
| | - M Dolores Delgado
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, Santander, Spain
- Departamento de Biología Molecular, Universidad de Cantabria, Santander, Spain
| | - Ignacio Varela
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, Santander, Spain
- Departamento de Biología Molecular, Universidad de Cantabria, Santander, Spain
| | - José R Regueiro
- Department of Immunology, Ophthalmology and ENT, Universidad Complutense, School of Medicine and 12 de Octubre Health Research Institute (imas12), Madrid, Spain
| | | | - Almudena R Ramiro
- Centro Nacional de Investigaciones Cardiovasculares-CNIC Carlos III, Madrid, Spain
| | - Javier León
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, Santander, Spain.
- Departamento de Biología Molecular, Universidad de Cantabria, Santander, Spain.
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Gondwe Y, Salima A, Manda A, Ozuah N, Mapurisa G, Brandt K, Gopal S, Tomoka T, Fedoriw Y, Westmoreland KD. Spatial distribution of incident pediatric Burkitt lymphoma in central and northern Malawi and association with malaria prevalence. Pediatr Blood Cancer 2022; 69:e29867. [PMID: 35731580 PMCID: PMC10846644 DOI: 10.1002/pbc.29867] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 05/27/2022] [Accepted: 06/09/2022] [Indexed: 11/06/2022]
Abstract
BACKGROUND Burkitt lymphoma (BL) accounts for 90% of pediatric lymphomas in sub-Saharan Africa. Plasmodium falciparum malaria is considered an etiological factor of BL. We describe the geographic distribution of pediatric BL in Malawi and association with P. falciparum malaria prevalence rate (PfPR). METHODS We enrolled 220 pathologically confirmed incident pediatric BL cases (2013-2018) into an observational clinical cohort at Kamuzu Central Hospital (KCH) in Lilongwe district. KCH is the main tertiary cancer referral center serving the central and northern regions of Malawi. Using an ecological study design, we calculated district-level annual BL incidence rate using census population estimates. District-level PfPR was extracted from the National Malaria Control Program 2010 report. BL incidence and PfPR maps were constructed in QGIS. Moran's I test was used to identify BL spatial clusters. Pearson's correlation and multiple linear regression analyses were used to statistically examine the relationship between PfPR and BL. RESULTS BL incidence was higher in central region districts (8.2 cases per million) than northern districts (2.9 cases per million) and was elevated in lakeshore districts. Districts with elevated PfPR tended to have elevated BL incidence. A low-risk BL cluster was detected in the north. Statistically, BL incidence was positively correlated with PfPR (r = .77, p < .01). A 1% increase in PfPR predicted an increase in BL incidence of 0.2 cases per million (p = .03), when controlling for travel time from referral district hospital to KCH. CONCLUSION Our study supports evidence for an association between P. falciparum and BL and highlights a need to improve geographic accessibility to tertiary cancer services in Malawi's northern region.
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Affiliation(s)
- Yolanda Gondwe
- University of North Carolina Project-Malawi, University of North Carolina, Lilongwe, Malawi
| | - Ande Salima
- University of North Carolina Project-Malawi, University of North Carolina, Lilongwe, Malawi
| | - Agness Manda
- University of North Carolina Project-Malawi, University of North Carolina, Lilongwe, Malawi
| | | | - Gugulethu Mapurisa
- University of North Carolina Project-Malawi, University of North Carolina, Lilongwe, Malawi
| | - Katerina Brandt
- Department of Geography, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Satish Gopal
- National Cancer Institute Center for Global Health, Bethesda, Maryland, USA
| | - Tamiwe Tomoka
- University of North Carolina Project-Malawi, University of North Carolina, Lilongwe, Malawi
| | - Yuri Fedoriw
- University of North Carolina Project-Malawi, University of North Carolina, Lilongwe, Malawi
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Katherine D Westmoreland
- University of North Carolina Project-Malawi, University of North Carolina, Lilongwe, Malawi
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
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The Epstein-Barr Virus Oncogene EBNA1 Suppresses Natural Killer Cell Responses and Apoptosis Early after Infection of Peripheral B Cells. mBio 2021; 12:e0224321. [PMID: 34781735 PMCID: PMC8593684 DOI: 10.1128/mbio.02243-21] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The innate immune system serves as frontline defense against pathogens, such as bacteria and viruses. Natural killer (NK) cells are a part of innate immunity and can both secrete cytokines and directly target cells for lysis. NK cells express several cell surface receptors, including NKG2D, which bind multiple ligands. People with deficiencies in NK cells are often susceptible to uncontrolled infection by herpesviruses, such as Epstein-Barr virus (EBV). Infection with EBV stimulates both innate and adaptive immunity, yet the virus establishes lifelong latent infection in memory B cells. We show that the EBV oncogene EBNA1, previously known to be necessary for maintaining EBV genomes in latently infected cells, also plays an important role in suppressing NK cell responses and cell death in newly infected cells. EBNA1 does so by downregulating the NKG2D ligands ULBP1 and ULBP5 and modulating expression of c-Myc. B cells infected with a derivative of EBV that lacks EBNA1 are more susceptible to NK cell-mediated killing and show increased levels of apoptosis. Thus, EBNA1 performs a previously unappreciated role in reducing immune response and programmed cell death after EBV infection, helping infected cells avoid immune surveillance and apoptosis and thus persist for the lifetime of the host. IMPORTANCE Epstein-Barr virus (EBV) is a ubiquitous human pathogen, infecting up to 95% of the world's adult population. Initial infection with EBV can cause infectious mononucleosis. EBV is also linked to several human malignancies, including lymphomas and carcinomas. Although infection by EBV alerts the immune system and causes an immune response, the virus persists for life in memory B cells. We show that the EBV protein EBNA1 can downregulate several components of the innate immune system linked to natural killer (NK) cells. This downregulation of NK cell activity translates to lower killing of EBV-infected cells and is likely one way that EBV escapes immune surveillance after infection. Additionally, we show that EBNA1 reduces apoptosis in newly infected B cells, allowing more of these cells to survive. Taken together, our findings uncover new functions of EBNA1 and provide insights into viral strategies to survive the initial immune response postinfection.
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6
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Yang YC, Sugden B. Epstein-Barr Virus Limits the Accumulation of IPO7, an Essential Gene Product. Front Microbiol 2021; 12:643327. [PMID: 33664726 PMCID: PMC7920963 DOI: 10.3389/fmicb.2021.643327] [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] [Received: 12/17/2020] [Accepted: 01/25/2021] [Indexed: 01/19/2023] Open
Abstract
Epstein-Barr virus (EBV) encodes more than 40 miRNAs that target cellular mRNAs to aid its infection, replication, and maintenance in individual cells and in its human host. Importin-7 (IPO7), also termed Imp7 or RanBPM7, is a nucleocytoplasmic transport protein that has been frequently identified as a target for two of these viral miRNAs. How the viral life cycle might benefit from regulating IPO7 has been unclear, though. We demonstrate with CRISPR-Cas9 mutagenesis that IPO7 is essential in at least three cells lines and that increasing its levels of expression inhibits growth of infected cells. EBV thus regulates the level of IPO7 to limit its accumulation consistent with its being required for survival of its host cell.
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Affiliation(s)
- Ya-Chun Yang
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI, United States
| | - Bill Sugden
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI, United States
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Guo R, Zhang Y, Teng M, Jiang C, Schineller M, Zhao B, Doench JG, O'Reilly RJ, Cesarman E, Giulino-Roth L, Gewurz BE. DNA methylation enzymes and PRC1 restrict B-cell Epstein-Barr virus oncoprotein expression. Nat Microbiol 2020; 5:1051-1063. [PMID: 32424339 PMCID: PMC7462085 DOI: 10.1038/s41564-020-0724-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 04/16/2020] [Indexed: 12/13/2022]
Abstract
To accomplish the remarkable task of lifelong infection, the Epstein-Barr virus (EBV) switches between four viral genome latency and lytic programmes to navigate the B-cell compartment and evade immune responses. The transforming programme, consisting of highly immunogenic EBV nuclear antigen (EBNA) and latent membrane proteins (LMPs), is expressed in newly infected B lymphocytes and in post-transplant lymphomas. On memory cell differentiation and in most EBV-associated Burkitt's lymphomas, all but one viral antigen are repressed for immunoevasion. To gain insights into the epigenetic mechanisms that restrict immunogenic oncoprotein expression, a genome-scale CRISPR-Cas9 screen was performed in EBV and Burkitt's lymphoma cells. Here, we show that the ubiquitin ligase ubiquitin-like PHD and RING finger domain-containing protein 1 (UHRF1) and its DNA methyltransferase partner DNA methyltransferase I (DNMT1) are critical for the restriction of EBNA and LMP expression. All UHRF1 reader and writer domains were necessary for silencing and DNMT3B was identified as an upstream viral genome CpG methylation initiator. Polycomb repressive complex I exerted a further layer of control over LMP expression, suggesting a second mechanism for latency programme switching. UHRF1, DNMT1 and DNMT3B are upregulated in germinal centre B cells, the Burkitt's lymphoma cell of origin, providing a molecular link between B-cell state and the EBV latency programme. These results suggest rational therapeutic targets to manipulate EBV oncoprotein expression.
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Affiliation(s)
- Rui Guo
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Yuchen Zhang
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Mingxiang Teng
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Chang Jiang
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Cancer Physiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Molly Schineller
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Bo Zhao
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - John G Doench
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Richard J O'Reilly
- Department of Pediatrics, Bone Marrow Transplant Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ethel Cesarman
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY, USA
| | | | - Benjamin E Gewurz
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
- Department of Microbiology, Harvard Medical School, Boston, MA, USA.
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
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Epstein-Barr Virus-Specific CD8 T Cells Selectively Infiltrate the Brain in Multiple Sclerosis and Interact Locally with Virus-Infected Cells: Clue for a Virus-Driven Immunopathological Mechanism. J Virol 2019; 93:JVI.00980-19. [PMID: 31578295 PMCID: PMC6880158 DOI: 10.1128/jvi.00980-19] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 09/24/2019] [Indexed: 12/14/2022] Open
Abstract
EBV establishes a lifelong and asymptomatic infection in most individuals and more rarely causes infectious mononucleosis and malignancies, like lymphomas. The virus is also strongly associated with MS, a chronic neuroinflammatory disease with unknown etiology. Infectious mononucleosis increases the risk of developing MS, and immune reactivity toward EBV is higher in persons with MS, indicating inadequate control of the virus. Previous studies have suggested that persistent EBV infection in the CNS stimulates an immunopathological response, causing bystander neural cell damage. To verify this, we need to identify the immune culprits responsible for the detrimental antiviral response in the CNS. In this study, we analyzed postmortem brains donated by persons with MS and show that CD8 cytotoxic T cells recognizing EBV enter the brain and interact locally with the virus-infected cells. This antiviral CD8 T cell-mediated immune response likely contributes to MS pathology. Epstein-Barr virus (EBV) is a ubiquitous herpesvirus strongly associated with multiple sclerosis (MS), a chronic inflammatory disease of the central nervous system (CNS). However, the mechanisms linking EBV infection to MS pathology are uncertain. Neuropathological and immunological studies suggest that a persistent EBV infection in the CNS can stimulate a CD8 T-cell response aimed at clearing the virus but inadvertently causing CNS injury. Inasmuch as in situ demonstration of EBV-specific CD8 T cells and their effector function is missing, we searched for EBV-specific CD8 T cells in MS brain tissue using the pentamer technique. Postmortem brain samples from 12 donors with progressive MS and known HLA class I genotype were analyzed. Brain sections were stained with HLA-matched pentamers coupled with immunogenic peptides from EBV-encoded proteins, control virus (cytomegalovirus and influenza A virus) proteins, and myelin basic protein. CD8 T cells recognizing proteins expressed in the latent and lytic phases of the EBV life cycle were visualized in white matter lesions and/or meninges of 11/12 MS donors. The fraction (median value) of CD8 T cells recognizing individual EBV epitopes ranged from 0.5 to 2.5% of CNS-infiltrating CD8 T cells. Cytomegalovirus-specific CD8 T cells were detected at a lower frequency (≤0.3%) in brain sections from 4/12 MS donors. CNS-infiltrating EBV-specific CD8 T cells were CD107a positive, suggesting a cytotoxic phenotype, and stuck to EBV-infected cells. Together with local EBV dysregulation, selective enrichment of EBV-specific CD8 T cells in the MS brain supports the notion that skewed immune responses toward EBV contribute to inflammation causing CNS injury. IMPORTANCE EBV establishes a lifelong and asymptomatic infection in most individuals and more rarely causes infectious mononucleosis and malignancies, like lymphomas. The virus is also strongly associated with MS, a chronic neuroinflammatory disease with unknown etiology. Infectious mononucleosis increases the risk of developing MS, and immune reactivity toward EBV is higher in persons with MS, indicating inadequate control of the virus. Previous studies have suggested that persistent EBV infection in the CNS stimulates an immunopathological response, causing bystander neural cell damage. To verify this, we need to identify the immune culprits responsible for the detrimental antiviral response in the CNS. In this study, we analyzed postmortem brains donated by persons with MS and show that CD8 cytotoxic T cells recognizing EBV enter the brain and interact locally with the virus-infected cells. This antiviral CD8 T cell-mediated immune response likely contributes to MS pathology.
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9
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Yang J, Zhang X, Blumenthal RM, Cheng X. Detection of DNA Modifications by Sequence-Specific Transcription Factors. J Mol Biol 2019:S0022-2836(19)30568-6. [PMID: 31626807 DOI: 10.1016/j.jmb.2019.09.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 09/16/2019] [Accepted: 09/17/2019] [Indexed: 12/16/2022]
Abstract
The establishment, detection, and alteration or elimination of epigenetic DNA modifications are essential to controlling gene expression ranging from bacteria to mammals. The DNA methylations occurring at cytosine and adenine are carried out by SAM-dependent methyltransferases. Successive oxidations of 5-methylcytosine (5mC) by Tet dioxygenases generate 5-hydroxymethyl (5hmC), 5-formyl (5fC), and 5-carboxyl (5caC) derivatives; thus, DNA elements with multiple methylation sites can have a wide range of modification states. In contrast, oxidation of N6-methyladenine by homologs of Escherichia coli AlkB removes the methyl group directly. Both Tet and AlkB enzymes are 2-oxoglutarate- and Fe(II)-dependent dioxygenases. DNA-binding proteins decode the modification status of specific genomic regions. This article centers on two families of sequence-specific transcription factors: bZIP (basic leucine-zipper) proteins, exemplified by the AP-1 and CEBPβ recognition of 5mC; and bHLH (basic helix-loop-helix) proteins, exemplified by MAX and TCF4 recognition of 5caC. We discuss the impact of template strand DNA modification on the activities of DNA and RNA polymerases, and the varied tendencies of modifications to alter base pairing and their interactions with DNA repair enzymes.
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Affiliation(s)
- Jie Yang
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xing Zhang
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Robert M Blumenthal
- Department of Medical Microbiology and Immunology, and Program in Bioinformatics, The University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA.
| | - Xiaodong Cheng
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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10
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Araújo Carvalho AC, Tavares Mendes ML, Santos VS, Tanajura DM, Prado Nunes MA, Martins-Filho PRS. Association between human herpes virus seropositivity and frailty in the elderly: A systematic review and meta-analysis. Ageing Res Rev 2018; 48:145-152. [PMID: 30391341 DOI: 10.1016/j.arr.2018.10.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 09/13/2018] [Accepted: 10/24/2018] [Indexed: 12/30/2022]
Abstract
Frailty is an emerging geriatric syndrome characterized by decreased physiologic reserve and increased vulnerability to environmental factors. Several studies have examined the association between persistent cytomegalovirus (CMV) infection and poor clinical outcomes in the elderly, but the results are often contradictory. Here, we performed a systematic review and meta-analysis to analyze the association between human herpesvirus seropositivity [CMV, Epstein-Barr virus (EBV), Varicella zoster virus (VZV), and Herpes simplex virus (HSV)] and frailty in elderly people. Searches were performed in PubMed, SCOPUS, Lilacs, IBECS, and Web of Science databases. We used the odds ratio (OR) as a measure of the association between herpesvirus infections and frailty. Summary estimates were calculated using random-effects models. Six studies were included in the present systematic review. The data from 2559 elderly subjects were analyzed; 1571 of the subjects had ages between 60 and 79 years, and 988 of the subjects were older than 80. We found an association between CMV seropositivity and frailty in the elderly aged 60-79 years (OR 2.33, CI 95% 1.48-3.67) but not in the oldest-old subjects (OR 0.67, CI 95% 0.42-1.05). Moreover, no association was found between EBV, VZV, and HSV infections and frailty. Current evidence suggests an association between CMV seropositivity and frailty in individuals aged 60-79 years old.
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11
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Ren R, Horton JR, Zhang X, Blumenthal RM, Cheng X. Detecting and interpreting DNA methylation marks. Curr Opin Struct Biol 2018; 53:88-99. [PMID: 30031306 DOI: 10.1016/j.sbi.2018.06.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 06/19/2018] [Indexed: 12/22/2022]
Abstract
The generation, alteration, recognition, and erasure of epigenetic modifications of DNA are fundamental to controlling gene expression in mammals. These covalent DNA modifications include cytosine methylation by AdoMet-dependent methyltransferases and 5-methylcytosine oxidation by Fe(II)-dependent and α-ketoglutarate-dependent dioxygenases. Sequence-specific transcription factors are responsible for interpreting the modification status of specific regions of chromatin. This review focuses on recent developments in characterizing the functional and structural links between the modification status of two DNA bases: 5-methylcytosine and 5-methyluracil (thymine).
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Affiliation(s)
- Ren Ren
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - John R Horton
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xing Zhang
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Robert M Blumenthal
- Department of Medical Microbiology and Immunology, and Program in Bioinformatics, The University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA
| | - Xiaodong Cheng
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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12
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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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13
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Mentis AFA, Dardiotis E, Grigoriadis N, Petinaki E, Hadjigeorgiou GM. Viruses and endogenous retroviruses in multiple sclerosis: From correlation to causation. Acta Neurol Scand 2017; 136:606-616. [PMID: 28542724 PMCID: PMC7159535 DOI: 10.1111/ane.12775] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/02/2017] [Indexed: 12/28/2022]
Abstract
Multiple sclerosis is an immune-mediated disease with an environmental component. According to a long-standing but unproven hypothesis dating to initial descriptions of multiple sclerosis (MS) at the end of the 19th century, viruses are either directly or indirectly implicated in MS pathogenesis. Whether viruses in MS are principally causal or simply contributory remains to be proven, but many viruses or viral elements-predominantly Epstein-Barr virus, human endogenous retroviruses (HERVs) and human herpesvirus 6 (HHV-6) but also less common viruses such as Saffold and measles viruses-are associated with MS. Here, we present an up-to-date and comprehensive review of the main candidate viruses implicated in MS pathogenesis and summarize how these viruses might cause or lead to the hallmark demyelinating and inflammatory lesions of MS. We review data from epidemiological, animal and in vitro studies and in doing so offer a transdisciplinary approach to the topic. We argue that it is crucially important not to interpret "absence of evidence" as "evidence of absence" and that future studies need to focus on distinguishing correlative from causative associations. Progress in the MS-virus field is expected to arise from an increasing body of knowledge on the interplay between viruses and HERVs in MS. Such interactions suggest common HERV-mediated pathways downstream of viral infection that cause both neuroinflammation and neurodegeneration. We also comment on the limitations of existing studies and provide future research directions for the field.
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Affiliation(s)
- A.-F. A. Mentis
- Department of Microbiology; University Hospital of Larissa; University of Thessaly; Larissa Greece
- The Johns Hopkins University, AAP; Baltimore MD USA
| | - E. Dardiotis
- Department of Neurology; University Hospital of Larissa; University of Thessaly; Larissa Greece
| | - N. Grigoriadis
- Laboratory of Experimental Neurology and Neuroimmunology; B’ Department of Neurology; AHEPA University Hospital; Aristotle University of Thessaloniki; Thessaloniki Greece
| | - E. Petinaki
- Department of Microbiology; University Hospital of Larissa; University of Thessaly; Larissa Greece
| | - G. M. Hadjigeorgiou
- Department of Neurology; University Hospital of Larissa; University of Thessaly; Larissa Greece
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14
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Chiu YF, Sugden AU, Fox K, Hayes M, Sugden B. Kaposi's sarcoma-associated herpesvirus stably clusters its genomes across generations to maintain itself extrachromosomally. J Cell Biol 2017; 216:2745-2758. [PMID: 28696226 PMCID: PMC5584176 DOI: 10.1083/jcb.201702013] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 05/23/2017] [Accepted: 05/31/2017] [Indexed: 02/08/2023] Open
Abstract
Genetic elements that replicate extrachromosomally are rare in mammals; however, several human tumor viruses, including the papillomaviruses and the gammaherpesviruses, maintain their plasmid genomes by tethering them to cellular chromosomes. We have uncovered an unprecedented mechanism of viral replication: Kaposi's sarcoma-associated herpesvirus (KSHV) stably clusters its genomes across generations to maintain itself extrachromosomally. To identify and characterize this mechanism, we developed two complementary, independent approaches: live-cell imaging and a predictive computational model. The clustering of KSHV requires the viral protein, LANA1, to bind viral genomes to nucleosomes arrayed on both cellular and viral DNA. Clustering affects both viral partitioning and viral genome numbers of KSHV. The clustering of KSHV plasmids provides it with an effective evolutionary strategy to rapidly increase copy numbers of genomes per cell at the expense of the total numbers of cells infected.
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MESH Headings
- Antigens, Viral/genetics
- Antigens, Viral/metabolism
- Chromosomes
- Computer Simulation
- DNA Replication
- DNA, Viral/biosynthesis
- DNA, Viral/genetics
- Evolution, Molecular
- Gene Expression Regulation, Viral
- Genome, Viral
- Genomic Instability
- HEK293 Cells
- HeLa Cells
- Herpesvirus 4, Human/genetics
- Herpesvirus 8, Human/genetics
- Herpesvirus 8, Human/growth & development
- Herpesvirus 8, Human/metabolism
- Host-Pathogen Interactions
- Humans
- In Situ Hybridization, Fluorescence
- Microscopy, Confocal
- Microscopy, Video
- Models, Genetic
- Nuclear Proteins/genetics
- Nuclear Proteins/metabolism
- Protein Binding
- Time Factors
- Time-Lapse Imaging
- Transfection
- Virus Replication
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Affiliation(s)
- Ya-Fang Chiu
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI
- Morgridge Institute for Research, University of Wisconsin-Madison, Madison, WI
- Research Center for Emerging Viral Infections, Chang-Gung University, Taoyuan, Taiwan
- Department of Microbiology and Immunology, Chang-Gung University, Taoyuan, Taiwan
- Department of Medical Laboratory, Chang-Gung Memorial Hospital, Taoyuan, Taiwan
| | - Arthur U Sugden
- Department of Neuroscience, Brown University, Providence, RI
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA
| | - Kathryn Fox
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI
- Flow Cytometry Laboratory, Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI
| | - Mitchell Hayes
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI
| | - Bill Sugden
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI
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15
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Hong S, Wang D, Horton JR, Zhang X, Speck SH, Blumenthal RM, Cheng X. Methyl-dependent and spatial-specific DNA recognition by the orthologous transcription factors human AP-1 and Epstein-Barr virus Zta. Nucleic Acids Res 2017; 45:2503-2515. [PMID: 28158710 PMCID: PMC5389525 DOI: 10.1093/nar/gkx057] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 01/21/2017] [Indexed: 12/22/2022] Open
Abstract
Activator protein 1 (AP-1) is a transcription factor that recognizes two versions of a 7-base pair response element, either 5΄-TGAGTCA-3΄ or 5΄-MGAGTCA-3΄ (where M = 5-methylcytosine). These two elements share the feature that 5-methylcytosine and thymine both have a methyl group in the same position, 5-carbon of the pyrimidine, so each of them has two methyl groups at nucleotide positions 1 and 5 from the 5΄ end, resulting in four methyl groups symmetrically positioned in duplex DNA. Epstein-Barr Virus Zta is a key transcriptional regulator of the viral lytic cycle that is homologous to AP-1. Zta recognizes several methylated Zta-response elements, including meZRE1 (5΄-TGAGMCA-3΄) and meZRE2 (5΄-TGAGMGA-3΄), where a methylated cytosine occupies one of the inner thymine residues corresponding to the AP-1 element, resulting in the four spatially equivalent methyl groups. Here, we study how AP-1 and Zta recognize these methyl groups within their cognate response elements. These methyl groups are in van der Waals contact with a conserved di-alanine in AP-1 dimer (Ala265 and Ala266 in Jun), or with the corresponding Zta residues Ala185 and Ser186 (via its side chain carbon Cβ atom). Furthermore, the two ZRE elements differ at base pair 6 (C:G versus G:C), forming a pseudo-symmetric sequence (meZRE1) or an asymmetric sequence (meZRE2). In vitro DNA binding assays suggest that Zta has high affinity for all four sequences examined, whereas AP-1 has considerably reduced affinity for the asymmetric sequence (meZRE2). We ascribe this difference to Zta Ser186 (a unique residue for Zta) whose side chain hydroxyl oxygen atom interacts with the two half sites differently, whereas the corresponding Ala266 of AP-1 Jun protein lacks such flexibility. Our analyses demonstrate a novel mechanism of 5mC/T recognition in a methylation-dependent, spatial and sequence-specific approach by basic leucine-zipper transcriptional factors.
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Affiliation(s)
- Samuel Hong
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA 30322, USA.,Molecular and Systems Pharmacology graduate program, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA 30322, USA
| | - Dongxue Wang
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA 30322, USA
| | - John R Horton
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA 30322, USA.,Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xing Zhang
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA 30322, USA.,Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Samuel H Speck
- Department of Microbiology & Immunology, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA 30322, USA.,Emory Vaccine Center, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA 30322, USA
| | - Robert M Blumenthal
- Department of Medical Microbiology and Immunology and Program in Bioinformatics, The University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA
| | - Xiaodong Cheng
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA 30322, USA.,Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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16
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Ma Y, Walsh MJ, Bernhardt K, Ashbaugh CW, Trudeau SJ, Ashbaugh IY, Jiang S, Jiang C, Zhao B, Root DE, Doench JG, Gewurz BE. CRISPR/Cas9 Screens Reveal Epstein-Barr Virus-Transformed B Cell Host Dependency Factors. Cell Host Microbe 2017; 21:580-591.e7. [PMID: 28494239 PMCID: PMC8938989 DOI: 10.1016/j.chom.2017.04.005] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 03/10/2017] [Accepted: 04/19/2017] [Indexed: 12/26/2022]
Abstract
Epstein-Barr virus (EBV) causes endemic Burkitt lymphoma (BL) and immunosuppression-related lymphomas. These B cell malignancies arise by distinct transformation pathways and have divergent viral and host expression programs. To identify host dependency factors resulting from these EBV+, B cell-transformed cell states, we performed parallel genome-wide CRISPR/Cas9 loss-of-function screens in BL and lymphoblastoid cell lines (LCLs). These highlighted 57 BL and 87 LCL genes uniquely important for their growth and survival. LCL hits were enriched for EBV-induced genes, including viral super-enhancer targets. Our systematic approach uncovered key mechanisms by which EBV oncoproteins activate the PI3K/AKT pathway and evade tumor suppressor responses. LMP1-induced cFLIP was found to be critical for LCL defense against TNFα-mediated programmed cell death, whereas EBV-induced BATF/IRF4 were critical for BIM suppression and MYC induction in LCLs. Finally, EBV super-enhancer-targeted IRF2 protected LCLs against Blimp1-mediated tumor suppression. Our results identify viral transformation-driven synthetic lethal targets for therapeutic intervention.
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Affiliation(s)
- Yijie Ma
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Michael J Walsh
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Program in Virology, Harvard Medical School, Boston, MA 02115, USA
| | - Katharina Bernhardt
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Camille W Ashbaugh
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Stephen J Trudeau
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Isabelle Y Ashbaugh
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Sizun Jiang
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Program in Virology, Harvard Medical School, Boston, MA 02115, USA
| | - Chang Jiang
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Bo Zhao
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - David E Root
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - John G Doench
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Benjamin E Gewurz
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Program in Virology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
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17
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Yang YC, Liem A, Lambert PF, Sugden B. Dissecting the regulation of EBV's BART miRNAs in carcinomas. Virology 2017; 505:148-154. [PMID: 28259048 PMCID: PMC5504693 DOI: 10.1016/j.virol.2017.02.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 01/31/2017] [Accepted: 02/14/2017] [Indexed: 12/11/2022]
Abstract
Epstein-Barr virus (EBV) encodes multiple miRNAs known to contribute to
its pathogenicity. Previous studies have found that the levels of some EBV
miRNAs are 10–100 fold higher in biopsies and in tumor xenografts than
in cells grown in culture. We have asked if these increased levels reflect
transcriptional enhancement resulting from the tumor microenvironment, selection
for increased levels of the EBV genome, or both. We measured the levels of BART
miRNAs and their DNA templates in tumor xenografts induced from EBV-positive
gastric carcinoma cells and EBV-negative gastric carcinoma cells expressing
plasmid replicons encoding these miRNAs. We focused on BART miRNAs which are
expressed in all tumors and found that they provide tumors selective growth
advantages as xenografts. Stem-loop PCR and real-time PCR revealed that the
xenografts expressed both higher levels of some miRNAs and viral DNA templates
than did the corresponding cells in culture.
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Affiliation(s)
- Ya-Chun Yang
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, 1111 Highland Avenue, Madison, WI 53705-2275, United States
| | - Amy Liem
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, 1111 Highland Avenue, Madison, WI 53705-2275, United States
| | - Paul F Lambert
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, 1111 Highland Avenue, Madison, WI 53705-2275, United States
| | - Bill Sugden
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, 1111 Highland Avenue, Madison, WI 53705-2275, United States.
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18
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Affiliation(s)
- Ya-Fang Chiu
- McArdle Laboratory for Cancer Research, University of Wisconsin–Madison, Madison, Wisconsin 53705;
- Morgridge Institute for Research, Madison, Wisconsin 53715
- Research Center for Emerging Viral Infections and Department of Microbiology and Immunology, Chang Gung University, Taoyuan 33302, Taiwan
- Department of Medical Laboratory, Chang Gung Memorial Hospital, Taoyuan 33305, Taiwan
| | - Bill Sugden
- McArdle Laboratory for Cancer Research, University of Wisconsin–Madison, Madison, Wisconsin 53705;
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19
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Hettmann A, Demcsák A, Decsi G, Bach Á, Pálinkó D, Rovó L, Nagy K, Takács M, Minarovits J. Infectious Agents Associated with Head and Neck Carcinomas. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 897:63-80. [PMID: 26563307 DOI: 10.1007/5584_2015_5005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In addition to traditional risk factors such as smoking habits and alcohol consumption, certain microbes also play an important role in the generation of head and neck carcinomas. Infection with high-risk human papillomavirus types is strongly associated with the development of oropharyngeal carcinoma, and Epstein-Barr virus appears to be indispensable for the development of non-keratinizing squamous cell carcinoma of the nasopharynx. Other viruses including torque teno virus and hepatitis C virus may act as co-carcinogens, increasing the risk of malignant transformation. A shift in the composition of the oral microbiome was associated with the development of oral squamous cell carcinoma, although the causal or casual role of oral bacteria remains to be clarified. Conversion of ethanol to acetaldehyde, a mutagenic compound, by members of the oral microflora as well as by fungi including Candida albicans and others is a potential mechanism that may increase oral cancer risk. In addition, distinct Candida spp. also produce NBMA (N-nitrosobenzylmethylamine), a potent carcinogen. Inflammatory processes elicited by microbes may also facilitate tumorigenesis in the head and neck region.
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Affiliation(s)
- Andrea Hettmann
- Division of Virology, National Center for Epidemiology, Albert F. ut 2-6, H-1097, Budapest, Hungary
| | - Anett Demcsák
- Faculty of Dentistry, Department of Oral Biology and Experimental Dental Research, University of Szeged, Szeged, Hungary
| | - Gábor Decsi
- Department of Oral Surgery, University of Szeged, Tisza Lajos krt. 64, H-6720, Szeged, Hungary
| | - Ádám Bach
- Faculty of Medicine, Department of Oto-Rhino-Laryngology and Head-Neck Surgery, University of Szeged, Tisza L. krt. 111, H-6725, Szeged, Hungary
| | - Dóra Pálinkó
- Faculty of Medicine, Department of Oto-Rhino-Laryngology and Head-Neck Surgery, University of Szeged, Tisza L. krt. 111, H-6725, Szeged, Hungary
| | - László Rovó
- Faculty of Medicine, Department of Oto-Rhino-Laryngology and Head-Neck Surgery, University of Szeged, Tisza L. krt. 111, H-6725, Szeged, Hungary
| | - Katalin Nagy
- Department of Oral Surgery, University of Szeged, Tisza Lajos krt. 64, H-6720, Szeged, Hungary
| | - Mária Takács
- Division of Virology, National Center for Epidemiology, Albert F. ut 2-6, H-1097, Budapest, Hungary
| | - Janos Minarovits
- Faculty of Dentistry, Department of Oral Biology and Experimental Dental Research, University of Szeged, Szeged, Hungary.
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20
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Chakravorty A, Sugden B. The AT-hook DNA binding ability of the Epstein Barr virus EBNA1 protein is necessary for the maintenance of viral genomes in latently infected cells. Virology 2015; 484:251-258. [PMID: 26122471 DOI: 10.1016/j.virol.2015.05.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 04/02/2015] [Accepted: 05/20/2015] [Indexed: 02/01/2023]
Abstract
Epstein Barr Virus (EBV) is a human tumor virus that is causally linked to malignancies such as Burkitt׳s lymphoma, and gastric and nasopharyngeal carcinomas. Tethering of EBV genomes to cellular chromosomes is required for the synthesis and persistence of viral plasmids in tumor cells. However, it is not established how EBV genomes are tethered to cellular chromosomes. We test the hypothesis that the viral protein EBNA1 tethers EBV genomes to chromosomes specifically through its N-terminal AT-hook DNA-binding domains by using a small molecule, netropsin, that has been shown to inhibit the AT-hook DNA-binding of EBNA1 in vitro. We show that netropsin forces the loss of EBV genomes from epithelial and lymphoid cells in an AT-hook dependent manner and that EBV-positive lymphoma cells are significantly more inhibited in their growth by netropsin than are corresponding EBV-negative cells.
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Affiliation(s)
- Adityarup Chakravorty
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI, United States
| | - Bill Sugden
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI, United States.
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