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Inagaki T, Kumar A, Komaki S, Nakajima KI, Izumiya Y. An atlas of chromatin landscape in KSHV-infected cells during de novo infection and reactivation. Virology 2024; 597:110146. [PMID: 38909515 DOI: 10.1016/j.virol.2024.110146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 06/04/2024] [Accepted: 06/18/2024] [Indexed: 06/25/2024]
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV) is an oncogenic γ-herpesvirus with a double-stranded DNA capable of establishing latent infection in the host cell. During latency, only a limited number of viral genes are expressed in infected host cells, and that helps the virus to evade host immune cell response. During primary infection, the KSHV genome is chromatinized and maintained as an episome, which is tethered to the host chromosome via Latency Associated Nuclear Antigen (LANA). The KSHV episome undergoes the same chromatin modification with the host cell chromosome and, therefore, is regulated by various epigenetic modifications, such as DNA methylation, histone methylation, and histone acetylation. The KSHV genome is also organized in a spatiotemporal manner by forming genomic loops, which enable simultaneous and coordinated control of dynamic gene transcription, particularly during the lytic replication phase. The genome-wide approaches and advancing bioinformatic tools have increased the resolution of studies on the dynamic transcriptional control and our understanding of KSHV latency-lytic switch regulation. We will summarize our current understanding of the epigenetic gene regulation on the KSHV chromatin.
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Affiliation(s)
- Tomoki Inagaki
- Department of Dermatology, School of Medicine, The University of California Davis, Sacramento, CA, USA.
| | - Ashish Kumar
- Department of Dermatology, School of Medicine, The University of California Davis, Sacramento, CA, USA
| | - Somayeh Komaki
- Department of Dermatology, School of Medicine, The University of California Davis, Sacramento, CA, USA
| | - Ken-Ichi Nakajima
- Department of Dermatology, School of Medicine, The University of California Davis, Sacramento, CA, USA
| | - Yoshihiro Izumiya
- Department of Dermatology, School of Medicine, The University of California Davis, Sacramento, CA, USA; Department of Biochemistry and Molecular Medicine, School of Medicine, UC Davis, Sacramento, CA, USA
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2
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Knickmann J, Staliunaite L, Puhach O, Ostermann E, Günther T, Nichols J, Jarvis MA, Voigt S, Grundhoff A, Davison AJ, Brune W. A simple method for rapid cloning of complete herpesvirus genomes. CELL REPORTS METHODS 2024; 4:100696. [PMID: 38266652 PMCID: PMC10921015 DOI: 10.1016/j.crmeth.2024.100696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 12/08/2023] [Accepted: 01/02/2024] [Indexed: 01/26/2024]
Abstract
Herpesviruses are large DNA viruses and include important human and veterinary pathogens. Their genomes can be cloned as bacterial artificial chromosomes (BACs) and genetically engineered in Escherichia coli using BAC recombineering methods. While the recombineering methods are efficient, the initial BAC-cloning step remains laborious. To overcome this limitation, we have developed a simple, rapid, and efficient BAC-cloning method based on single-step transformation-associated recombination (STAR) in Saccharomyces cerevisiae. The linear viral genome is directly integrated into a vector comprising a yeast centromeric plasmid and a BAC replicon. Following transfer into E. coli, the viral genome can be modified using standard BAC recombineering techniques. We demonstrate the speed, fidelity, and broad applicability of STAR by cloning two strains of both rat cytomegalovirus (a betaherpesvirus) and Kaposi's sarcoma-associated herpesvirus (a gammaherpesvirus). STAR cloning facilitates the functional genetic analysis of herpesviruses and other large DNA viruses and their use as vaccines and therapeutic vectors.
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Affiliation(s)
- Jan Knickmann
- Leibniz Institute of Virology (LIV), Hamburg, Germany
| | | | - Olha Puhach
- Leibniz Institute of Virology (LIV), Hamburg, Germany
| | | | | | - Jenna Nichols
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Michael A Jarvis
- School of Biomedical Sciences, University of Plymouth, Plymouth, UK; The Vaccine Group Ltd., Plymouth, UK
| | - Sebastian Voigt
- Institute for Virology, University Hospital Essen, Essen, Germany
| | | | - Andrew J Davison
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Wolfram Brune
- Leibniz Institute of Virology (LIV), Hamburg, Germany.
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3
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Izumiya Y, Algalil A, Espera JM, Miura H, Izumiya C, Inagaki T, Kumar A. Kaposi's sarcoma-associated herpesvirus terminal repeat regulates inducible lytic gene promoters. J Virol 2024; 98:e0138623. [PMID: 38240593 PMCID: PMC10878276 DOI: 10.1128/jvi.01386-23] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 01/02/2024] [Indexed: 02/21/2024] Open
Abstract
The Kaposi's sarcoma-associated herpesvirus (KSHV) genome consists of an approximately 140-kb unique coding region flanked by 30-40 copies of a 0.8-kb terminal repeat (TR) sequence. A gene enhancer recruits transcription-related enzymes by having arrays of transcription factor binding sites. Here, we show that KSHV TR possesses transcription regulatory function with latency-associated nuclear antigen (LANA). Cleavage under targets and release using nuclease demonstrated that TR fragments were occupied by LANA-interacting histone-modifying enzymes in naturally infected cells. The TR was enriched with histone H3K27 acetylation (H3K27Ac) and H3K4 tri-methylation (H3K4me3) modifications and also expressed nascent RNAs. The sites of H3K27Ac and H3K4me3 modifications were also conserved in the KSHV unique region among naturally infected primary effusion lymphoma cells. KSHV origin of lytic replication (Ori-Lyt) showed similar protein and histone modification occupancies with that of TR. In the Ori-Lyt region, the LANA and LANA-interacting proteins colocalized with an H3K27Ac-modified nucleosome along with paused RNA polymerase II. The KSHV transactivator KSHV replication and transcription activator (K-Rta) recruitment sites franked the LANA-bound nucleosome, and reactivation evicted the LANA-bound nucleosome. Including TR fragments in reporter plasmid enhanced inducible viral gene promoter activities independent of the orientations. In the presence of TR in reporter plasmids, K-Rta transactivation was drastically increased, while LANA acquired the promoter repression function. KSHV TR, therefore, functions as an enhancer for KSHV inducible genes. However, in contrast to cellular enhancers bound by multiple transcription factors, perhaps the KSHV enhancer is predominantly regulated by the LANA nuclear body.IMPORTANCEEnhancers are a crucial regulator of differential gene expression programs. Enhancers are the cis-regulatory sequences determining target genes' spatiotemporal and quantitative expression. Here, we show that Kaposi's sarcoma-associated herpesvirus (KSHV) terminal repeats fulfill the enhancer definition for KSHV inducible gene promoters. The KSHV enhancer is occupied by latency-associated nuclear antigen (LANA) and its interacting proteins, such as CHD4. Neighboring terminal repeat (TR) fragments to lytic gene promoters drastically enhanced KSHV replication and transcription activator and LANA transcription regulatory functions. This study, thus, proposes a new latency-lytic switch model in which TR accessibility to the KSHV gene promoters regulates viral inducible gene expression.
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Affiliation(s)
- Yoshihiro Izumiya
- Department of Dermatology, School of Medicine, University of California Davis, Sacramento, California, USA
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California Davis, Sacramento, California, USA
| | - Adhraa Algalil
- Department of Dermatology, School of Medicine, University of California Davis, Sacramento, California, USA
- Midwestern University College of Dental Medicine, Glendale, Arizona, USA
| | - Jonna M. Espera
- Department of Dermatology, School of Medicine, University of California Davis, Sacramento, California, USA
| | - Hiroki Miura
- Department of Dermatology, School of Medicine, University of California Davis, Sacramento, California, USA
| | - Chie Izumiya
- Department of Dermatology, School of Medicine, University of California Davis, Sacramento, California, USA
| | - Tomoki Inagaki
- Department of Dermatology, School of Medicine, University of California Davis, Sacramento, California, USA
| | - Ashish Kumar
- Department of Dermatology, School of Medicine, University of California Davis, Sacramento, California, USA
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4
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Schulz TF, Freise A, Stein SC. Kaposi sarcoma-associated herpesvirus latency-associated nuclear antigen: more than a key mediator of viral persistence. Curr Opin Virol 2023; 61:101336. [PMID: 37331160 DOI: 10.1016/j.coviro.2023.101336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 05/03/2023] [Accepted: 05/22/2023] [Indexed: 06/20/2023]
Abstract
Kaposi sarcoma-associated herpesvirus (KSHV), or human herpesvirus-8, is an oncogenic herpesvirus. Its latency-associated nuclear antigen (LANA) is essential for the persistence of KSHV in latently infected cells. LANA mediates replication of the latent viral genome during the S phase of a dividing cell and partitions episomes to daughter cells by attaching them to mitotic chromosomes. It also mediates the establishment of latency in newly infected cells through epigenetic mechanisms and suppresses the activation of the productive replication cycle. Furthermore, LANA promotes the proliferation of infected cell by acting as a transcriptional regulator and by modulating the cellular proteome through the recruitment of several cellular ubiquitin ligases. Finally, LANA interferes with the innate and adaptive immune system to facilitate the immune escape of infected cells.
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Affiliation(s)
- Thomas F Schulz
- Institute of Virology, Hannover Medical School, Germany; Cluster of Excellence 2155 RESIST, Germany; German Center for Infection Research, Hannover-Braunschweig Site, Germany.
| | - Anika Freise
- Institute of Virology, Hannover Medical School, Germany
| | - Saskia C Stein
- Institute of Virology, Hannover Medical School, Germany; Cluster of Excellence 2155 RESIST, Germany
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5
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Damania B, Dittmer DP. Today's Kaposi sarcoma is not the same as it was 40 years ago, or is it? J Med Virol 2023; 95:e28773. [PMID: 37212317 PMCID: PMC10266714 DOI: 10.1002/jmv.28773] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/20/2023] [Accepted: 04/22/2023] [Indexed: 05/23/2023]
Abstract
This review will provide an overview of the notion that Kaposi sarcoma (KS) is a disease that manifests under diverse and divergent circumstances. We begin with a historical introduction of KS and KS-associated herpesvirus (KSHV), highlight the diversity of clinical presentations of KS, summarize what we know about the cell of origin for this tumor, explore KSHV viral load as a potential biomarker for acute KSHV infections and KS-associated complications, and discuss immune modulators that impact KSHV infection, KSHV persistence, and KS disease.
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Affiliation(s)
- Blossom Damania
- Lineberger Comprehensive Cancer Center, Department of Microbiology and Immunology, School of Medicine, University of North Carolina at Chapel Hill, 450 West Drive CB#7295, Rm 12-048, Chapel Hill, NC 27599
| | - Dirk P. Dittmer
- Lineberger Comprehensive Cancer Center, Department of Microbiology and Immunology, School of Medicine, University of North Carolina at Chapel Hill, 450 West Drive CB#7295, Rm 12-048, Chapel Hill, NC 27599
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Scholl A, De S. Epigenetic Regulation by Polycomb Complexes from Drosophila to Human and Its Relation to Communicable Disease Pathogenesis. Int J Mol Sci 2022; 23:ijms232012285. [PMID: 36293135 PMCID: PMC9603650 DOI: 10.3390/ijms232012285] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 10/04/2022] [Accepted: 10/10/2022] [Indexed: 12/05/2022] Open
Abstract
Although all cells in the human body are made of the same DNA, these cells undergo differentiation and behave differently during development, through integration of external and internal stimuli via 'specific mechanisms.' Epigenetics is one such mechanism that comprises DNA/RNA, histone modifications, and non-coding RNAs that regulate transcription without changing the genetic code. The discovery of the first Polycomb mutant phenotype in Drosophila started the study of epigenetics more than 80 years ago. Since then, a considerable number of Polycomb Group (PcG) genes in Drosophila have been discovered to be preserved in mammals, including humans. PcG proteins exert their influence through gene repression by acting in complexes, modifying histones, and compacting the chromatin within the nucleus. In this article, we discuss how our knowledge of the PcG repression mechanism in Drosophila translates to human communicable disease research.
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PRC1-independent binding and activity of RYBP on the KSHV genome during de novo infection. PLoS Pathog 2022; 18:e1010801. [PMID: 36026503 PMCID: PMC9455864 DOI: 10.1371/journal.ppat.1010801] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 09/08/2022] [Accepted: 08/08/2022] [Indexed: 11/19/2022] Open
Abstract
Kaposi’s sarcoma-associated herpesvirus (KSHV) is an oncogenic virus that causes lifelong infection in humans by establishing latency after primary infection. Latent infection is a prerequisite for both persistent infection and the development of KSHV-associated cancers. While viral lytic genes are transiently expressed after primary infection, their expression is significantly restricted and concomitant with the binding of host epigenetic repressors Polycomb Repressive Complex 1 and 2 (PRC1 and PRC2) to lytic genes. PRC1 and PRC2 mediate the repressive histone marks H2AK119ub and H3K27me3, respectively, and maintain heterochromatin structure on KSHV lytic genes to inhibit their expression. In contrast to PRC2, little is known about the recruitment and role of PRC1 factors on the KSHV genome following de novo infection. Thus, the goal of this study was to examine the function of PRC1 factors in the establishment of KSHV latency. To address this question, we performed an shRNA screen targeting 7 different components of the canonical and non-canonical PRC1 complexes during primary KSHV infection. We found that RYBP, a main subunit of the non-canonical PRC1 complexes, is a potent repressor of KSHV lytic genes that can bind to the viral genome and inhibit lytic genes as early as 4 hours post infection. Surprisingly, our ChIP analyses showed that RYBP binds to lytic viral gene promoters in a PRC1-independent manner, does not affect PRC1 activity on the KSHV genome, and can reduce the level of histone marks associated with transcription elongation. Our data also suggest that RYBP can repress the viral lytic cycle after primary infection by inhibiting the transcription elongation of the lytic cycle inducer KSHV gene RTA. Based on our results we propose that RYBP uses a PRC1-independent mechanism to block KSHV RTA expression thereby promoting the establishment of KSHV latency following de novo infection.
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8
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Impact of Cultured Neuron Models on α-Herpesvirus Latency Research. Viruses 2022; 14:v14061209. [PMID: 35746680 PMCID: PMC9228292 DOI: 10.3390/v14061209] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 05/26/2022] [Accepted: 05/27/2022] [Indexed: 02/01/2023] Open
Abstract
A signature trait of neurotropic α-herpesviruses (α-HV) is their ability to establish stable non-productive infections of peripheral neurons termed latency. This specialized gene expression program is the foundation of an evolutionarily successful strategy to ensure lifelong persistence in the host. Various physiological stresses can induce reactivation in a subset of latently-infected neurons allowing a new cycle of viral productive cycle gene expression and synthesis of infectious virus. Recurring reactivation events ensure transmission of the virus to new hosts and contributes to pathogenesis. Efforts to define the molecular basis of α-HV latency and reactivation have been notoriously difficult because the neurons harboring latent virus in humans and in experimentally infected live-animal models, are rare and largely inaccessible to study. Increasingly, researchers are turning to cultured neuron infection models as simpler experimental platforms from which to explore latency and reactivation at the molecular level. In this review, I reflect on the strengths and weaknesses of existing neuronal models and briefly summarize the important mechanistic insights these models have provided. I also discuss areas where prioritization will help to ensure continued progress and integration.
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Kumar A, Lyu Y, Yanagihashi Y, Chantarasrivong C, Majerciak V, Salemi M, Wang KH, Inagaki T, Chuang F, Davis RR, Tepper CG, Nakano K, Izumiya C, Shimoda M, Nakajima KI, Merleev A, Zheng ZM, Campbell M, Izumiya Y. KSHV episome tethering sites on host chromosomes and regulation of latency-lytic switch by CHD4. Cell Rep 2022; 39:110788. [PMID: 35545047 PMCID: PMC9153692 DOI: 10.1016/j.celrep.2022.110788] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 02/11/2022] [Accepted: 04/14/2022] [Indexed: 12/25/2022] Open
Abstract
Kaposi sarcoma-associated herpesvirus (KSHV) establishes a latent infection in the cell nucleus, but where KSHV episomal genomes are tethered and the mechanisms underlying KSHV lytic reactivation are unclear. Here, we study the nuclear microenvironment of KSHV episomes and show that the KSHV latency-lytic replication switch is regulated via viral long non-coding (lnc)RNA-CHD4 (chromodomain helicase DNA binding protein 4) interaction. KSHV episomes localize with CHD4 and ADNP proteins, components of the cellular ChAHP complex. The CHD4 and ADNP proteins occupy the 5'-region of the highly inducible lncRNAs and terminal repeats of the KSHV genome together with latency-associated nuclear antigen (LANA). Viral lncRNA binding competes with CHD4 DNA binding, and KSHV reactivation sequesters CHD4 from the KSHV genome, which is also accompanied by detachment of KSHV episomes from host chromosome docking sites. We propose a model in which robust KSHV lncRNA expression determines the latency-lytic decision by regulating LANA/CHD4 binding to KSHV episomes.
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Affiliation(s)
- Ashish Kumar
- Department of Dermatology School of Medicine, University of California Davis (UC Davis), Sacramento, CA 95817, USA
| | - Yuanzhi Lyu
- Department of Dermatology School of Medicine, University of California Davis (UC Davis), Sacramento, CA 95817, USA
| | | | | | - Vladimir Majerciak
- Tumor Virus RNA Biology Section, HIV Dynamics and Replication Program, National Cancer Institute, NIH, Frederick, MD 21702, USA
| | - Michelle Salemi
- Genome Center, Proteomics Core, Genome and Biomedical Sciences Facility, UC Davis, Davis, CA 95616, USA
| | - Kang-Hsin Wang
- Department of Dermatology School of Medicine, University of California Davis (UC Davis), Sacramento, CA 95817, USA
| | - Tomoki Inagaki
- Department of Dermatology School of Medicine, University of California Davis (UC Davis), Sacramento, CA 95817, USA
| | - Frank Chuang
- Department of Biochemistry and Molecular Medicine, School of Medicine, UC Davis, Sacramento, CA 95817, USA
| | - Ryan R Davis
- Department of Pathology and Laboratory Medicine, School of Medicine, UC Davis, Sacramento, CA 95817, USA
| | - Clifford G Tepper
- Department of Biochemistry and Molecular Medicine, School of Medicine, UC Davis, Sacramento, CA 95817, USA; Viral Oncology and Pathogen-Associated Malignancies Initiative, UC Davis Comprehensive Cancer Center, Sacramento, CA 95817, USA
| | - Kazushi Nakano
- Lifescience Division, Lifematics, Osaka, Osaka 541-0046, Japan
| | - Chie Izumiya
- Department of Dermatology School of Medicine, University of California Davis (UC Davis), Sacramento, CA 95817, USA
| | - Michiko Shimoda
- Department of Dermatology School of Medicine, University of California Davis (UC Davis), Sacramento, CA 95817, USA; Viral Oncology and Pathogen-Associated Malignancies Initiative, UC Davis Comprehensive Cancer Center, Sacramento, CA 95817, USA
| | - Ken-Ichi Nakajima
- Department of Dermatology School of Medicine, University of California Davis (UC Davis), Sacramento, CA 95817, USA
| | - Alexander Merleev
- Department of Dermatology School of Medicine, University of California Davis (UC Davis), Sacramento, CA 95817, USA
| | - Zhi-Ming Zheng
- Tumor Virus RNA Biology Section, HIV Dynamics and Replication Program, National Cancer Institute, NIH, Frederick, MD 21702, USA
| | - Mel Campbell
- Department of Dermatology School of Medicine, University of California Davis (UC Davis), Sacramento, CA 95817, USA.
| | - Yoshihiro Izumiya
- Department of Dermatology School of Medicine, University of California Davis (UC Davis), Sacramento, CA 95817, USA; Department of Biochemistry and Molecular Medicine, School of Medicine, UC Davis, Sacramento, CA 95817, USA; Viral Oncology and Pathogen-Associated Malignancies Initiative, UC Davis Comprehensive Cancer Center, Sacramento, CA 95817, USA.
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10
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Tan M, Li S, Juillard F, Chitas R, Custódio TF, Xue H, Szymula A, Sun Q, Liu B, Álvarez ÁL, Chen S, Huang J, Simas JP, McVey CE, Kaye KM. MLL1 is regulated by KSHV LANA and is important for virus latency. Nucleic Acids Res 2021; 49:12895-12911. [PMID: 34850113 PMCID: PMC8682764 DOI: 10.1093/nar/gkab1094] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 09/29/2021] [Accepted: 10/20/2021] [Indexed: 01/19/2023] Open
Abstract
Mixed lineage leukemia 1 (MLL1) is a histone methyltransferase. Kaposi's sarcoma-associated herpesvirus (KSHV) is a leading cause of malignancy in AIDS. KSHV latently infects tumor cells and its genome is decorated with epigenetic marks. Here, we show that KSHV latency-associated nuclear antigen (LANA) recruits MLL1 to viral DNA where it establishes H3K4me3 modifications at the extensive KSHV terminal repeat elements during primary infection. LANA interacts with MLL1 complex members, including WDR5, integrates into the MLL1 complex, and regulates MLL1 activity. We describe the 1.5-Å crystal structure of N-terminal LANA peptide complexed with MLL1 complex member WDR5, which reveals a potential regulatory mechanism. Disruption of MLL1 expression rendered KSHV latency establishment highly deficient. This deficiency was rescued by MLL1 but not by catalytically inactive MLL1. Therefore, MLL1 is LANA regulable and exerts a central role in virus infection. These results suggest broad potential for MLL1 regulation, including by non-host factors.
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Affiliation(s)
- Min Tan
- Departments of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Shijun Li
- Departments of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Franceline Juillard
- Departments of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Rute Chitas
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras 2780-157, Portugal
| | - Tânia F Custódio
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras 2780-157, Portugal
| | - Han Xue
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 200031 Shanghai, China
| | - Agnieszka Szymula
- Departments of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Qiming Sun
- Departments of Biochemistry and Cardiology, Second Affiliated Hospital Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Bing Liu
- Departments of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Ángel L Álvarez
- Departments of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - She Chen
- Proteomics Center, National Institute of Biological Sciences, Beijing 102206, China
| | - Jing Huang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine 200125 Shanghai, China
| | - J Pedro Simas
- Instituto de Medicina Molecular, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal.,Católica Biomedical Research, Católica Medical School, Universidade Católica Portuguesa, Palma de Cima, 1649-023 Lisboa, Portugal
| | - Colin E McVey
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras 2780-157, Portugal
| | - Kenneth M Kaye
- Departments of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
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11
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Ferguson J, Campos-León K, Pentland I, Stockton JD, Günther T, Beggs AD, Grundhoff A, Roberts S, Noyvert B, Parish JL. The chromatin insulator CTCF regulates HPV18 transcript splicing and differentiation-dependent late gene expression. PLoS Pathog 2021; 17:e1010032. [PMID: 34735550 PMCID: PMC8594839 DOI: 10.1371/journal.ppat.1010032] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 11/16/2021] [Accepted: 10/13/2021] [Indexed: 11/18/2022] Open
Abstract
The ubiquitous host protein, CCCTC-binding factor (CTCF), is an essential regulator of cellular transcription and functions to maintain epigenetic boundaries, stabilise chromatin loops and regulate splicing of alternative exons. We have previously demonstrated that CTCF binds to the E2 open reading frame (ORF) of human papillomavirus (HPV) 18 and functions to repress viral oncogene expression in undifferentiated keratinocytes by co-ordinating an epigenetically repressed chromatin loop within HPV episomes. Keratinocyte differentiation disrupts CTCF-dependent chromatin looping of HPV18 episomes promoting induction of enhanced viral oncogene expression. To further characterise CTCF function in HPV transcription control we utilised direct, long-read Nanopore RNA-sequencing which provides information on the structure and abundance of full-length transcripts. Nanopore analysis of primary human keratinocytes containing HPV18 episomes before and after synchronous differentiation allowed quantification of viral transcript species, including the identification of low abundance novel transcripts. Comparison of transcripts produced in wild type HPV18 genome-containing cells to those identified in CTCF-binding deficient genome-containing cells identifies CTCF as a key regulator of differentiation-dependent late promoter activation, required for efficient E1^E4 and L1 protein expression. Furthermore, our data show that CTCF binding at the E2 ORF promotes usage of the downstream weak splice donor (SD) sites SD3165 and SD3284, to the dominant E4 splice acceptor site at nucleotide 3434. These findings demonstrate that in the HPV life cycle both early and late virus transcription programmes are facilitated by recruitment of CTCF to the E2 ORF. Oncogenic human papillomavirus (HPV) infection is the cause of a subset of epithelial cancers of the uterine cervix, other anogenital areas and the oropharynx. HPV infection is established in the basal cells of epithelia where a restricted programme of viral gene expression is required for replication and maintenance of the viral episome. Completion of the HPV life cycle is dependent on the maturation (differentiation) of infected cells which induces enhanced viral gene expression and induction of capsid production. We previously reported that the host cell transcriptional regulator, CTCF, is hijacked by HPV to control viral gene expression. In this study, we use long-read mRNA sequencing to quantitatively map the variety and abundance of HPV transcripts produced in early and late stages of the HPV life cycle and to dissect the function of CTCF in controlling HPV gene expression and transcript processing.
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Affiliation(s)
- Jack Ferguson
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, West Midlands, United Kingdom
| | - Karen Campos-León
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, West Midlands, United Kingdom
| | - Ieisha Pentland
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, West Midlands, United Kingdom
| | - Joanne D. Stockton
- Genomics Birmingham, University of Birmingham, Birmingham, West Midlands, United Kingdom
| | - Thomas Günther
- Heinrich-Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Andrew D. Beggs
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, West Midlands, United Kingdom
- Genomics Birmingham, University of Birmingham, Birmingham, West Midlands, United Kingdom
| | - Adam Grundhoff
- Heinrich-Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Sally Roberts
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, West Midlands, United Kingdom
| | - Boris Noyvert
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, West Midlands, United Kingdom
- CRUK Birmingham Centre and Centre for Computational Biology, University of Birmingham, Birmingham, West Midlands, United Kingdom
| | - Joanna L. Parish
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, West Midlands, United Kingdom
- * E-mail:
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12
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De Novo Polycomb Recruitment: Lessons from Latent Herpesviruses. Viruses 2021; 13:v13081470. [PMID: 34452335 PMCID: PMC8402699 DOI: 10.3390/v13081470] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/22/2021] [Accepted: 07/24/2021] [Indexed: 12/11/2022] Open
Abstract
The Human Herpesviruses persist in the form of a latent infection in specialized cell types. During latency, the herpesvirus genomes associate with cellular histone proteins and the viral lytic genes assemble into transcriptionally repressive heterochromatin. Although there is divergence in the nature of heterochromatin on latent herpesvirus genomes, in general, the genomes assemble into forms of heterochromatin that can convert to euchromatin to permit gene expression and therefore reactivation. This reversible form of heterochromatin is known as facultative heterochromatin and is most commonly characterized by polycomb silencing. Polycomb silencing is prevalent on the cellular genome and plays a role in developmentally regulated and imprinted genes, as well as X chromosome inactivation. As herpesviruses initially enter the cell in an un-chromatinized state, they provide an optimal system to study how de novo facultative heterochromatin is targeted to regions of DNA and how it contributes to silencing. Here, we describe how polycomb-mediated silencing potentially assembles onto herpesvirus genomes, synergizing what is known about herpesvirus latency with facultative heterochromatin targeting to the cellular genome. A greater understanding of polycomb silencing of herpesviruses will inform on the mechanism of persistence and reactivation of these pathogenic human viruses and provide clues regarding how de novo facultative heterochromatin forms on the cellular genome.
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13
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Abstract
Among all of the known biological carcinogens, Epstein-Barr virus (EBV) and Kaposi's sarcoma-associated herpesvirus (KSHV) are two of the classical oncogenic herpesviruses known to induce the oncogenic phenotype. Many studies have revealed important functions related to epigenetic alterations of the EBV and KSHV genomes that mediate oncogenesis, but the detailed mechanisms are not fully understood. It is also challenging to fully describe the critical cellular events that drive oncogenesis as well as a comprehensive map of the molecular contributors. This review introduces the roles of epigenetic modifications of these viral genomes, including DNA methylation, histone modification, chromatin remodeling, and noncoding RNA expression, and elucidates potential strategies utilized for inducing oncogenesis by these human gammaherpesviruses.
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Affiliation(s)
- Yonggang Pei
- Departments of Otorhinolaryngology-Head and Neck Surgery and Microbiology, Tumor Virology Program, Abramson Comprehensive Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA;
| | - Josiah Hiu-Yuen Wong
- Departments of Otorhinolaryngology-Head and Neck Surgery and Microbiology, Tumor Virology Program, Abramson Comprehensive Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA;
| | - Erle S Robertson
- Departments of Otorhinolaryngology-Head and Neck Surgery and Microbiology, Tumor Virology Program, Abramson Comprehensive Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA;
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14
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Clinical Manifestations and Epigenetic Regulation of Oral Herpesvirus Infections. Viruses 2021; 13:v13040681. [PMID: 33920978 PMCID: PMC8071331 DOI: 10.3390/v13040681] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/13/2021] [Accepted: 04/13/2021] [Indexed: 12/20/2022] Open
Abstract
The oral cavity is often the first site where viruses interact with the human body. The oral epithelium is a major site of viral entry, replication and spread to other cell types, where chronic infection can be established. In addition, saliva has been shown as a primary route of person-to-person transmission for many viruses. From a clinical perspective, viral infection can lead to several oral manifestations, ranging from common intraoral lesions to tumors. Despite the clinical and biological relevance of initial oral infection, little is known about the mechanism of regulation of the viral life cycle in the oral cavity. Several viruses utilize host epigenetic machinery to promote their own life cycle. Importantly, viral hijacking of host chromatin-modifying enzymes can also lead to the dysregulation of host factors and in the case of oncogenic viruses may ultimately play a role in promoting tumorigenesis. Given the known roles of epigenetic regulation of viral infection, epigenetic-targeted antiviral therapy has been recently explored as a therapeutic option for chronic viral infection. In this review, we highlight three herpesviruses with known roles in oral infection, including herpes simplex virus type 1, Epstein–Barr virus and Kaposi’s sarcoma-associated herpesvirus. We focus on the respective oral clinical manifestations of these viruses and their epigenetic regulation, with a specific emphasis on the viral life cycle in the oral epithelium.
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15
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Regulation of KSHV Latency and Lytic Reactivation. Viruses 2020; 12:v12091034. [PMID: 32957532 PMCID: PMC7551196 DOI: 10.3390/v12091034] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 09/10/2020] [Accepted: 09/12/2020] [Indexed: 02/06/2023] Open
Abstract
Kaposi’s sarcoma-associated herpesvirus (KSHV) is associated with three malignancies— Kaposi’s sarcoma (KS), primary effusion lymphoma (PEL), and multicentric Castleman’s disease (MCD). Central to the pathogenesis of these diseases is the KSHV viral life cycle, which is composed of a quiescent latent phase and a replicative lytic phase. While the establishment of latency enables persistent KSHV infection and evasion of the host immune system, lytic replication is essential for the dissemination of the virus between hosts and within the host itself. The transition between these phases, known as lytic reactivation, is controlled by a complex set of environmental, host, and viral factors. The effects of these various factors converge on the regulation of two KSHV proteins whose functions facilitate each phase of the viral life cycle—latency-associated nuclear antigen (LANA) and the master switch of KSHV reactivation, replication and transcription activator (RTA). This review presents the current understanding of how the transition between the phases of the KSHV life cycle is regulated, how the various phases contribute to KSHV pathogenesis, and how the viral life cycle can be exploited as a therapeutic target.
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16
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Czech-Sioli M, Günther T, Therre M, Spohn M, Indenbirken D, Theiss J, Riethdorf S, Qi M, Alawi M, Wülbeck C, Fernandez-Cuesta I, Esmek F, Becker JC, Grundhoff A, Fischer N. High-resolution analysis of Merkel Cell Polyomavirus in Merkel Cell Carcinoma reveals distinct integration patterns and suggests NHEJ and MMBIR as underlying mechanisms. PLoS Pathog 2020; 16:e1008562. [PMID: 32833988 PMCID: PMC7470373 DOI: 10.1371/journal.ppat.1008562] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 09/03/2020] [Accepted: 07/08/2020] [Indexed: 12/17/2022] Open
Abstract
Merkel Cell Polyomavirus (MCPyV) is the etiological agent of the majority of Merkel Cell Carcinomas (MCC). MCPyV positive MCCs harbor integrated, defective viral genomes that constitutively express viral oncogenes. Which molecular mechanisms promote viral integration, if distinct integration patterns exist, and if integration occurs preferentially at loci with specific chromatin states is unknown. We here combined short and long-read (nanopore) next-generation sequencing and present the first high-resolution analysis of integration site structure in MCC cell lines as well as primary tumor material. We find two main types of integration site structure: Linear patterns with chromosomal breakpoints that map closely together, and complex integration loci that exhibit local amplification of genomic sequences flanking the viral DNA. Sequence analysis suggests that linear patterns are produced during viral replication by integration of defective/linear genomes into host DNA double strand breaks via non-homologous end joining, NHEJ. In contrast, our data strongly suggest that complex integration patterns are mediated by microhomology-mediated break-induced replication, MMBIR. Furthermore, we show by ChIP-Seq and RNA-Seq analysis that MCPyV preferably integrates in open chromatin and provide evidence that viral oncogene expression is driven by the viral promoter region, rather than transcription from juxtaposed host promoters. Taken together, our data explain the characteristics of MCPyV integration and may also provide a model for integration of other oncogenic DNA viruses such as papillomaviruses.
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Affiliation(s)
- Manja Czech-Sioli
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Thomas Günther
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Marlin Therre
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Michael Spohn
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Daniela Indenbirken
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Juliane Theiss
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Sabine Riethdorf
- Institute of Tumorbiology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Minyue Qi
- Bioinformatics Core, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Malik Alawi
- Bioinformatics Core, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Corinna Wülbeck
- Translational skin cancer research, German Cancer Consortium (DKTK), University Hospital Essen, Essen, Germany
| | - Irene Fernandez-Cuesta
- Institute of Nanostructure- and Solid State Physics (INF), Center for Hybrid Nanostructures (CHyN), University of Hamburg, Hamburg, Germany
| | - Franziska Esmek
- Institute of Nanostructure- and Solid State Physics (INF), Center for Hybrid Nanostructures (CHyN), University of Hamburg, Hamburg, Germany
| | - Jürgen C. Becker
- Translational skin cancer research, German Cancer Consortium (DKTK), University Hospital Essen, Essen, Germany
- Deutsches Krebsforschungszentrum, Heidelberg, Germany
| | - Adam Grundhoff
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
- * E-mail: (AG); (NF)
| | - Nicole Fischer
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- * E-mail: (AG); (NF)
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17
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Campbell M, Yang WS, Yeh WW, Kao CH, Chang PC. Epigenetic Regulation of Kaposi's Sarcoma-Associated Herpesvirus Latency. Front Microbiol 2020; 11:850. [PMID: 32508765 PMCID: PMC7248258 DOI: 10.3389/fmicb.2020.00850] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 04/08/2020] [Indexed: 12/17/2022] Open
Abstract
Kaposi’s sarcoma-associated herpesvirus (KSHV) is an oncogenic γ-herpesvirus that infects humans and exhibits a biphasic life cycle consisting of latent and lytic phases. Following entry into host cells, the KSHV genome undergoes circularization and chromatinization into an extrachromosomal episome ultimately leading to the establishment of latency. The KSHV episome is organized into distinct chromatin domains marked by variations in repressive or activating epigenetic modifications, including DNA methylation, histone methylation, and histone acetylation. Thus, the development of KSHV latency is believed to be governed by epigenetic regulation. In the past decade, interrogation of the KSHV epitome by genome-wide approaches has revealed a complex epigenetic mark landscape across KSHV genome and has uncovered the important regulatory roles of epigenetic modifications in governing the development of KSHV latency. Here, we highlight many of the findings regarding the role of DNA methylation, histone modification, post-translational modification (PTM) of chromatin remodeling proteins, the contribution of long non-coding RNAs (lncRNAs) in regulating KSHV latency development, and the role of higher-order episomal chromatin architecture in the maintenance of latency and the latent-to-lytic switch.
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Affiliation(s)
- Mel Campbell
- UC Davis Cancer Center, University of California, Davis, Davis, CA, United States
| | - Wan-Shan Yang
- Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan
| | - Wayne W Yeh
- Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan
| | - Chen-Hsuan Kao
- Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan
| | - Pei-Ching Chang
- Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan
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18
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Buschle A, Hammerschmidt W. Epigenetic lifestyle of Epstein-Barr virus. Semin Immunopathol 2020; 42:131-142. [PMID: 32232535 PMCID: PMC7174264 DOI: 10.1007/s00281-020-00792-2] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 02/14/2020] [Indexed: 12/13/2022]
Abstract
Epstein-Barr virus (EBV) is a model of herpesvirus latency and epigenetic changes. The virus preferentially infects human B-lymphocytes (and also other cell types) but does not turn them straight into virus factories. Instead, it establishes a strictly latent infection in them and concomitantly induces the activation and proliferation of infected B cells. How the virus establishes latency in its target cells is only partially understood, but its latent state has been studied intensively by many. During latency, several copies of the viral genome are maintained as minichromosomes in the nucleus. In latently infected cells, most viral genes are epigenetically repressed by cellular chromatin constituents and DNA methylation, but certain EBV genes are spared and remain expressed to support the latent state of the virus in its host cell. Latency is not a dead end, but the virus can escape from this state and reactivate. Reactivation is a coordinated process that requires the removal of repressive chromatin components and a gain in accessibility for viral and cellular factors and machines to support the entire transcriptional program of EBV's ensuing lytic phase. We have a detailed picture of the initiating events of EBV's lytic phase, which are orchestrated by a single viral protein - BZLF1. Its induced expression can lead to the expression of all lytic viral proteins, but initially it fosters the non-licensed amplification of viral DNA that is incorporated into preformed capsids. In the virions, the viral DNA is free of histones and lacks methylated cytosine residues which are lost during lytic DNA amplification. This review provides an overview of EBV's dynamic epigenetic changes, which are an integral part of its ingenious lifestyle in human host cells.
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Affiliation(s)
- Alexander Buschle
- Research Unit Gene Vectors, Helmholtz Zentrum München, German Research Center for Environmental Health and German Centre for Infection Research (DZIF), Partner site Munich, Marchioninistr. 25, D-81377, Munich, Germany
| | - Wolfgang Hammerschmidt
- Research Unit Gene Vectors, Helmholtz Zentrum München, German Research Center for Environmental Health and German Centre for Infection Research (DZIF), Partner site Munich, Marchioninistr. 25, D-81377, Munich, Germany.
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19
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Rainbow Kaposi's Sarcoma-Associated Herpesvirus Revealed Heterogenic Replication with Dynamic Gene Expression. J Virol 2020; 94:JVI.01565-19. [PMID: 31969436 PMCID: PMC7108829 DOI: 10.1128/jvi.01565-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Accepted: 01/02/2020] [Indexed: 12/25/2022] Open
Abstract
Molecular mechanisms of Kaposi's sarcoma-associated herpesvirus (KSHV) reactivation have been studied primarily by measuring the total or average activity of an infected cell population, which often consists of a mixture of both nonresponding and reactivating cells that in turn contain KSHVs at various stages of replication. Studies on KSHV gene regulation at the individual cell level would allow us to better understand the basis for this heterogeneity, and new preventive measures could be developed based on findings from nonresponding cells exposed to reactivation stimuli. Here, we generated a recombinant reporter virus, which we named "Rainbow-KSHV," that encodes three fluorescence-tagged KSHV proteins (mBFP2-ORF6, mCardinal-ORF52, and mCherry-LANA). Rainbow-KSHV replicated similarly to a prototype reporter-KSHV, KSHVr.219, and wild-type BAC16 virus. Live imaging revealed unsynchronized initiation of reactivation and KSHV replication with diverse kinetics between individual cells. Cell fractionation revealed temporal gene regulation, in which early lytic gene expression was terminated in late protein-expressing cells. Finally, isolation of fluorescence-positive cells from nonresponders increased dynamic ranges of downstream experiments 10-fold. Thus, this study demonstrates a tool to examine heterogenic responses of KSHV reactivation for a deeper understanding of KSHV replication.IMPORTANCE Sensitivity and resolution of molecular analysis are often compromised by the use of techniques that measure the ensemble average of large cell populations. Having a research tool to nondestructively identify the KSHV replication stage in an infected cell would not only allow us to effectively isolate cells of interest from cell populations but also enable more precise sample selection for advanced single-cell analysis. We prepared a recombinant KSHV that can report on its replication stage in host cells by differential fluorescence emission. Consistent with previous host gene expression studies, our experiments reveal the highly heterogenic nature of KSHV replication/gene expression at individual cell levels. The utilization of a newly developed reporter-KSHV and initial characterization of KSHV replication in single cells are presented.
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20
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Fröhlich J, Grundhoff A. Epigenetic control in Kaposi sarcoma-associated herpesvirus infection and associated disease. Semin Immunopathol 2020; 42:143-157. [PMID: 32219477 PMCID: PMC7174275 DOI: 10.1007/s00281-020-00787-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 01/20/2020] [Indexed: 12/15/2022]
Abstract
Kaposi sarcoma-associated herpesvirus (KSHV) is the etiologic agent of several malignancies of endothelial and B-cell origin. The fact that latently infected tumor cells in these malignancies do not express classical viral oncogenes suggests that pathogenesis of KSHV-associated disease results from multistep processes that, in addition to constitutive viral gene expression, may require accumulation of cellular alterations. Heritable changes of the epigenome have emerged as an important co-factor that contributes to the pathogenesis of many non-viral cancers. Since KSHV encodes a number of factors that directly or indirectly manipulate host cell chromatin, it is an intriguing possibility that epigenetic reprogramming also contributes to the pathogenesis of KSHV-associated tumors. The fact that heritable histone modifications have also been shown to regulate viral gene expression programs in KSHV-infected tumor cells underlines the importance of epigenetic control during latency and tumorigenesis. We here review what is presently known about the role of epigenetic regulation of viral and host chromatin in KSHV infection and discuss how viral manipulation of these processes may contribute to the development of KSHV-associated disease.
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Affiliation(s)
- Jacqueline Fröhlich
- Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Adam Grundhoff
- Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany.
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21
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Epigenetic factor siRNA screen during primary KSHV infection identifies novel host restriction factors for the lytic cycle of KSHV. PLoS Pathog 2020; 16:e1008268. [PMID: 31923286 PMCID: PMC6977772 DOI: 10.1371/journal.ppat.1008268] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 01/23/2020] [Accepted: 12/09/2019] [Indexed: 12/12/2022] Open
Abstract
Establishment of viral latency is not only essential for lifelong Kaposi’s sarcoma-associated herpesvirus (KSHV) infection, but it is also a prerequisite of viral tumorigenesis. The latent viral DNA has a complex chromatin structure, which is established in a stepwise manner regulated by host epigenetic factors during de novo infection. However, despite the importance of viral latency in KSHV pathogenesis, we still have limited information about the repertoire of epigenetic factors that are critical for the establishment and maintenance of KSHV latency. Therefore, the goal of this study was to identify host epigenetic factors that suppress lytic KSHV genes during primary viral infection, which would indicate their role in latency establishment. We performed an siRNA screen targeting 392 host epigenetic factors during primary infection and analyzed which ones affect the expression of the viral replication and transcription activator (RTA) and/or the latency-associated nuclear antigen (LANA), which are viral genes essential for lytic replication and latency, respectively. As a result, we identified the Nucleosome Remodeling and Deacetylase (NuRD) complex, Tip60 and Tip60-associated co-repressors, and the histone demethylase KDM2B as repressors of KSHV lytic genes during both de novo infection and the maintenance of viral latency. Furthermore, we showed that KDM2B rapidly binds to the incoming viral DNA as early as 8 hpi, and can limit the enrichment of activating histone marks on the RTA promoter favoring the downregulation of RTA expression even prior to the polycomb proteins-regulated heterochromatin establishment on the viral genome. Strikingly, KDM2B can also suppress viral gene expression and replication during lytic infection of primary gingival epithelial cells, revealing that KDM2B can act as a host restriction factor of the lytic cycle of KSHV during both latent and lytic infections in multiple different cell types. Latent viral infection of cancer cells in KSHV-associated tumors is critical for the growth and survival of the cancer. Thus, revealing how lytic viral genes get suppressed through epigenetic regulation following de novo KSHV infection, resulting in the establishment of latency, is central to understanding the pathogenesis of KSHV infection. Importantly, the epigenetic factors that we identified as suppressors of KSHV lytic genes are not only crucial for the establishment and maintenance of KSHV latency in different cell types, but also several of them can block lytic KSHV infection in oral epithelial cells. Since herpesviruses often rely on similar sets of host epigenetic factors, the characterization of these newly identified epigenetic factors in KSHV infection may help to better understand fundamental epigenetic mechanisms that may also be utilized by other herpesviruses to establish latency following primary infection.
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