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Collins-McMillen D, De Oliveira Pessoa D, Zarrella K, Parkins CJ, Daily M, Moorman NJ, Kamil JP, Caposio P, Padi M, Goodrum FD. Viral and host network analysis of the human cytomegalovirus transcriptome in latency. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.21.594597. [PMID: 38826434 PMCID: PMC11142044 DOI: 10.1101/2024.05.21.594597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
HCMV genes UL135 and UL138 play opposing roles regulating latency and reactivation in CD34+ human progenitor cells (HPCs). Using the THP-1 cell line model for latency and reactivation, we designed an RNA sequencing study to compare the transcriptional profile of HCMV infection in the presence and absence of these genes. The loss of UL138 results in elevated levels of viral gene expression and increased differentiation of cell populations that support HCMV gene expression and genome synthesis. The loss of UL135 results in diminished viral gene expression during an initial burst that occurs as latency is established and no expression of eleven viral genes from the ULb' region even following stimulation for differentiation and reactivation. Transcriptional network analysis revealed host transcription factors with potential to regulate the ULb' genes in coordination with pUL135. These results reveal roles for UL135 and UL138 in regulation of viral gene expression and potentially hematopoietic differentiation.
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Affiliation(s)
- Donna Collins-McMillen
- BIO5 Institute, University of Arizona, Tucson, Arizona, United States of America
- Department of Immunobiology, University of Arizona, Tucson, Arizona, United States of America
| | - Diogo De Oliveira Pessoa
- Bioinformatics Shared Resource, Arizona Cancer Center, University of Arizona, Tucson, Arizona, United States of America
| | - Kristen Zarrella
- Department of Immunobiology, University of Arizona, Tucson, Arizona, United States of America
| | - Christopher J. Parkins
- Vaccine and Gene Therapy Institute, Oregon Health Science University, Beaverton, Oregon, United States of America
| | - Michael Daily
- Vaccine and Gene Therapy Institute, Oregon Health Science University, Beaverton, Oregon, United States of America
| | - Nathaniel J. Moorman
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Jeremy P. Kamil
- Department of Microbiology and Immunology, Louisiana State University Health Sciences Center, Shreveport, Louisiana, United States of America
| | - Patrizia Caposio
- Vaccine and Gene Therapy Institute, Oregon Health Science University, Beaverton, Oregon, United States of America
| | - Megha Padi
- Bioinformatics Shared Resource, Arizona Cancer Center, University of Arizona, Tucson, Arizona, United States of America
- University of Arizona Cancer Center, University of Arizona, Tucson, Arizona, United States of America
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, United States of America
| | - Felicia D. Goodrum
- BIO5 Institute, University of Arizona, Tucson, Arizona, United States of America
- Department of Immunobiology, University of Arizona, Tucson, Arizona, United States of America
- University of Arizona Cancer Center, University of Arizona, Tucson, Arizona, United States of America
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, United States of America
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2
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Mason R, Bradley E, Wills M, Sinclair J, Reeves M. Repression of the major immediate early promoter of human cytomegalovirus allows transcription from an alternate promoter. J Gen Virol 2023; 104. [PMID: 37702591 DOI: 10.1099/jgv.0.001894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/14/2023] Open
Abstract
Following infection, the human cytomegalovirus (HCMV) genome becomes rapidly associated with host histones which can contribute to the regulation of viral gene expression. This can be seen clearly during HCMV latency where silencing of the major immediate early promoter (MIEP), normally responsible for expression of the key lytic proteins IE72 and IE86, is mediated by histone methylation and recruitment of heterochromatin protein 1. Crucially, reversal of these histone modifications coupled with histone acetylation drives viral reactivation which can be blocked with specific histone acetyltransferase inhibitors (HATi). In lytic infection, a role for HATi is less clear despite the well-established enhancement of viral replication observed with histone deacetylase inhibitors. Here we report that a number of different broad-acting HATi have a minor impact on viral infection and replication during lytic infection with the more overt phenotypes observed at lower multiplicities of infection. However, specific analyses of the regulation of major immediate early (MIE) gene expression reveal that the HATi C646, which targets p300/CBP, transiently repressed MIE gene expression via inhibition of the MIEP but by 24 h post-infection MIE gene expression was rescued due to compensatory activation of an alternative IE promoter, ip2. This suggested that silencing of the MIEP promoted alternative ip2 promoter activity in lytic infection and, consistent with this, ip2 transcription is impaired in cells infected with a recombinant HCMV that does not auto-repress the MIEP at late times of infection. Furthermore, inhibition of the histone methyltransferases known to be responsible for auto-repression is similarly inhibitory to ip2 transcription in wild-type infected cells. We also observe that these discrete transcriptional activities of the MIEP and ip2 promoter are also reflected in reactivation; essentially in cells where the MIEP is silenced, ip2 activity is easier to detect at very early times post-reactivation whereas in cells where robust activation of the MIEP is observed ip2 transcription is reduced or delayed. Finally, we observe that inhibition of pathways demonstrated to be important for reactivation of HCMV in dendritic cells, e.g. in response to IL-6, are preferentially important for activation of the MIEP and not the ip2 promoter. Together, these data add to the hypothesis that the existence of multiple promoters within the MIE region of HCMV can drive reactivation in a cell type- and ligand-specific manner and also suggest that inter-dependent regulatory activity between the two promoters exists.
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Affiliation(s)
- Rebecca Mason
- Institute of Immunity & Transplantation, Royal Free Campus, Division of Infection & Immunity, UCL, London, UK
| | - Eleanor Bradley
- Institute of Immunity & Transplantation, Royal Free Campus, Division of Infection & Immunity, UCL, London, UK
| | - Mark Wills
- Department of Medicine, Addenbrooke's Hospital, University of Cambridge, Cambridge, UK
| | - John Sinclair
- Department of Medicine, Addenbrooke's Hospital, University of Cambridge, Cambridge, UK
| | - Matthew Reeves
- Institute of Immunity & Transplantation, Royal Free Campus, Division of Infection & Immunity, UCL, London, UK
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3
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McMahon‑Cole H, Johnson A, Sadat Aghamiri S, Helikar T, Crawford LB. Modeling and Remodeling the Cell: How Digital Twins and HCMV Can Elucidate the Complex Interactions of Viral Latency, Epigenetic Regulation, and Immune Responses. CURRENT CLINICAL MICROBIOLOGY REPORTS 2023; 10:141-151. [PMID: 37901689 PMCID: PMC10601359 DOI: 10.1007/s40588-023-00201-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/12/2023] [Indexed: 10/31/2023]
Abstract
Purpose of Review Human cytomegalovirus (HCMV), while asymptomatic in most, causes significant complications during fetal development, following transplant or in immunosuppressed individuals. The host-virus interactions regulating viral latency and reactivation and viral control of the cellular environment (immune regulation, differentiation, epigenetics) are highly complex. Understanding these processes is essential to controlling infection and can be leveraged as a novel approach for understanding basic cell biology. Recent Findings Immune digital twins (IDTs) are digital simulations integrating knowledge of human immunology, physiology, and patient-specific clinical data to predict individualized immune responses and targeted treatments. Recent studies used IDTs to elucidate mechanisms of T cells, dendritic cells, and epigenetic control-all key to HCMV biology. Summary Here, we discuss how leveraging the unique biology of HCMV and IDTs will clarify immune response dynamics, host-virus interactions, and viral latency and reactivation and serve as a powerful IDT-validation platform for individualized and holistic health management.
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Affiliation(s)
- Hana McMahon‑Cole
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Alicia Johnson
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Sara Sadat Aghamiri
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Tomáš Helikar
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Lindsey B. Crawford
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, USA
- Nebraska Center for Virology, Lincoln, NE, USA
- Nebraska Center for Integrated Biomolecular Communication, Lincoln, NE, USA
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4
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Abstract
Human cytomegalovirus (HCMV) is a betaherpesvirus that establishes lifelong infection in its host and can cause severe comorbidities in individuals with suppressed or compromised immune systems. The lifecycle of HCMV consists of lytic and latent phases, largely dependent upon the cell type infected and whether transcription from the major immediate early locus can ensue. Control of this locus, which acts as a critical "switch" region from where the lytic gene expression cascade originates, as well as regulation of the additional ~235 kilobases of virus genome, occurs through chromatinization with cellular histone proteins after infection. Upon infection of a host cell, an initial intrinsic antiviral response represses gene expression from the incoming genome, which is relieved in permissive cells by viral and host factors in concert. Latency is established in a subset of hematopoietic cells, during which viral transcription is largely repressed while the genome is maintained. As these latently infected cells differentiate, the cellular milieu and epigenetic modifications change, giving rise to the initial stages of virus reactivation from latency. Thus, throughout the cycle of infection, chromatinization, chromatin modifiers, and the recruitment of specific transcription factors influence the expression of genes from the HCMV genome. In this review, we discuss epigenetic regulation of the HCMV genome during the different phases of infection, with an emphasis on recent reports that add to our current perspective.
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Affiliation(s)
- Stephen M. Matthews
- Infection Biology, Global Center for Pathogen and Human Health Research, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Ian J. Groves
- Infection Biology, Global Center for Pathogen and Human Health Research, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
- Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland Clinic, Cleveland, Ohio, USA
| | - Christine M. O'Connor
- Infection Biology, Global Center for Pathogen and Human Health Research, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
- Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland Clinic, Cleveland, Ohio, USA
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5
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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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6
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Abstract
While many viral infections are limited and eventually resolved by the host immune response or by death of the host, other viruses establish long-term relationships with the host by way of a persistent infection, that range from chronic viruses that may be eventually cleared to those that establish life-long persistent or latent infection. Viruses infecting hosts from bacteria to humans establish quiescent infections that must be reactivated to produce progeny. For mammalian viruses, most notably herpesviruses, this quiescent maintenance of viral genomes in the absence of virus replication is referred to as latency. The latent strategy allows the virus to persist quiescently within a single host until conditions indicate a need to reactivate to reach a new host or, to re-seed a reservoir within the host. Here, I review common themes in viral strategies to regulate the latent cycle and reactivate from it ranging from bacteriophage to herpesviruses with a focus on human cytomegalovirus (HCMV). Themes central to herpesvirus latency include, epigenetic repression of viral gene expression and mechanisms to regulate host signaling and survival. Critical to the success of a latent program are mechanisms by which the virus can "sense" fluctuations in host biology (within the host) or environment (outside the host) and make appropriate "decisions" to maintain latency or re-initiate the replicative program. The signals or environments that indicate the establishment of a latent state, the very nature of the latent state, as well as the signals driving reactivation have been topics of intense study from bacteriophage to human viruses, as these questions encompass the height of complexity in virus-host interactions-where the host and the virus coexist.
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Affiliation(s)
- Felicia Goodrum
- Department of Immunobiology, BIO5 Institute, University of Arizona, Tucson, AZ, United States.
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7
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Hong YM, Min SY, Kim D, Kim S, Seo D, Lee KH, Han SH. Human MicroRNAs Attenuate the Expression of Immediate Early Proteins and HCMV Replication during Lytic and Latent Infection in Connection with Enhancement of Phosphorylated RelA/p65 (Serine 536) That Binds to MIEP. Int J Mol Sci 2022; 23:ijms23052769. [PMID: 35269913 PMCID: PMC8911160 DOI: 10.3390/ijms23052769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 02/24/2022] [Accepted: 02/28/2022] [Indexed: 02/05/2023] Open
Abstract
Attenuating the expression of immediate early (IE) proteins is essential for controlling the lytic replication of human cytomegalovirus (HCMV). The human microRNAs (hsa-miRs), miR-200b-3p and miR-200c-3p, have been identified to bind the 3′-untranslated region (3′-UTR) of the mRNA encoding IE proteins. However, whether hsa-miRs can reduce IE72 expression and HCMV viral load or exhibit a crosstalk with the host cellular signaling machinery, most importantly the NF-κB cascade, has not been evaluated. In this study, argonaute-crosslinking and immunoprecipitation-seq revealed that miR-200b-3p and miR-200c-3p bind the 3′-UTR of UL123, which is a gene that encodes IE72. The binding of these miRNAs to the 3′-UTR of UL123 was verified in transfected cells stably expressing GFP. We used miR-200b-3p/miR-200c-3p mimics to counteract the downregulation of these miRNA after acute HCMV infection. This resulted in reduced IE72/IE86 expression and HCMV VL during lytic infection. We determined that IE72/IE86 alone can inhibit the phosphorylation of RelA/p65 at the Ser536 residue and that p-Ser536 RelA/p65 binds to the major IE promoter/enhancer (MIEP). The upregulation of miR-200b-3p and miR-200c-3p resulted in the phosphorylation of RelA/p65 at Ser536 through the downregulation of IE, and the binding of the resultant p-Ser536 RelA/p65 to MIEP resulted in a decreased production of pro-inflammatory cytokines. Overall, miR-200b-3p and miR-200c-3p—together with p-Ser536 RelA/p65—can prevent lytic HCMV replication during acute and latent infection
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Affiliation(s)
- Yeon-Mi Hong
- Division of Infectious Disease, Department of Internal Medicine, Yonsei University College of Medicine, Seoul 06273, Korea; (Y.-M.H.); (S.Y.M.); (D.K.); (S.K.); (K.H.L.)
| | - Seo Yeon Min
- Division of Infectious Disease, Department of Internal Medicine, Yonsei University College of Medicine, Seoul 06273, Korea; (Y.-M.H.); (S.Y.M.); (D.K.); (S.K.); (K.H.L.)
| | - Dayeong Kim
- Division of Infectious Disease, Department of Internal Medicine, Yonsei University College of Medicine, Seoul 06273, Korea; (Y.-M.H.); (S.Y.M.); (D.K.); (S.K.); (K.H.L.)
| | - Subin Kim
- Division of Infectious Disease, Department of Internal Medicine, Yonsei University College of Medicine, Seoul 06273, Korea; (Y.-M.H.); (S.Y.M.); (D.K.); (S.K.); (K.H.L.)
| | - Daekwan Seo
- Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul 06273, Korea;
| | - Kyoung Hwa Lee
- Division of Infectious Disease, Department of Internal Medicine, Yonsei University College of Medicine, Seoul 06273, Korea; (Y.-M.H.); (S.Y.M.); (D.K.); (S.K.); (K.H.L.)
| | - Sang Hoon Han
- Division of Infectious Disease, Department of Internal Medicine, Yonsei University College of Medicine, Seoul 06273, Korea; (Y.-M.H.); (S.Y.M.); (D.K.); (S.K.); (K.H.L.)
- Correspondence: ; Tel.: +82-2-2019-3319; Fax: +82-2-3463-3882
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8
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Inhibition of histone demethylase KDM4 by ML324 induces apoptosis through the unfolded protein response and Bim upregulation in hepatocellular carcinoma cells. Chem Biol Interact 2022; 353:109806. [PMID: 34999051 DOI: 10.1016/j.cbi.2022.109806] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 09/30/2021] [Accepted: 01/05/2022] [Indexed: 02/06/2023]
Abstract
Hepatocellular carcinoma (HCC) is an extremely aggressive malignancy that ranks as the sixth-leading cause of cancer-associated death worldwide. Recently, various epigenetic mechanisms including gene methylation were reported to be potential next era HCC therapeutics and biomarkers. Although inhibition of epigenetic enzymes including histone lysine demethylase 4 (KDM4) enhanced cell death in HCC cells, the detailed mechanism of cell death machinery is poorly understood. In this study, we found that ML324, a small molecule KDM4-specific inhibitor, induced the death of HCC cells in a general cell culture system and 3D spheroid culture with increased cleavage of caspase-3. Mechanistically, we identified that unfolded protein responses (UPR) were involved in ML324-induced HCC cell death. Incubation of HCC cells with ML324 upregulated death receptor 5 (DR5) expression through the activation transcription factor 3 (ATF3)-C/EBP homologous protein (CHOP)-dependent pathway. Moreover, we identified BIM protein as a mediator of ML324-induced apoptosis using CRISPR/Cas9 knockout analysis. We showed that the loss of Bim suppressed ML324-induced apoptosis by flow cytometry analysis, colony formation assay, and caspase-3 activation assay. Interestingly, BIM protein expression by ML324 was regulated by ATF3, CHOP, and DR5 which are factors involved in UPR. Specifically, we confirmed the regulating roles of KDM4E in Bim and CHOP expression using a chromatin immune precipitation (ChIP) assay. Physical binding of KDM4E to Bim and CHOP promoters decreased the response to ML324. Our findings suggest that KDM4 inhibition is a potent anti-tumor therapeutic strategy for human HCC, and further studies of UPR-induced apoptosis and the associated epigenetic functional mechanisms may lead to the discovery of novel target for future cancer therapy.
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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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10
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Epigenetic reprogramming of host and viral genes by Human Cytomegalovirus infection in Kasumi-3 myeloid progenitor cells at early times post-infection. J Virol 2021; 95:JVI.00183-21. [PMID: 33731453 PMCID: PMC10021080 DOI: 10.1128/jvi.00183-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
HCMV establishes latency in myeloid cells. Using the Kasumi-3 latency model, we previously showed that lytic gene expression is activated prior to establishment of latency in these cells. The early events in infection may have a critical role in shaping establishment of latency. Here, we have used an integrative multi-omics approach to investigate dynamic changes in host and HCMV gene expression and epigenomes at early times post infection. Our results show dynamic changes in viral gene expression and viral chromatin. Analyses of Pol II, H3K27Ac and H3K27me3 occupancy of the viral genome showed that 1) Pol II occupancy was highest at the MIEP at 4 hours post infection. However, it was observed throughout the genome; 2) At 24 hours, H3K27Ac was localized to the major immediate early promoter/enhancer and to a possible second enhancer in the origin of replication OriLyt; 3) viral chromatin was broadly accessible at 24 hpi. In addition, although HCMV infection activated expression of some host genes, we observed an overall loss of de novo transcription. This was associated with loss of promoter-proximal Pol II and H3K27Ac, but not with changes in chromatin accessibility or a switch in modification of H3K27.Importance.HCMV is an important human pathogen in immunocompromised hosts and developing fetuses. Current anti-viral therapies are limited by toxicity and emergence of resistant strains. Our studies highlight emerging concepts that challenge current paradigms of regulation of HCMV gene expression in myeloid cells. In addition, our studies show that HCMV has a profound effect on de novo transcription and the cellular epigenome. These results may have implications for mechanisms of viral pathogenesis.
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11
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Groves IJ, Jackson SE, Poole EL, Nachshon A, Rozman B, Schwartz M, Prinjha RK, Tough DF, Sinclair JH, Wills MR. Bromodomain proteins regulate human cytomegalovirus latency and reactivation allowing epigenetic therapeutic intervention. Proc Natl Acad Sci U S A 2021; 118:e2023025118. [PMID: 33619107 PMCID: PMC7936348 DOI: 10.1073/pnas.2023025118] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Reactivation of human cytomegalovirus (HCMV) from latency is a major health consideration for recipients of stem-cell and solid organ transplantations. With over 200,000 transplants taking place globally per annum, virus reactivation can occur in more than 50% of cases leading to loss of grafts as well as serious morbidity and even mortality. Here, we present the most extensive screening to date of epigenetic inhibitors on HCMV latently infected cells and find that histone deacetylase inhibitors (HDACis) and bromodomain inhibitors are broadly effective at inducing virus immediate early gene expression. However, while HDACis, such as myeloid-selective CHR-4487, lead to production of infectious virions, inhibitors of bromodomain (BRD) and extraterminal proteins (I-BETs), including GSK726, restrict full reactivation. Mechanistically, we show that BET proteins (BRDs) are pivotally connected to regulation of HCMV latency and reactivation. Through BRD4 interaction, the transcriptional activator complex P-TEFb (CDK9/CycT1) is sequestered by repressive complexes during HCMV latency. Consequently, I-BETs allow release of P-TEFb and subsequent recruitment to promoters via the superelongation complex (SEC), inducing transcription of HCMV lytic genes encoding immunogenic antigens from otherwise latently infected cells. Surprisingly, this occurs without inducing many viral immunoevasins and, importantly, while also restricting viral DNA replication and full HCMV reactivation. Therefore, this pattern of HCMV transcriptional dysregulation allows effective cytotoxic immune targeting and killing of latently infected cells, thus reducing the latent virus genome load. This approach could be safely used to pre-emptively purge the virus latent reservoir prior to transplantation, thereby reducing HCMV reactivation-related morbidity and mortality.
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MESH Headings
- Azepines/pharmacology
- Bacterial Proteins/genetics
- Bacterial Proteins/metabolism
- Benzodiazepines/pharmacology
- Cell Cycle Proteins/antagonists & inhibitors
- Cell Cycle Proteins/genetics
- Cell Cycle Proteins/immunology
- Cyclin T/genetics
- Cyclin T/immunology
- Cyclin-Dependent Kinase 9/genetics
- Cyclin-Dependent Kinase 9/immunology
- Cytomegalovirus/drug effects
- Cytomegalovirus/genetics
- Cytomegalovirus/immunology
- Cytomegalovirus Infections/genetics
- Cytomegalovirus Infections/immunology
- Cytomegalovirus Infections/pathology
- DNA Replication/drug effects
- DNA, Viral/antagonists & inhibitors
- DNA, Viral/genetics
- DNA, Viral/immunology
- Epigenesis, Genetic
- Genes, Immediate-Early
- Genes, Reporter
- Histone Deacetylase Inhibitors/pharmacology
- Histone Deacetylases/genetics
- Histone Deacetylases/immunology
- Host-Pathogen Interactions
- Humans
- Luminescent Proteins/genetics
- Luminescent Proteins/metabolism
- Models, Biological
- Positive Transcriptional Elongation Factor B/genetics
- Positive Transcriptional Elongation Factor B/immunology
- Primary Cell Culture
- Promoter Regions, Genetic
- T-Lymphocytes, Cytotoxic/drug effects
- T-Lymphocytes, Cytotoxic/immunology
- T-Lymphocytes, Cytotoxic/virology
- THP-1 Cells
- Thalidomide/analogs & derivatives
- Thalidomide/pharmacology
- Transcription Factors/antagonists & inhibitors
- Transcription Factors/genetics
- Transcription Factors/immunology
- Transcription, Genetic
- Virus Activation/drug effects
- Virus Latency/drug effects
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Affiliation(s)
- Ian J Groves
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, CB2 0QQ, United Kingdom;
| | - Sarah E Jackson
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, CB2 0QQ, United Kingdom
| | - Emma L Poole
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, CB2 0QQ, United Kingdom
| | - Aharon Nachshon
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Batsheva Rozman
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Michal Schwartz
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Rab K Prinjha
- Adaptive Immunity Research Unit, GlaxoSmithKline Medicines Research Centre, Stevenage, SG1 2NY, United Kingdom
| | - David F Tough
- Adaptive Immunity Research Unit, GlaxoSmithKline Medicines Research Centre, Stevenage, SG1 2NY, United Kingdom
| | - John H Sinclair
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, CB2 0QQ, United Kingdom
| | - Mark R Wills
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, CB2 0QQ, United Kingdom;
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12
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New Insights Into the Molecular Mechanisms and Immune Control of Cytomegalovirus Reactivation. Transplantation 2020; 104:e118-e124. [PMID: 31996662 PMCID: PMC7790173 DOI: 10.1097/tp.0000000000003138] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Cytomegalovirus (CMV) is a β-herpesvirus that establishes lifelong latency in infected hosts. Following transplantation of a latently infected organ, reactivation can occur and consists of a spectrum of clinically apparent syndromes from mild symptoms to tissue-invasive, resulting in both direct and indirect sequelae. Before the advent of effective antiviral agents, the primary treatment was reduction in immunosuppression (IS). While antiviral agents provide effective prophylaxis, there are several important caveats associated with their use, including drug toxicity and resistance. The traditional view attributes CMV reactivation and the ensuing clinical disease primarily to IS, either intrinsic to disease-related immune compromise or from the extrinsic administration of IS agents. However, previous data from both animal models and human subjects showed that inflammatory signals could induce upregulation of latent viral gene expression. New data demonstrate that ischemia/reperfusion is necessary and sufficient to induce CMV reactivation following murine transplantation of a latently infected graft. In this article, we review a growing body of evidence that suggests that reactivation of both human CMV and murine CMV is first triggered by molecular events that activate CMV gene expression and lytic infection and viral dissemination are then facilitated by IS. The initial activation of viral gene expression may be mediated by oxidative stress, DNA damage, or inflammatory cytokines, and these factors may act synergistically. New therapeutic approaches are needed to capture this complex array of targets.
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Abdurakhmanova ER, Brusnakov MY, Golovchenko OV, Pilyo SG, Velychko NV, Harden EA, Prichard MN, James SH, Zhirnov VV, Brovarets VS. Synthesis and in vitro anticytomegalovirus activity of 5-hydroxyalkylamino-1,3-oxazoles derivatives. Med Chem Res 2020. [DOI: 10.1007/s00044-020-02593-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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14
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Forte E, Zhang Z, Thorp EB, Hummel M. Cytomegalovirus Latency and Reactivation: An Intricate Interplay With the Host Immune Response. Front Cell Infect Microbiol 2020; 10:130. [PMID: 32296651 PMCID: PMC7136410 DOI: 10.3389/fcimb.2020.00130] [Citation(s) in RCA: 113] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 03/10/2020] [Indexed: 12/16/2022] Open
Abstract
CMV is an ancient herpesvirus that has co-evolved with its host over millions of years. The 236 kbp genome encodes at least 165 genes, four non-coding RNAs and 14 miRNAs. Of the protein-coding genes, 43-44 are core replication genes common to all herpesviruses, while ~30 are unique to betaherpesviruses. Many CMV genes are involved in evading detection by the host immune response, and others have roles in cell tropism. CMV replicates systemically, and thus, has adapted to various biological niches within the host. Different biological niches may place competing demands on the virus, such that genes that are favorable in some contexts are unfavorable in others. The outcome of infection is dependent on the cell type. In fibroblasts, the virus replicates lytically to produce infectious virus. In other cell types, such as myeloid progenitor cells, there is an initial burst of lytic gene expression, which is subsequently silenced through epigenetic repression, leading to establishment of latency. Latently infected monocytes disseminate the virus to various organs. Latency is established through cell type specific mechanisms of transcriptional silencing. In contrast, reactivation is triggered through pathways activated by inflammation, infection, and injury that are common to many cell types, as well as differentiation of myeloid cells to dendritic cells. Thus, CMV has evolved a complex relationship with the host immune response, in which it exploits cell type specific mechanisms of gene regulation to establish latency and to disseminate infection systemically, and also uses the inflammatory response to infection as an early warning system which allows the virus to escape from situations in which its survival is threatened, either by cellular damage or infection of the host with another pathogen. Spontaneous reactivation induced by cellular aging/damage may explain why extensive expression of lytic genes has been observed in recent studies using highly sensitive transcriptome analyses of cells from latently infected individuals. Recent studies with animal models highlight the potential for harnessing the host immune response to blunt cellular injury induced by organ transplantation, and thus, prevent reactivation of CMV and its sequelae.
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Affiliation(s)
- Eleonora Forte
- Department of Surgery, Comprehensive Transplant Center, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Zheng Zhang
- Department of Surgery, Comprehensive Transplant Center, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Edward B. Thorp
- Department of Pathology and Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Mary Hummel
- Department of Surgery, Comprehensive Transplant Center, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
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15
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Zhang X, Liu L, Yuan X, Wei Y, Wei X. JMJD3 in the regulation of human diseases. Protein Cell 2019; 10:864-882. [PMID: 31701394 PMCID: PMC6881266 DOI: 10.1007/s13238-019-0653-9] [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: 11/27/2018] [Accepted: 06/11/2019] [Indexed: 02/06/2023] Open
Abstract
In recent years, many studies have shown that histone methylation plays an important role in maintaining the active and silent state of gene expression in human diseases. The Jumonji domain-containing protein D3 (JMJD3), specifically demethylate di- and trimethyl-lysine 27 on histone H3 (H3K27me2/3), has been widely studied in immune diseases, infectious diseases, cancer, developmental diseases, and aging related diseases. We will focus on the recent advances of JMJD3 function in human diseases, and looks ahead to the future of JMJD3 gene research in this review.
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Affiliation(s)
- Xiangxian Zhang
- Laboratory of Aging Research and Nanotoxicology, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Li Liu
- Laboratory of Aging Research and Nanotoxicology, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xia Yuan
- Laboratory of Aging Research and Nanotoxicology, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yuquan Wei
- Laboratory of Aging Research and Nanotoxicology, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xiawei Wei
- Laboratory of Aging Research and Nanotoxicology, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China.
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16
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Lee JH, Pasquarella JR, Kalejta RF. Cell Line Models for Human Cytomegalovirus Latency Faithfully Mimic Viral Entry by Macropinocytosis and Endocytosis. J Virol 2019; 93:e01021-19. [PMID: 31391271 PMCID: PMC6803280 DOI: 10.1128/jvi.01021-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 08/05/2019] [Indexed: 02/06/2023] Open
Abstract
Human cytomegalovirus (HCMV) enters primary CD34+ hematopoietic progenitor cells by macropinocytosis, where it establishes latency in part because its tegument-transactivating protein, pp71, remains associated with endosomes and is therefore unable to initiate productive, lytic replication. Here we show that multiple HCMV strains also enter cell line models used to study latency by macropinocytosis and endocytosis. In all latency models tested, tegument-delivered pp71 was found to be colocalized with endosomal markers and was not associated with the seven other cytoplasmic localization markers tested. Like the capsid-associated pp150 tegument protein, we initially detected capsid proteins in association with endosomes but later detected them in the nucleus. Inhibitors of macropinocytosis and endocytosis reduced latent viral gene expression and precluded reactivation. Importantly, we utilized electron microscopy to observe entry by macropinocytosis and endocytosis, providing additional visual corroboration of the findings of our functional studies. Our demonstration that HCMV enters cell line models for latency in a manner indistinguishable from that of its entry into primary cells illustrates the utility of these cell lines for probing the mechanisms, host genetics, and small-molecule-mediated inhibition of HCMV entry into the cell types where it establishes latency.IMPORTANCE Primary cells cultured in vitro currently provide the highest available relevance for examining molecular and genetic requirements for the establishment, maintenance, and reactivation of HCMV latency. However, their expense, heterogeneity, and intransigence to both long-term culture and molecular or genetic modification create rigor and reproducibility challenges for HCMV latency studies. There are several cell line models for latency not obstructed by deficiencies inherent in primary cells. However, many researchers view cell line studies of latency to be physiologically irrelevant because of the perception that these models display numerous and significant differences from primary cells. Here, we show that the very first step in a latent HCMV infection, entry of the virus into cells, occurs in cell line models in a manner indistinguishable from that in which it occurs in primary CD34+ hematopoietic progenitor cells. Our data argue that experimental HCMV latency is much more similar than it is different in cell lines and primary cells.
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Affiliation(s)
- Jeong-Hee Lee
- Institute for Molecular Virology and McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Joseph R Pasquarella
- Institute for Molecular Virology and McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Robert F Kalejta
- Institute for Molecular Virology and McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin, USA
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17
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Zhang Z, Qiu L, Yan S, Wang JJ, Thomas PM, Kandpal M, Zhao L, Iovane A, Liu XF, Thorp EB, Chen Q, Hummel M, Kanwar YS, Abecassis MM. A clinically relevant murine model unmasks a "two-hit" mechanism for reactivation and dissemination of cytomegalovirus after kidney transplant. Am J Transplant 2019; 19:2421-2433. [PMID: 30947382 PMCID: PMC6873708 DOI: 10.1111/ajt.15376] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 03/17/2019] [Accepted: 03/24/2019] [Indexed: 01/25/2023]
Abstract
Reactivation of latent cytomegalovirus remains an important complication after transplant. Although immunosuppression (IS) has been implicated as a primary cause, we have previously shown that the implantation response of a kidney allograft can lead to early transcriptional activation of latent murine cytomegalovirus (MCMV) genes in an immune-competent host and to MCMV reactivation and dissemination to other organs in a genetically immune-deficient recipient. We now describe a model that allows us to separately analyze the impact of the implantation effect vs that of a clinically relevant IS regimen. Treatment with IS of latently infected mice alone does not induce viral reactivation, but transplant of latently infected allogeneic kidneys combined with IS facilitates MCMV reactivation in the graft and dissemination to other organs. The IS regimen effectively dampens allo-immune inflammatory pathways and depletes recipient anti-MCMV but does not affect ischemia-reperfusion injury pathways. MCMV reactivation similar to that seen in allogeneic transplants combined with also occurs after syngeneic transplants. Thus, our data strongly suggest that while ischemia-reperfusion injury of the implanted graft is sufficient and necessary to initiate transcriptional reactivation of latent MCMV ("first hit"), IS is permissive to the first hit and facilitates dissemination to other organs ("second hit").
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Affiliation(s)
- Zheng Zhang
- Comprehensive Transplant Center, Northwestern University, Feinberg School of Medicine, Chicago, Illinois,Department of Surgery, Northwestern University, Feinberg School of Medicine, Chicago, Illinois
| | - Longhui Qiu
- Comprehensive Transplant Center, Northwestern University, Feinberg School of Medicine, Chicago, Illinois
| | - Shixian Yan
- Comprehensive Transplant Center, Northwestern University, Feinberg School of Medicine, Chicago, Illinois
| | - Jiao-Jing Wang
- Comprehensive Transplant Center, Northwestern University, Feinberg School of Medicine, Chicago, Illinois
| | - Paul M. Thomas
- Department of Chemistry and Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois
| | - Manoj Kandpal
- Comprehensive Transplant Center, Northwestern University, Feinberg School of Medicine, Chicago, Illinois,Preventive Medicine, Northwestern University, Feinberg School of Medicine, Chicago, Illinois
| | - Lihui Zhao
- Comprehensive Transplant Center, Northwestern University, Feinberg School of Medicine, Chicago, Illinois,Preventive Medicine, Northwestern University, Feinberg School of Medicine, Chicago, Illinois
| | - Andre Iovane
- Comprehensive Transplant Center, Northwestern University, Feinberg School of Medicine, Chicago, Illinois
| | - Xue-feng Liu
- Comprehensive Transplant Center, Northwestern University, Feinberg School of Medicine, Chicago, Illinois,Department of Surgery, Northwestern University, Feinberg School of Medicine, Chicago, Illinois
| | - Edward B. Thorp
- Department of Pathology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois
| | - Qing Chen
- Department of Pathology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois
| | - Mary Hummel
- Comprehensive Transplant Center, Northwestern University, Feinberg School of Medicine, Chicago, Illinois,Department of Surgery, Northwestern University, Feinberg School of Medicine, Chicago, Illinois,Department of Microbiology and Immunology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois
| | - Yashpal S. Kanwar
- Department of Pathology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois,Department of Nephrology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois
| | - Michael M. Abecassis
- Comprehensive Transplant Center, Northwestern University, Feinberg School of Medicine, Chicago, Illinois,Department of Surgery, Northwestern University, Feinberg School of Medicine, Chicago, Illinois,Department of Microbiology and Immunology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois
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18
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Martínez-Cano J, Campos-Sánchez E, Cobaleda C. Epigenetic Priming in Immunodeficiencies. Front Cell Dev Biol 2019; 7:125. [PMID: 31355198 PMCID: PMC6635466 DOI: 10.3389/fcell.2019.00125] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 06/26/2019] [Indexed: 12/17/2022] Open
Abstract
Immunodeficiencies (IDs) are disorders of the immune system that increase susceptibility to infections and cancer, and are therefore associated with elevated morbidity and mortality. IDs can be primary (not caused by other condition or exposure) or secondary due to the exposure to different agents (infections, chemicals, aging, etc.). Most primary immunodeficiencies (PIDs) are of genetic origin, caused by mutations affecting genes with key roles in the development or function of the cells of the immune system. A large percentage of PIDs are associated with a defective development and/or function of lymphocytes and, especially, B cells, the ones in charge of generating the different types of antibodies. B-cell development is a tightly regulated process in which many different factors participate. Among the regulators of B-cell differentiation, a correct epigenetic control of cellular identity is essential for normal cell function. With the advent of next-generation sequencing (NGS) techniques, more and more alterations in different types of epigenetic regulators are being described at the root of PIDs, both in humans and in animal models. At the same time, it is becoming increasingly clear that epigenetic alterations triggered by the exposure to environmental agents have a key role in the development of secondary immunodeficiencies (SIDs). Due to their largely reversible nature, epigenetic modifications are quickly becoming key therapeutic targets in other diseases where their contribution has been known for more time, like cancer. Here, we establish a parallelism between IDs and the nowadays accepted role of epigenetics in cancer initiation and progression, and propose that epigenetics forms a "third axis" (together with genetics and external agents) to be considered in the etiology of IDs, and linking PIDs and SIDs at the molecular level. We therefore postulate that IDs arise due to a variable contribution of (i) genetic, (ii) environmental, and (iii) epigenetic causes, which in fact form a continuum landscape of all possible combinations of these factors. Additionally, this implies the possibility of a fully epigenetically triggered mechanism for some IDs. This concept would have important prophylactic and translational implications, and would also imply a more blurred frontier between primary and secondary immunodeficiencies.
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Affiliation(s)
| | | | - César Cobaleda
- Department of Cell Biology and Immunology, Centro de Biología Molecular Severo Ochoa (Consejo Superior de Investigaciones Científicas –Universidad Autónoma de Madrid), Madrid, Spain
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19
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Kachaeva MV, Pilyo SG, Hartline CB, Harden EA, Prichard MN, Zhirnov VV, Brovarets VS. In vitro activity of novel derivatives of 1,3-oxazole-4-carboxylate and 1,3-oxazole-4-carbonitrile against human cytomegalovirus. Med Chem Res 2019. [DOI: 10.1007/s00044-019-02365-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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20
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Nehme Z, Pasquereau S, Herbein G. Control of viral infections by epigenetic-targeted therapy. Clin Epigenetics 2019; 11:55. [PMID: 30917875 PMCID: PMC6437953 DOI: 10.1186/s13148-019-0654-9] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 03/13/2019] [Indexed: 12/13/2022] Open
Abstract
Epigenetics is defined as the science that studies the modifications of gene expression that are not owed to mutations or changes in the genetic sequence. Recently, strong evidences are pinpointing toward a solid interplay between such epigenetic alterations and the outcome of human cytomegalovirus (HCMV) infection. Guided by the previous possibly promising experimental trials of human immunodeficiency virus (HIV) epigenetic reprogramming, the latter is paving the road toward two major approaches to control viral gene expression or latency. Reactivating HCMV from the latent phase ("shock and kill" paradigm) or alternatively repressing the virus lytic and reactivation phases ("block and lock" paradigm) by epigenetic-targeted therapy represent encouraging options to overcome latency and viral shedding or otherwise replication and infectivity, which could lead eventually to control the infection and its complications. Not limited to HIV and HCMV, this concept is similarly studied in the context of hepatitis B and C virus, herpes simplex virus, and Epstein-Barr virus. Therefore, epigenetic manipulations stand as a pioneering research area in modern biology and could constitute a curative methodology by potentially consenting the development of broad-spectrum antivirals to control viral infections in vivo.
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Affiliation(s)
- Zeina Nehme
- Department Pathogens & Inflammation-EPILAB, UPRES EA4266, University of Franche-Comté, University of Bourgogne Franche-Comté, 16 route de Gray, F-25030 Besançon cedex, France
- Université Libanaise, Beirut, Lebanon
| | - Sébastien Pasquereau
- Department Pathogens & Inflammation-EPILAB, UPRES EA4266, University of Franche-Comté, University of Bourgogne Franche-Comté, 16 route de Gray, F-25030 Besançon cedex, France
| | - Georges Herbein
- Department Pathogens & Inflammation-EPILAB, UPRES EA4266, University of Franche-Comté, University of Bourgogne Franche-Comté, 16 route de Gray, F-25030 Besançon cedex, France
- Department of Virology, CHRU Besancon, F-25030 Besançon, France
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21
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Botto S, Abraham J, Mizuno N, Pryke K, Gall B, Landais I, Streblow DN, Fruh KJ, DeFilippis VR. Human Cytomegalovirus Immediate Early 86-kDa Protein Blocks Transcription and Induces Degradation of the Immature Interleukin-1β Protein during Virion-Mediated Activation of the AIM2 Inflammasome. mBio 2019; 10:e02510-18. [PMID: 30755509 PMCID: PMC6372796 DOI: 10.1128/mbio.02510-18] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 01/02/2019] [Indexed: 12/11/2022] Open
Abstract
Secretion of interleukin-1β (IL-1β) represents a fundamental innate immune response to microbial infection that, at the molecular level, occurs following activation of proteolytic caspases that cleave the immature protein into a secretable form. Human cytomegalovirus (HCMV) is the archetypal betaherpesvirus that is invariably capable of lifelong infection through the activity of numerous virally encoded immune evasion phenotypes. Innate immune pathways responsive to cytoplasmic double-stranded DNA (dsDNA) are known to be activated in response to contact between HCMV and host cells. Here, we used clustered regularly interspaced short palindromic repeat (CRISPR)-CRISPR-associated protein 9 (Cas9) genome editing to demonstrate that the dsDNA receptor absent in melanoma 2 (AIM2) is required for secretion of IL-1β following HCMV infection. Furthermore, dsDNA-responsive innate signaling induced by HCMV infection that leads to activation of the type I interferon response is also shown, unexpectedly, to play a contributory role in IL-1β secretion. Importantly, we also show that rendering virus particles inactive by UV exposure leads to substantially increased IL-1β processing and secretion and that live HCMV can inhibit this, suggesting the virus encodes factors that confer an inhibitory effect on this response. Further examination revealed that ectopic expression of the immediate early (IE) 86-kDa protein (IE86) is actually associated with a block in transcription of the pro-IL-1β gene and, independently, diminishment of the immature protein. Overall, these results reveal two new and distinct phenotypes conferred by the HCMV IE86 protein, as well as an unusual circumstance in which a single herpesviral protein exhibits inhibitory effects on multiple molecular processes within the same innate immune response.IMPORTANCE Persistent infection with HCMV is associated with the operation of diverse evasion phenotypes directed at antiviral immunity. Obstruction of intrinsic and innate immune responses is typically conferred by viral proteins either associated with the viral particle or expressed immediately after entry. In line with this, numerous phenotypes are attributed to the HCMV IE86 protein that involve interference with innate immune processes via transcriptional and protein-directed mechanisms. We describe novel IE86-mediated phenotypes aimed at virus-induced secretion of IL-1β. Intriguingly, while many viruses target the function of the molecular scaffold required for IL-1β maturation to prevent this response, we find that HCMV and IE86 target the IL-1β protein specifically. Moreover, we show that IE86 impairs both the synthesis of the IL-1β transcript and the stability of the immature protein. This indicates an unusual phenomenon in which a single viral protein exhibits two molecularly separate evasion phenotypes directed at a single innate cytokine.
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Affiliation(s)
- Sara Botto
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Portland, Oregon, USA
| | - Jinu Abraham
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Portland, Oregon, USA
| | - Nobuyo Mizuno
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Portland, Oregon, USA
| | - Kara Pryke
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Portland, Oregon, USA
| | - Bryan Gall
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Portland, Oregon, USA
| | - Igor Landais
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Portland, Oregon, USA
| | - Daniel N Streblow
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Portland, Oregon, USA
| | - Klaus J Fruh
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Portland, Oregon, USA
| | - Victor R DeFilippis
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Portland, Oregon, USA
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22
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Collins-McMillen D, Buehler J, Peppenelli M, Goodrum F. Molecular Determinants and the Regulation of Human Cytomegalovirus Latency and Reactivation. Viruses 2018; 10:E444. [PMID: 30127257 PMCID: PMC6116278 DOI: 10.3390/v10080444] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 08/16/2018] [Accepted: 08/17/2018] [Indexed: 02/06/2023] Open
Abstract
Human cytomegalovirus (HCMV) is a beta herpesvirus that establishes a life-long persistence in the host, like all herpesviruses, by way of a latent infection. During latency, viral genomes are maintained in a quieted state. Virus replication can be reactivated from latency in response to changes in cellular signaling caused by stress or differentiation. The past decade has brought great insights into the molecular basis of HCMV latency. Here, we review the complex persistence of HCMV with consideration of latent reservoirs, viral determinants and their host interactions, and host signaling and the control of cellular and viral gene expression that contributes to the establishment of and reactivation from latency.
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Affiliation(s)
| | - Jason Buehler
- BIO5 Institute, University of Arizona, Tucson, AZ 85721, USA.
| | | | - Felicia Goodrum
- BIO5 Institute, University of Arizona, Tucson, AZ 85721, USA.
- Department of Immunobiology, University of Arizona, Tucson, AZ 85721, USA.
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23
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Rumlová M, Ruml T. In vitro methods for testing antiviral drugs. Biotechnol Adv 2018; 36:557-576. [PMID: 29292156 PMCID: PMC7127693 DOI: 10.1016/j.biotechadv.2017.12.016] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 12/22/2017] [Accepted: 12/27/2017] [Indexed: 12/24/2022]
Abstract
Despite successful vaccination programs and effective treatments for some viral infections, humans are still losing the battle with viruses. Persisting human pandemics, emerging and re-emerging viruses, and evolution of drug-resistant strains impose continuous search for new antiviral drugs. A combination of detailed information about the molecular organization of viruses and progress in molecular biology and computer technologies has enabled rational antivirals design. Initial step in establishing efficacy of new antivirals is based on simple methods assessing inhibition of the intended target. We provide here an overview of biochemical and cell-based assays evaluating the activity of inhibitors of clinically important viruses.
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Affiliation(s)
- Michaela Rumlová
- Department of Biotechnology, University of Chemistry and Technology, Prague 166 28, Czech Republic.
| | - Tomáš Ruml
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague 166 28, Czech Republic.
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24
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Shnayder M, Nachshon A, Krishna B, Poole E, Boshkov A, Binyamin A, Maza I, Sinclair J, Schwartz M, Stern-Ginossar N. Defining the Transcriptional Landscape during Cytomegalovirus Latency with Single-Cell RNA Sequencing. mBio 2018; 9:e00013-18. [PMID: 29535194 PMCID: PMC5850328 DOI: 10.1128/mbio.00013-18] [Citation(s) in RCA: 124] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 02/13/2018] [Indexed: 12/17/2022] Open
Abstract
Primary infection with human cytomegalovirus (HCMV) results in a lifelong infection due to its ability to establish latent infection, with one characterized viral reservoir being hematopoietic cells. Although reactivation from latency causes serious disease in immunocompromised individuals, our molecular understanding of latency is limited. Here, we delineate viral gene expression during natural HCMV persistent infection by analyzing the massive transcriptome RNA sequencing (RNA-seq) atlas generated by the Genotype-Tissue Expression (GTEx) project. This systematic analysis reveals that HCMV persistence in vivo is prevalent in diverse tissues. Notably, we find only viral transcripts that resemble gene expression during various stages of lytic infection with no evidence of any highly restricted latency-associated viral gene expression program. To further define the transcriptional landscape during HCMV latent infection, we also used single-cell RNA-seq and a tractable experimental latency model. In contrast to some current views on latency, we also find no evidence for any highly restricted latency-associated viral gene expression program. Instead, we reveal that latency-associated gene expression largely mirrors a late lytic viral program, albeit at much lower levels of expression. Overall, our work has the potential to revolutionize our understanding of HCMV persistence and suggests that latency is governed mainly by quantitative changes, with a limited number of qualitative changes, in viral gene expression.IMPORTANCE Human cytomegalovirus is a prevalent pathogen, infecting most of the population worldwide and establishing lifelong latency in its hosts. Although reactivation from latency causes significant morbidity and mortality in immunocompromised hosts, our molecular understanding of the latent state remains limited. Here, we examine the viral gene expression during natural and experimental latent HCMV infection on a transcriptome-wide level. In contrast to the classical views on herpesvirus latency, we find no evidence for a restricted latency-associated viral gene expression program. Instead, we reveal that latency gene expression largely resembles a late lytic viral profile, albeit at much lower levels of expression. Taken together, our data transform the current view of HCMV persistence and suggest that latency is mainly governed by quantitative rather than qualitative changes in viral gene expression.
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Affiliation(s)
- Miri Shnayder
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Aharon Nachshon
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Benjamin Krishna
- Department of Medicine, Addenbrooke's Hospital, University of Cambridge, Cambridge, United Kingdom
| | - Emma Poole
- Department of Medicine, Addenbrooke's Hospital, University of Cambridge, Cambridge, United Kingdom
| | - Alina Boshkov
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Amit Binyamin
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Itay Maza
- Department of Gastroenterology, Rambam Health Care Campus and Bruce Rappaport School of Medicine, Technion, Institute of Technology, Haifa, Israel
| | - John Sinclair
- Department of Medicine, Addenbrooke's Hospital, University of Cambridge, Cambridge, United Kingdom
| | - Michal Schwartz
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Noam Stern-Ginossar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
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Ren Y, Choi E, Zhang K, Chen Y, Ye S, Deng X, Zhang K, Bao X. Detection of Nuclear Protein Profile Changes by Human Metapneumovirus M2-2 Protein Using Quantitative Differential Proteomics. Vaccines (Basel) 2017; 5:vaccines5040045. [PMID: 29207503 PMCID: PMC5748611 DOI: 10.3390/vaccines5040045] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 11/14/2017] [Accepted: 11/29/2017] [Indexed: 01/28/2023] Open
Abstract
Human metapneumovirus (hMPV) is a leading cause of lower respiratory infection in pediatric populations globally. This study examined proteomic profile changes in A549 cells infected with hMPV and two attenuated mutants with deleted PDZ domain-binding motif(s) in the M2-2 protein. These motifs are involved in the interruption of antiviral signaling, namely the interaction between the TNF receptor associated factor (TRAF) and mitochondrial antiviral-signaling (MAVS) proteins. The aim of this study was to provide insight into the overall and novel impact of M2-2 motifs on cellular responses via an unbiased comparison. Tandem mass tagging, stable isotope labeling, and high-resolution mass spectrometry were used for quantitative proteomic analysis. Using quantitative proteomics and Venn analysis, 1248 common proteins were detected in all infected samples of both technical sets. Hierarchical clustering of the differentiated proteome displayed distinct proteomic signatures that were controlled by the motif(s). Bioinformatics and experimental analysis confirmed the differentiated proteomes, revealed novel cellular biological events, and implicated key pathways controlled by hMPV M2-2 PDZ domain-binding motif(s). This provides further insight for evaluating M2-2 mutants as potent vaccine candidates.
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Affiliation(s)
- Yuping Ren
- Department of Pediatrics, University of Texas Medical Branch, Galveston, TX 77555, USA.
- Department of Plastic Surgery, TongJi Hospital, TongJi Medical College, Huazhong University of Science and Technology, Wuhan 430073, China.
| | - Eunjin Choi
- Department of Pediatrics, University of Texas Medical Branch, Galveston, TX 77555, USA.
| | - Ke Zhang
- Department of Biochemistry, Baylor University, Waco, TX 76706, USA.
| | - Yu Chen
- Department of Pediatrics, University of Texas Medical Branch, Galveston, TX 77555, USA.
- Department of Pediatrics, TongJi Hospital, TongJi Medical College, Huazhong University of Science and Technology, Wuhan 430073, China.
| | - Sha Ye
- Department of Pediatrics, University of Texas Medical Branch, Galveston, TX 77555, USA.
- Department of Gynecologic Oncology Ward V, Hunan Cancer Hospital, Xiangya School of Medicine, Central South University, Changsha 410008, China.
| | - Xiaoling Deng
- Department of Pediatrics, University of Texas Medical Branch, Galveston, TX 77555, USA.
| | - Kangling Zhang
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77555, USA.
| | - Xiaoyong Bao
- Department of Pediatrics, University of Texas Medical Branch, Galveston, TX 77555, USA.
- Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, TX 77555, USA.
- The Institute of Translational Science, University of Texas Medical Branch, Galveston, TX 77555, USA.
- The Institute for Human Infections & Immunity, University of Texas Medical Branch, Galveston, TX 77555, USA.
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