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Open accessJournal ArticleDOI: 10.1073/PNAS.2023025118

Bromodomain proteins regulate human cytomegalovirus latency and reactivation allowing epigenetic therapeutic intervention

02 Mar 2021-Proceedings of the National Academy of Sciences of the United States of America (National Academy of Sciences)-Vol. 118, Iss: 9
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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Topics: Human cytomegalovirus (56%), Transplantation (50%)
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6 results found


Open accessJournal ArticleDOI: 10.3390/V13050817
01 May 2021-Viruses
Abstract: Human cytomegalovirus (HCMV) is a ubiquitous human herpesvirus. In healthy people, primary infection is generally asymptomatic, and the virus can go on to establish lifelong latency in cells of the myeloid lineage. However, HCMV often causes severe disease in the immunosuppressed: transplant recipients and people living with AIDS, and also in the immunonaive foetus. At present, there are several antiviral drugs licensed to control HCMV disease. However, these are all faced with problems of poor bioavailability, toxicity and rapidly emerging viral resistance. Furthermore, none of them are capable of fully clearing the virus from the host, as they do not target latent infection. Consequently, reactivation from latency is a significant source of disease, and there remains an unmet need for treatments that also target latent infection. This review briefly summarises the most common HCMV antivirals used in clinic at present and discusses current research into targeting the latent HCMV reservoir.

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Topics: Human cytomegalovirus (56.99%)

2 Citations


Open accessJournal ArticleDOI: 10.3389/FIMMU.2021.657945
Abstract: Human cytomegalovirus (HCMV) infection is not cleared by the initial immune response but persists for the lifetime of the host, in part due to its ability to establish a latent infection in cells of the myeloid lineage. HCMV has been shown to manipulate the secretion of cellular proteins during both lytic and latent infection; with changes caused by latent infection mainly investigated in CD34+ progenitor cells. Whilst CD34+ cells are generally bone marrow resident, their derivative CD14+ monocytes migrate to the periphery where they briefly circulate until extravasation into tissue sites. We have analyzed the effect of HCMV latent infection on the secretome of CD14+ monocytes, identifying an upregulation of both CCL8 and CXCL10 chemokines in the CD14+ latency-associated secretome. Unlike CD34+ cells, the CD14+ latency-associated secretome did not induce migration of resting immune cell subsets but did induce migration of activated NK and T cells expressing CXCR3 in a CXCL10 dependent manner. As reported in CD34+ latent infection, the CD14+ latency-associated secretome also suppressed the anti-viral activity of stimulated CD4+ T cells. Surprisingly, however, co-culture of activated autologous CD4+ T cells with latently infected monocytes resulted in reactivation of HCMV at levels comparable to those observed using M-CSF and IL-1β cytokines. We propose that these events represent a potential strategy to enable HCMV reactivation and local dissemination of the virus at peripheral tissue sites.

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Topics: Chemokine (54%), CXCL10 (54%), Human cytomegalovirus (54%) ... show more

1 Citations


Open accessPosted ContentDOI: 10.1101/2021.06.23.449602
Bergstedt J1, Azzou Sak2, Tsuo K2, Jaquaniello A2  +9 moreInstitutions (3)
24 Jun 2021-bioRxiv
Abstract: Epigenetic changes are required for normal development and health, and can also underlie disease states; yet, the nature and respective contribution of factors that drive epigenetic variation in humans remain to be fully characterized. Here, we assessed how the blood DNA methylome of 958 adults is affected by genetic variation, aging, sex and 139 diverse environmental exposures, and investigated whether these effects are direct or mediated by changes in cellular composition, measured by deep immunophenotyping. We show that cellular heterogeneity and DNA sequence variation are the strongest predictors of DNA methylation levels. We identify latent cytomegalovirus infection as a major driver of DNA methylation variation and delineate three distinct effects of aging on DNA methylation, including increased dispersion consistent with epigenetic drift. Our rich dataset provides a unique resource for the design and interpretation of epigenetic studies and highlight critical factors in medical epigenomics studies.

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Topics: Epigenomics (64%), DNA methylation (61%), Epigenetics (59%)

1 Citations


Open accessPosted ContentDOI: 10.1101/2021.06.04.21256785
Altaf M1, Irfan Ma2, Naheed N, Nm A3Institutions (3)
04 Jun 2021-medRxiv
Abstract: Background Deficiencies in CMV-specific T cell immunity pre-transplant increase patient risk of CMV reactivation and disease post-transplantation. The aim of this study was to investigate and compare CMV-specific cellular immunity in healthy virus carriers and lung transplant candidates pre-transplant to identify key immune mediators associated with functional defects in CMV-specific T cells. Methods A prospective cohort study of 43 adult lung transplant candidates and 14 healthy virus carriers was conducted in Brisbane, Australia. Intracellular cytokine staining and immune phenotyping (by multiparametric flow cytometry) were performed to explore phenotypic and functional characteristics of CMV-specific T cells. Results In this study, 60% of lung transplant candidates were CMV-seropositive pre-transplant. The numbers of CMV-specific T cells in the periphery were comparable between CMV-seropositive lung transplant candidates and healthy virus carriers. Effector molecule (CD107a, IFN-γ, TNF-α, and IL-2) expression on CMV-specific CD8+ and CD4+ T cells was significantly higher in CMV-seropositive lung transplant candidates compared to healthy virus carriers. However, expression of key T cell function mediators (CD11a, CD29, CD49f, and Granzyme B) was significantly higher in CMV-seropositive lung transplant candidates compared to healthy virus carriers. Conversely, expression levels of CD49d, CD103, and Eomes on T cells and CMV-specific T cells were significantly lower in CMV-seropositive lung transplant candidates compared to healthy virus carriers. Conclusions The findings from this study reveal significant phenotypic differences between healthy virus carriers and lung transplant candidates. Assessment of pre-existing CMV-specific T-cell immunity in lung transplant candidates may help to inform and personalise post-transplant clinical management.

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Topics: T cell (57.99%), Immune system (55%), Cellular immunity (54%) ... show more

Open accessPosted ContentDOI: 10.1101/2021.07.26.453763
26 Jul 2021-bioRxiv
Abstract: Primary infection with Human cytomegalovirus (HCMV) results in a persistent lifelong infection due to its ability to establish latent infection. During productive HCMV infection, viral genes are expressed in a coordinated cascade that is characteristic of all herpesviruses and traditionally relies on the dependencies of viral genes on protein synthesis and viral DNA replication. In contrast, the transcriptional landscape associated with HCMV latency is still disputed and poorly understood. Here, we examine viral transcriptomic dynamics during the establishment of both productive and latent HCMV infections. These temporal measurements reveal that viral gene expression dynamics along productive infection and their dependencies on protein synthesis and viral DNA replication, do not fully align. This illustrates that the regulation of herpesvirus genes does not represent a simple sequential transcriptional cascade and surprisingly many viral genes are regulated by multiple independent modules. Using our improved classification of viral gene expression kinetics in conjunction with transcriptome-wide measurements of the effects of a wide array of chromatin modifiers, we unbiasedly show that a defining characteristic of latent cells is the unique repression of immediate early (IE) genes. In particular, we demonstrate that IE1 (a central IE protein) expression is the principal barrier for achieving a full productive cycle. Altogether, our findings provide an unbiased and elaborate definition of HCMV gene expression in lytic and latent infection states.

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Topics: Lytic cycle (55%), Human cytomegalovirus (55%), Gene (51%) ... show more

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72 results found


Open accessJournal ArticleDOI: 10.1093/NAR/30.1.207
Ron Edgar1, Michael Domrachev1, Alex E. Lash1Institutions (1)
Abstract: The Gene Expression Omnibus (GEO) project was initiated in response to the growing demand for a public repository for high-throughput gene expression data. GEO provides a flexible and open design that facilitates submission, storage and retrieval of heterogeneous data sets from high-throughput gene expression and genomic hybridization experiments. GEO is not intended to replace in house gene expression databases that benefit from coherent data sets, and which are constructed to facilitate a particular analytic method, but rather complement these by acting as a tertiary, central data distribution hub. The three central data entities of GEO are platforms, samples and series, and were designed with gene expression and genomic hybridization experiments in mind. A platform is, essentially, a list of probes that define what set of molecules may be detected. A sample describes the set of molecules that are being probed and references a single platform used to generate its molecular abundance data. A series organizes samples into the meaningful data sets which make up an experiment. The GEO repository is publicly accessible through the World Wide Web at http://www.ncbi.nlm.nih.gov/geo.

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Topics: Hybridization Array (55%)

9,336 Citations


Open accessJournal ArticleDOI: 10.1126/SCIENCE.1247651
14 Feb 2014-Science
Abstract: In multicellular organisms, biological function emerges when heterogeneous cell types form complex organs. Nevertheless, dissection of tissues into mixtures of cellular subpopulations is currently challenging. We introduce an automated massively parallel single-cell RNA sequencing (RNA-seq) approach for analyzing in vivo transcriptional states in thousands of single cells. Combined with unsupervised classification algorithms, this facilitates ab initio cell-type characterization of splenic tissues. Modeling single-cell transcriptional states in dendritic cells and additional hematopoietic cell types uncovers rich cell-type heterogeneity and gene-modules activity in steady state and after pathogen activation. Cellular diversity is thereby approached through inference of variable and dynamic pathway activity rather than a fixed preprogrammed cell-type hierarchy. These data demonstrate single-cell RNA-seq as an effective tool for comprehensive cellular decomposition of complex tissues.

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Topics: Cell type (52%)

1,307 Citations


Open accessJournal ArticleDOI: 10.1038/NATURE10509
27 Oct 2011-Nature
Abstract: Recurrent chromosomal translocations involving the mixed lineage leukaemia (MLL) gene initiate aggressive forms of leukaemia, which are often refractory to conventional therapies1. Many MLL-fusion partners are members of the super elongation complex (SEC), a critical regulator of transcriptional elongation, suggesting that aberrant control of this process has an important role in leukaemia induction2, 3. Here we use a global proteomic strategy to demonstrate that MLL fusions, as part of SEC2, 3 and the polymerase-associated factor complex (PAFc)4, 5, are associated with the BET family of acetyl-lysine recognizing, chromatin ‘adaptor’ proteins. These data provided the basis for therapeutic intervention in MLL-fusion leukaemia, via the displacement of the BET family of proteins from chromatin. We show that a novel small molecule inhibitor of the BET family, GSK1210151A (I-BET151), has profound efficacy against human and murine MLL-fusion leukaemic cell lines, through the induction of early cell cycle arrest and apoptosis. I-BET151 treatment in two human leukaemia cell lines with different MLL fusions alters the expression of a common set of genes whose function may account for these phenotypic changes. The mode of action of I-BET151 is, at least in part, due to the inhibition of transcription at key genes (BCL2, C-MYC and CDK6) through the displacement of BRD3/4, PAFc and SEC components from chromatin. In vivo studies indicate that I-BET151 has significant therapeutic value, providing survival benefit in two distinct mouse models of murine MLL–AF9 and human MLL–AF4 leukaemia. Finally, the efficacy of I-BET151 against human leukaemia stem cells is demonstrated, providing further evidence of its potent therapeutic potential. These findings establish the displacement of BET proteins from chromatin as a promising epigenetic therapy for these aggressive leukaemias.

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Topics: Chromatin (56.99%), BET inhibitor (55%), Chromatin immunoprecipitation (53%) ... show more

1,261 Citations


Open accessJournal ArticleDOI: 10.1084/JEM.20050882
Abstract: Human cytomegalovirus (HCMV) infections of immunocompetent hosts are characterized by a dynamic, life-long interaction in which host immune responses, particularly of T cells, restrain viral replication and prevent disease but do not eliminate the virus or preclude transmission. Because HCMV is among the largest and most complex of known viruses, the T cell resources committed to maintaining this balance have never been characterized completely. Here, using cytokine flow cytometry and 13,687 overlapping 15mer peptides comprising 213 HCMV open reading frames (ORFs), we found that 151 HCMV ORFs were immunogenic for CD4 + and/or CD8 + T cells, and that ORF immunogenicity was influenced only modestly by ORF expression kinetics and function. We further documented that total HCMV-specific T cell responses in seropositive subjects were enormous, comprising on average ∼10% of both the CD4 + and CD8 + memory compartments in blood, whereas cross-reactive recognition of HCMV proteins in seronegative individuals was limited to CD8 + T cells and was rare. These data provide the first glimpse of the total human T cell response to a complex infectious agent and will provide insight into the rules governing immunodominance and cross-reactivity in complex viral infections of humans.

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Topics: T cell (60%), Cytotoxic T cell (59%), Human cytomegalovirus (57.99%) ... show more

1,184 Citations


Open accessJournal ArticleDOI: 10.1126/SCIENCE.1227919
23 Nov 2012-Science
Abstract: The human cytomegalovirus (HCMV) genome was sequenced 20 years ago. However, like those of other complex viruses, our understanding of its protein coding potential is far from complete. We used ribosome profiling and transcript analysis to experimentally define the HCMV translation products and follow their temporal expression. We identified hundreds of previously unidentified open reading frames and confirmed a fraction by means of mass spectrometry. We found that regulated use of alternative transcript start sites plays a broad role in enabling tight temporal control of HCMV protein expression and allowing multiple distinct polypeptides to be generated from a single genomic locus. Our results reveal an unanticipated complexity to the HCMV coding capacity and illustrate the role of regulated changes in transcript start sites in generating this complexity.

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Topics: Ribosome profiling (54%), ORFeome (51%), Human cytomegalovirus (51%) ... show more

508 Citations


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