The Smc5/6 Complex Restricts HBV when Localized to ND10 without Inducing an Innate Immune Response and is Counteracted by the HBV X Protein Shortly after Infection
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE93153 | GEO | 2017/03/01
SECONDARY ACCESSION(S): PRJNA360143
REPOSITORIES: GEO
Similar Datasets
Project description:The structural maintenance of chromosome 5/6 complex (Smc5/6) is a restriction factor that represses hepatitis B virus (HBV) transcription. HBV counters this restriction by expressing HBV X protein (HBx), which targets Smc5/6 for degradation. However, the mechanism by which Smc5/6 suppresses HBV transcription and how HBx is initially expressed is not known. In this study we characterized viral kinetics and the host response during HBV infection of primary human hepatocytes (PHH) to address these unresolved questions. We determined that Smc5/6 localizes with Nuclear Domain 10 (ND10) in PHH. Co-localization has functional implications since depletion of ND10 structural components alters the nuclear distribution of Smc6 and induces HBV gene expression in the absence of HBx. We also found that HBV infection and replication does not induce a prominent global host transcriptional response in PHH, either shortly after infection when Smc5/6 is present, or at later times post-infection when Smc5/6 has been degraded. Notably, HBV and an HBx-negative virus establish high level infection in PHH without inducing expression of interferon-stimulated genes or production of interferons or other cytokines. Our study also revealed that Smc5/6 is degraded in the majority of infected PHH by the time cccDNA transcription could be detected and that HBx RNA is present in cell culture-derived virus preparations as well as HBV patient plasma. Collectively, these data indicate that Smc5/6 is an intrinsic antiviral restriction factor that suppresses HBV transcription when localized to ND10 without inducing a detectable innate immune response. Our data also suggest that HBx protein may be initially expressed by delivery of extracellular HBx RNA into HBV-infected cells.
| S-EPMC5240991 | biostudies-literature
Project description:Hepatitis B virus (HBV) is known for its ability to interact with the host cell DNA methylation machinery. In HBV-infected hepatocytes, this interaction leads to chronic liver diseases, including hepatocellular carcinoma (HCC). We studied the extent of genomic changes induced by natural HBV infection in human primary hepatocytes. Transcriptome and methylome profiles were obtained at different time points post-infection to identify HBV-specific alterations. Although gene expression and DNA methylation do not directly correlate, they both seem to reflect the effect of cell culture and viral infection at different levels.These changes in the hepatocyte cellular program shed light on the initial events leading to HBV-associated liver diseases.
2016-01-01 | GSE72068 | GEO
Project description:Background and Aims: Recent identification of intracellular DNA sensing pathways and involvement in numerous diverse disease processes including viral pathogenesis and autoimmunity suggests a role for these processes in liver pathology. The presence of these pathways in the liver and their role in HBV infection is unknown. Methods: In order to characterize the role of DNA sensing pathways in the liver, we utilized in vitro models. Microarray was performed on DNA treated and HBV infected hepatoma primary human hepatocytes. Results: Here we show that HBV infection and foreign DNA results in a significant innate immune response characterized by the production of inflammatory chemokines. The goal of this study is to characterize the changes in gene expression triggered by HBV and foreign DNA in primary human hepatocytes. PHHs were infected with HBV (MO.I = 50) for 40 hours. PHHs were transfected with 1μg/mL of ISD/dsDNA90 for 12 or 24 hours. Three replicates were performed for each condition.
2016-08-09 | E-GEOD-69590 | biostudies-arrayexpress
Project description:Purpose: The goal of this study is to identify genes and pathways in macrophages that may be altered by hepatocytes with replicating HBV Methods: THP-1 monocytic cells were treated with PMA for differentiation into macrophages (M0). These macrophages were co-cultured for 4 days with HepAD38 cells with (HBV-) or without (HBV+) the treatmetn of tetracycline and then lysed for the isolation of RNA using NEBNext Ultra II RNA Library Prep Kit for Illumina. The polyA+ RNA-seq was conducted in triplicate, and about 30 million sequence reads per sample that passed quality filters were analyzed by Partek Flow. The qRT–PCR validation of the results was performed using SYBR Green assays. M0 macrophages without co-culturing with HepAD38 cells were also analyzed to serve as the control (M0). Results: To understand how HBV might affect THP-1 macrophages and how macrophages suppressed HBV replication, we conducted the RNA-seq analysis to determine the gene expression profiles in THP-1 macrophages (Mϕ) without co-culturing with HepAD38 cells (M0), THP-1 macrophages co-cultured with HepAD38 cells in the presence of tetracycline (HBV-), and THP-1 macrophages co-cultured with HepAD38 cells in the absence of tetracycline (HBV+). The analysis of RNA-seq results revealed 3946 differentially expressed genes (DEGs) between Mϕ(HBV+) and Mϕ(M0) cells, 3333 DEGs between Mϕ(HBV-) and Mϕ(M0) cells, and 783 DEGs between Mϕ(HBV+) and Mϕ(HBV-) cells (Figure 2A). The heatmap analysis revealed that Mϕ(HBV+) cells expressed significant higher levels of M1 markers including IL-1β and lower levels of M2 markers than in Mϕ(HBV-) cells (Figure 2B). The induction of IL-1β in Mϕ(HBV+) cells was also highly prominent when the cytokine expression profiles were analyzed by the volcano plot (Figure 2C). This induction of IL-1β was confirmed by RT-qPCR analysis (Figure S2E). These results indicated that THP-1 macrophages co-cultured with cells containing replicating HBV would undergo the M1 polarization. Interestingly, the heat map analysis of top 20 DEGs, based on low false discovery rate and high Log2 fold changes, between Mϕ(HBV+) and Mϕ(HBV-) cells revealed that seven of them were mitochondria-encoded genes that regulate the OXPHOS (Figure 2D). The pathway analysis indicated that the OXPHOS pathway was indeed upregulated in MΦ(HBV+) cells, although some pathways in these cells were also downregulated (e.g., Sirtuin signaling) and some were not affected (e.g., insulin receptor signaling) (Figure 2E). Conclusions: Our study provided the detailed analysis of the response of macrophages to hepatocytes containing replicating HBV. Our results indicated that HBV-could induce the M1 polarization of THP-1-derived macrophage. The induction of CXCL1 expression in macrophages by HBV likely plays an important role in the hepatic infiltration of neutrophils, whih express a high level of CXCR1 , the receptor of CXCL1. Our finding of an increased expression of mitochondria-encoded genes that regulate OXPHOS also suggested that HBV might promote OXPHOS in macrophages.
2022-02-18 | GSE179618 | GEO
Project description:In the HBV transgenic mouse model of chronic infection, the forkhead box protein A/hepatocyte nuclear factor 3 (Foxa/HNF3) family of pioneer transcription factors are required to support postnatal viral demethylation and subsequent HBV transcription and replication. Liver-specific Foxa-deficient mice with hepatic expression of only Foxa3 do not support HBV replication but display biliary epithelial hyperplasia with bridging fibrosis. However, liver-specific Foxa-deficient mice with hepatic expression of only Foxa1 or Foxa2 also successfully restrict viral transcription and replication but display only minimal alterations in liver physiology. These observations suggest that the level of Foxa activity, rather than the combination of specific Foxa genes, is a key determinant of HBV biosynthesis. Together, these findings suggest that targeting Foxa activity could lead to HBV DNA methylation and transcriptional inactivation, resulting in the resolution of chronic HBV infections which are responsible for approximately one million deaths annually worldwide.
2024-07-16 | GSE263120 | GEO
Project description:Several classes of capsid assembly modulators (CAMs) are currently being developed for chronic hepatitis B (CHB) cure. Both class A (CAM-A) and class E (CAM-E) CAMs disrupt nucleocapsid assembly and reduce extracellular hepatitis B virus (HBV) DNA. However, only CAM-As have been shown to reduce the number of HBV-infected cells in the animal models. However, there has been limited efficacy to date of CAM-A molecules achieving this secondary mechanism of HBV-infected cell clearance in CHB clinical trials. To investigate this disconnect, we performed comparative experiments with tool compounds from each class to further explore these unique features and antiviral activity of CAM-A across HBV-infected primary human hepatocytes (PHH), as well as in two different HBV mouse models (immunodeficient mice repopulated with human hepatocytes and AAV-HBV). Mechanistic studies in HBV-infected PHH revealed that CAM-A, but not CAM-E, induced dose-dependent aggregation of HBV core protein (HBc) in the nucleus. Experiments with siRNA, resulted in identification of the ubiquitin-binding protein p62 as a factor negatively regulating the size of these aggregates. Furthermore, we found that only the CAM-A is able to induce HBc-positive cell death in vivo with the loss of HBV-infected cells positively correlated to the levels of intrahepatic HBc. Profiling of intrahepatic HBc levels across CHB patient liver biopsies demonstrated a significantly lower level of HBc per hepatocyte than either of the HBV mouse models. Taken together, these data demonstrate that CAMs of class A have a unique secondary mechanism that has potential to specifically affect viability of HBV-infected hepatocytes. At the same time, the clearance of infected hepatocytes may depend on the level of HBc expression thereby limiting the therapeutic potential for this class of molecules.
2024-05-21 | GSE260966 | GEO
Project description:In hepatocyte nuclei, hepatitis B virus (HBV) genomes occur episomally as covalently closed circular DNA (cccDNA). The HBV X protein (HBx) is required to initiate and maintain HBV replication and acts as host gene trans-regulator. However, functionally relevant spatiotemporal localization and interactions of cccDNA and HBx remain to be understood. This is the first study utilizing circularized chromosome conformation capture (4C) to identify regional virus-host genome interactions. We combined 4C with RNA-seq and ChIP-seq to illuminate the nuclear landscape associated with HBV episomes and HBx. Moreover, we functionally studied HBx-binding to episomal HBV DNA. In human HBV-positive HepaRG hepatocytes, 4C and ChIP revealed specific nuclear localization of HBV episomes and HBx associated with actively transcribed nuclear domains correlating well in size with constrained topological units built up by chromatin fibre loops, which are believed to constitute fundamental cell nuclear architectural units. Interestingly, HBx alone occupied transcribed chromatin domains, and its binding to HBV episomes depended on its C-terminus in vitro. In conclusion, HBx and HBV DNA similarly follow higher-order nuclear assembly patterns, specifically favoring transcriptionally active nuclear compartments. These novel observations may shed light on important unsolved problems: to understand the long-term episomal stability and the facilitation of viral persistence.
2018-04-30 | GSE100400 | GEO
Project description:Background and Aims: Recent identification of intracellular DNA sensing pathways and involvement in numerous diverse disease processes including viral pathogenesis and autoimmunity suggests a role for these processes in liver pathology. The presence of these pathways in the liver and their role in HBV infection is unknown. Methods: In order to characterize the role of DNA sensing pathways in the liver, we utilized in vitro models. Microarray was performed on DNA treated and HBV infected hepatoma primary human hepatocytes. Results: Here we show that HBV infection and foreign DNA results in a significant innate immune response characterized by the production of inflammatory chemokines. The goal of this study is to characterize the changes in gene expression triggered by HBV and foreign DNA in primary human hepatocytes.
2016-08-09 | GSE69590 | GEO
Project description:In the HBV transgenic mouse model of chronic infection, the forkhead box protein A/hepatocyte nuclear factor 3 (Foxa/HNF3) family of pioneer transcription factors are required to support postnatal viral demethylation and subsequent HBV transcription and replication. Liver-specific Foxa-deficient mice with hepatic expression of only Foxa3 do not support HBV replication but display biliary epithelial hyperplasia with bridging fibrosis. However, liver-specific Foxa-deficient mice with hepatic expression of only Foxa1 or Foxa2 also successfully restrict viral transcription and replication but display only minimal alterations in liver physiology. These observations suggest that the level of Foxa activity, rather than the combination of specific Foxa genes, is a key determinant of HBV biosynthesis. Together, these findings suggest that targeting Foxa activity could lead to HBV DNA methylation and transcriptional inactivation, resulting in the resolution of chronic HBV infections which are responsible for approximately one million deaths annually worldwide.
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2017-03-29 | MSV000080794 | MassIVE