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RNA Sequencing Reveals that Kaposi Sarcoma-Associated Herpesvirus Infection Mimics Hypoxia Gene Expression Signature

ABSTRACT: RNA Sequencing Reveals that Kaposi Sarcoma-Associated Herpesvirus Infection Mimics Hypoxia Gene Expression Signature

OTHER RELATED OMICS DATASETS IN: GSE79032GSE79030

PROVIDER: PRJNA314763 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR3213400_1.fastq.gz	Fastqsanger.gz
	SRR3213400_2.fastq.gz	Fastqsanger.gz
	SRR3213401_1.fastq.gz	Fastqsanger.gz
	SRR3213401_2.fastq.gz	Fastqsanger.gz
	SRR3213402_1.fastq.gz	Fastqsanger.gz

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Transcription profiling of human lymphatic endothelial cells response to Kaposi-sarcoma herpesvirus

Project description:Assessment of the effect of Kaposi-sarcoma herpesvirus upon the transcriptome of lymphatic endothelial cells and its contribution to the transcriptome of Kaposi sarcoma.

2006-10-23 | E-MEXP-561 | biostudies-arrayexpress

Immunization of mice with virus-like vesicles of Kaposi sarcoma-associated herpesvirus reveals a role of ORF4 in complement-mediated neutralization

Project description:The development of a prophylactic vaccine for Kaposi sarcoma-associated Herpesvirus (KSHV) would prevent consequences from infection including disorders such as Kaposi sarcoma and primary effusion lymphoma. Here, we study the immunogenicity of noninfectious virus-like vesicles (VLVs) of KSHV as a potential future vaccine platform. VLVs present a repertoire of viral structural proteins but are noninfectious due to a defect in capsid formation that prevents viral DNA packaging. Immunization of mice with adjuvanted VLVs results in virus-specific antibodies and T cells. These antibodies neutralize viral infection, and this neutralization is enhanced by the complement system. Complement-enhanced neutralization is dependent on antibodies targeting the SCR region of viral ORF4. However, this activity was not present in serum from KSHV-infected humans. Our study highlights an important role of antibody effector functions in the development of a future KSHV vaccine

2023-02-01 | PXD035478 | Pride

RNA Sequencing Reveals that Kaposi Sarcoma-Associated Herpesvirus Infection Mimics Hypoxia Gene Expression Signature.

Project description:Kaposi sarcoma-associated herpesvirus (KSHV) causes several tumors and hyperproliferative disorders. Hypoxia and hypoxia-inducible factors (HIFs) activate latent and lytic KSHV genes, and several KSHV proteins increase the cellular levels of HIF. Here, we used RNA sequencing, qRT-PCR, Taqman assays, and pathway analysis to explore the miRNA and mRNA response of uninfected and KSHV-infected cells to hypoxia, to compare this with the genetic changes seen in chronic latent KSHV infection, and to explore the degree to which hypoxia and KSHV infection interact in modulating mRNA and miRNA expression. We found that the gene expression signatures for KSHV infection and hypoxia have a 34% overlap. Moreover, there were considerable similarities between the genes up-regulated by hypoxia in uninfected (SLK) and in KSHV-infected (SLKK) cells. hsa-miR-210, a HIF-target known to have pro-angiogenic and anti-apoptotic properties, was significantly up-regulated by both KSHV infection and hypoxia using Taqman assays. Interestingly, expression of KSHV-encoded miRNAs was not affected by hypoxia. These results demonstrate that KSHV harnesses a part of the hypoxic cellular response and that a substantial portion of hypoxia-induced changes in cellular gene expression are induced by KSHV infection. Therefore, targeting hypoxic pathways may be a useful way to develop therapeutic strategies for KSHV-related diseases.

| S-EPMC5234848 | biostudies-literature

An Updated overview of the Virion Proteome of Kaposi Sarcoma Associated Herpesvirus

Project description:The virion proteins of Kaposi Sarcoma Associated Herpesvirus (KSHV) were initially characterized in 2005 in two separate studies that combined detected 24 viral proteins and a few cellular components via LC-MS/MS or MALDI-TOF. Despite considerable advances in the sensitivity and specificity of mass spectrometry instrumentation in recent years, leading to significantly higher yields in detections, the KSHV virion proteome has not been revisited. In this study, we have re-examined the protein composition of purified KSHV virions via Ultra-High Resolution Qq-Time-Of-Flight mass spectrometry (UHR-QqTOF). Our results confirm the detection of all previously reported virion proteins, in addition to 17 other viral proteins, some of which have been characterized as virion-associated using other methods, and 10 novel proteins identified as virion-associated for the first time in this study. These results add KSHV ORF9, ORF23, ORF35, ORF48, ORF58, ORF72/vCyclin, K3, K9/vIRF1, K10/vIRF4, and K10.5/vIRF3 to the list of KSHV proteins that can be incorporated into virions. The addition of these proteins to the KSHV virion proteome provides novel and important insight into early events in KSHV infection mediated by virion-associated proteins.

2020-12-10 | PXD022626 | Pride

Kaposi’s Sarcoma-associated Herpesvirus Reactivation by Bacteria Promotes the Hypoxia Response and Epigenetic Regulation

Project description:Herpesviruses are frequently co-present with bacterial infection at multiple sites within the body, including the mouth, gut, and genitourinary tract. The detection of replicating virus in these compartments prompted investigation into the relationship between bacterial infection and Kaposi’s Sarcoma-associated Herpesvirus (KSHV) reactivation. Using a cell line latently infected with KSHV, we examined the ability of crude spent media containing metabolic products from periodontal and gut pathogens to reactivate KSHV. Upon incubation with crude spent media, KSHV was reactivated and we detected the up-regulation of viral early and late genes, linear viral genomes, and virions. Furthermore, KSHV reactivation was associated with global increases in histone H3 and histone H4 acetylation, consistent with viral expression. To explore the transcriptional consequences of spent media, we compared the gene expression changes following reactivation by P. gingivalis spent medium to those of two well-established pharmacological activators of KSHV reactivation, tetradecanolyl phorbol acetate and sodium butyrate. Microarray analyses revealed a unique gene expression signature with P. gingivalis-associated reactivation. Concurrent with KSHV reactivation, P. gingivalis spent medium increased the hypoxia response. Hypoxia was associated with effects on epigenetic regulators, including down-regulation of UHRF1, a modulator of DNA methylation. Our findings demonstrate that products secreted by oral bacteria not only stimulate a hypoxia response, but also result in global changes in epigenetic modifications and modifiers. These findings suggest that epigenetic changes induced by P. gingivalis underlie the KSHV reactivation pathway.

2018-03-20 | GSE67532 | GEO

Epigenetic reprogramming of Kaposi’s sarcoma-associated herpesvirus during hypoxic reactivation

Project description:Chromatin Immuno-precipitaion sequencing was performed using H3-Ac, H3K4Me3, H3K9Me3, H3K27Me3, LANA, RTA and DNA Polymerase 1 alpha antibodies to investigate its enrichment on Kaposi's sarcoma associated herpesvirus (KSHV) genome in BC3 cells under normoxic or hypoxic conditions

2022-08-15 | GSE202670 | GEO

RNA Sequencing Reveals that Kaposi Sarcoma-Associated Herpesvirus Infection Mimics Hypoxia Gene Expression Signature

Project description:This SuperSeries is composed of the SubSeries listed below.

2016-12-21 | GSE79032 | GEO

Hypoxia and Intrinsic Transcriptomic Subtyping of Soft Tissue Sarcoma

Project description:The heterogeneity and multiple histological categories of soft tissue sarcoma (STS) underlie a need for better classification schemes to improve their management. As none are currently available, we aimed to derive hypoxia and intrinsic molecular subtype mRNA abundance signatures for localized soft tissue sarcoma. RNA sequencing was used to identify genes induced by hypoxia in seven STS cell lines.

2017-11-17 | E-MTAB-6087 | biostudies-arrayexpress

Deregulation of lncRNAs by Kaposi's sarcoma-associated herpesvirus

Project description:Deregulation of host lncRNAs following infection with Kaposi’s sarcoma-associated herpesvirus (KSHV) was assessed. Total RNA was prepared from uninfected TIVE cells (telomerase-immortalized vein endothelial cells), and from TIVE cells latently infected with either wild-type KSHV or with a deletion mutant (Δcluster-KSHV) lacking ten of the twelve KSHV microRNA genes. The RNA was converted to labeled cRNA and used to probe a human lncRNA microarray. The goal was to investigate which host lncRNAs were either up- or down-regulated during latent infection with KSHV, and to determine if deregulation of host lncRNAs was dependent on KSHV miRNAs.

2017-07-12 | GSE89114 | GEO

Hypoxia and Hypoxia mimics

Project description:Comparison between hypoxia (1%O2) and cobalt chloride (100 uM) and deferoxamine (100 uM) and Nickel Chloride (100 uM) in Hep3B cells (human hepatocellular carcinoma cells) Keywords = Hep3B Keywords = hypoxia Keywords = cobalt Keywords = deferoxamine Keywords = Nickel Keywords: ordered

2004-02-27 | GSE1056 | GEO

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