Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

173 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The Epstein-Barr virus induced tumor suppressor miR-34a is growth promoting in EBV-infected B cells

ABSTRACT: Epstein-Barr virus (EBV) infection of primary human B cells drives their indefinite proliferation into lymphoblastoid cell lines (LCLs). B cell immortalization depends on expression of viral latency genes as well as the regulation of host genes. Given the important role of miRNAs in regulating fundamental cellular processes, in this study we assayed changes in host miRNA expression during primary B cell infection by EBV. We observed and validated dynamic changes in several miRNAs from early proliferation through immortalization; oncogenic miRNAs were induced and tumor suppressor miRNAs were largely repressed. However, one miRNA described as a p53-targeted tumor suppressor, miR-34a, was strongly induced by EBV infection and expressed in many EBV and KSHV-infected lymphoma cell lines. The EBV latent membrane protein 1 (LMP1) was sufficient to induce miR-34a requiring downstream NFM-NM-:B activation, but independent of functional p53. Furthermore, over-expression of miR-34a was not toxic in several B lymphoma cell lines and inhibition of miR-34a impaired the growth of EBV transformed cells. This study identifies a pro-growth role for a tumor suppressive miRNA in oncogenic virus-mediated transformation highlighting the importance of studying miRNA function in different cellular contexts. miRNA expression profiling of human B-cells, EBV-infected, proliferating B cells and Monoclonal LCLs from 3 different donors was conducted with the use of up to 2 M-NM-

ORGANISM(S): Homo sapiens

SUBMITTER: Dereje Jima

PROVIDER: E-GEOD-36926 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

The viral and cellular microRNA targetome in lymphoblastoid cell lines

Project description:Epstein-Barr virus (EBV) is a human herpesvirus linked to a number of B cell cancers and lymphoproliferative disorders. During latent infection, EBV expresses 25 viral pre-microRNAs (miRNAs) and induces the expression of specific host miRNAs, such as miR-155 and miR-21, which potentially play a role in viral oncogenesis. To date, a limited number of EBV miRNA targets have been identified; thus, the role of EBV miRNAs in viral pathogenesis is not well defined. Here, we used photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation (PAR-CLIP) combined with deep sequencing and computational analysis to comprehensively examine the viral and cellular miRNA targetome in EBV B95-8-infected lymphoblastoid cell lines (LCLs). We identified 7,827 miRNA-interaction sites in 3,492 cellular 3'UTRs. 531 of these sites contained seed-matches to viral miRNAs. 24 PAR-CLIP-identified miRNA:3'UTR interactions were confirmed by reporter assays. Our results reveal that EBV miRNAs predominantly target cellular transcripts during latent infection, thereby manipulating the host environment. Furthermore, targets of EBV miRNAs are involved in multiple cellular processes that are directly relevant to viral infection, including innate immunity, cell survival, and cell proliferation. Finally, we present evidence that myc-regulated host miRNAs from the miR-17/92 cluster can regulate latent viral gene expression. This comprehensive survey of the miRNA targetome in EBV-infected B cells represents a key step towards defining the functions of EBV-encoded miRNAs, and potentially, identifying novel therapeutic targets for EBVassociated malignancies. Ago2 (Argonaute 2) PAR-CLIP and small RNA deep sequencing of Epstein-Barr virus B95.8-infected lymphoblastoid cell lines (LCLs).

2012-10-16 | E-GEOD-41437 | biostudies-arrayexpress

Identification of SART3 as a pre-miR-34a–binding protein

Project description:MicroRNAs (miRNAs or miRs) are small, noncoding RNAs that are implicated in the regulation of nearly all biological processes. Global miRNA biogenesis is altered in many cancers and RNA-binding proteins (RBPs) have been shown to play a role in this process, presenting a promising avenue for targeting miRNA dysregulation in disease. miR-34a exhibits tumor-suppressive functions by targeting cell cycle regulators CDK4/6 and anti-apoptotic factor Bcl-2, among other regulatory pathways such as Wnt, TGF-, and Notch signaling. Many cancers show downregulation or loss of miR-34a, and synthetic miR-34a supplementation has been shown to inhibit tumor growth in vivo; however, the post-transcriptional mechanisms by which miR-34a is lost in cancer are not entirely understood. Here, we have used a proteomics-mediated approach to identify Squamous cell carcinoma antigen recognized by T-cells 3 (SART3) as a putative pre-miR-34a-binding protein. SART3 is a spliceosome recycling factor and nuclear RBP with no previously reported role in miRNA regulation. We demonstrate that SART3 binds pre-miR-34a with specificity over pre-let-7d and begin to elucidate a new functional role for this protein in non-small lung cancer cells. Overexpression of SART3 led to increased miR-34a levels, downregulation of the miR-34a target genes CDK4 and CDK6, and cell cycle arrest in the G1 phase. In vitro binding studies showed that the RNA-recognition motifs within the SART3 sequence are responsible for selective pre-miR-34a binding. Collectively, our results present evidence for an influential role of SART3 in miR-34a biogenesis and cell cycle progression.

2019-10-14 | PXD015278 | Pride

The Epstein-Barr virus induced tumor suppressor miR-34a is growth promoting in EBV-infected B cells

Project description:Epstein-Barr virus (EBV) infection of primary human B cells drives their indefinite proliferation into lymphoblastoid cell lines (LCLs). B cell immortalization depends on expression of viral latency genes as well as the regulation of host genes. Given the important role of miRNAs in regulating fundamental cellular processes, in this study we assayed changes in host miRNA expression during primary B cell infection by EBV. We observed and validated dynamic changes in several miRNAs from early proliferation through immortalization; oncogenic miRNAs were induced and tumor suppressor miRNAs were largely repressed. However, one miRNA described as a p53-targeted tumor suppressor, miR-34a, was strongly induced by EBV infection and expressed in many EBV and KSHV-infected lymphoma cell lines. The EBV latent membrane protein 1 (LMP1) was sufficient to induce miR-34a requiring downstream NFκB activation, but independent of functional p53. Furthermore, over-expression of miR-34a was not toxic in several B lymphoma cell lines and inhibition of miR-34a impaired the growth of EBV transformed cells. This study identifies a pro-growth role for a tumor suppressive miRNA in oncogenic virus-mediated transformation highlighting the importance of studying miRNA function in different cellular contexts.

2012-04-20 | GSE36926 | GEO

Mapping effective microRNA pairing beyond the seed using abasic modifications

Project description:MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression by base-pairing to complementary sites in mRNAs. The primary element for site recognition is the seed region (nucleotides 2-8 in the miRNA), but for a minority of sites pairing outside the seed increases efficiency, with the supplementary region (nucleotides 13-16) typically having the greatest impact. However, the structural determinants of effective pairing outside the seed are not fully understood. Here, we use abasic modified nucleotides to disrupt pairing to residues 13 and 14 of miR-34a and measure the effect of this modification compared to wild-type miR-34a on the cellular transcriptome and proteome using RNA-seq and mass spectrometry. We find that a subset of sites with predicted supplementary pairing are affected by miRNA transfection, with up to two-fold decreases in site repression at the mRNA level, although the effect at the protein level is less pronounced. Overall, this study demonstrates a novel methodological approach for elucidating the role of specific miRNA residues in target site selection, advancing our understanding of miRNA-mediated gene regulation.

2025-05-07 | PXD059550 | Pride

Metabolic stress is a barrier to Epstein-Barr virus mediated B-cell immortalization

Project description:Early after infection, Epstein-Barr Virus (EBV) induces a transient period of hyper-proliferation that is suppressed by the activation of the DNA damage response and a G1/S phase growth arrest. This growth arrest prevents long-term outgrowth of the majority of infected cells. We developed a method to isolate and characterize infected cells that arrest after this early burst of proliferation. We used microarray analysis to uncover changes in gene expression that could give us a better understanding of the pathways that attenuate immortalization. Human PBMCs were labeled with CellTrace Violet and infected with the B95-8 strain of EBV. At 4 days post-infection, the cells were labeled with a second proliferation dye, CFSE. Cells that proliferated are called PP and those that initially proliferated and then arrested are called PA. Total mRNA was isolated from sorted PA and PP cells using an RNeasy kit . The RNA was processed using an Ambion MessageAmp Premier Package and hybridized to a Human Genome U133 Plus. 2.0 Chip by the Duke Center for Genomic and Computational Biology Microarray Core. The resultant CEL files were RMA normalized (Partek) and the data was analyzed with GenePattern and GSEA v2.

2015-12-19 | E-GEOD-76137 | biostudies-arrayexpress

Epstein-Barr virus growth/latency III program alters cellular microRNA expression

Project description:The Epstein-Barr virus (EBV) is associated with lymphoid and epithelial cancers. Initial EBV infection alters lymphocyte gene expression, inducing cellular proliferation and differentiation as the virus transitions through consecutive latency transcription programs. Cellular microRNAs (miRNAs) are important regulators of signaling pathways and are implicated in carcinogenesis. The extent to which EBV exploits cellular miRNAs is unknown. Using micro-array analysis and quantitative PCR, we demonstrate differential expression of cellular miRNAs in type III versus type I EBV latency including elevated expression of miR-21, miR-23a, miR-24, miR-27a, miR-34a, miR-146a and b, and miR-155. In contrast, miR-28 expression was found to be lower in type III latency. The EBV-mediated regulation of cellular miRNAs may contribute to EBV signaling and associated cancers.

2008-10-07 | GSE13056 | GEO

Impact of miRNAs on the USSC proteome after XXL-differentiation

Project description:The contribution of microRNA-mediated posttranscriptional regulation on the final proteome in differentiating cells remains elusive. Here, we evaluated the impact of microRNAs (miRNAs) on the proteome of human umbilical cord blood-derived unrestricted somatic stem cells (USSC) during retinoic acid (RA) differentiation by a systemic approach using next generation sequencing analysing mRNA and miRNA expression and quantitative mass spectrometry-based proteome analyses. Interestingly, regulation of mRNAs and their dedicated proteins highly correlated during RA-incubation. Additionally, RA-induced USSC demonstrated a clear separation from native USSC thereby shifting from a proliferating to a metabolic phenotype. Bioinformatic integration of up- and downregulated miRNAs and proteins initially implied a strong impact of the miRNome on the XXL-USSC proteome. However, quantitative proteome analysis of the miRNA contribution on the final proteome after ectopic overexpression of downregulated miR-27a-5p and miR-221-5p or inhibition of upregulated miR-34a-5p, respectively, followed by RA-induction revealed only minor proportions of differentially abundant proteins. In addition, only small overlaps of these regulated proteins with inversely abundant proteins in non-transfected RA-treated USSC were observed. Hence, mRNA transcription rather than miRNA-mediated regulation is the driving force for protein regulation upon RA-incubation, strongly suggesting that miRNAs are fine-tuning regulators rather than active primary switches during RA-induction of USSC.

2020-01-31 | PXD016915 | Pride

Identification of novel Epstein-Barr Virus miRNA genes from Nasopharyngeal Carcinomas

Project description:MicroRNAs (miRNAs) represent a conserved class of small non-coding RNAs that are found in all higher eukaryotes as well as some DNA viruses. MiRNAs are 20-25 nucleotides (nt) in length and have important regulatory functions in biological processes such as embryonic development, cell differentiation, hormone secretion or metabolism. Furthermore, miRNAs have been implicated in the pathology of various diseases including cancer. MiRNA expression profiles not only classify different types of cancer but also may even help to characterize distinct tumor stages, therefore constituting a valuable tool for prognosis. Here we report the miRNA profile of Epstein-Barr Virus (EBV)-positive nasopharyngeal carcinoma (NPC) tissue samples characterized by cloning and sequencing. We find that all EBV miRNAs from the BART region are expressed in NPC tissues whereas ebv-miRNAs from the BHRF1 region are not found. Moreover, we identify two novel EBV miRNA genes originating from the BART region that have not been found in other tissues or cell lines before. We also identify three new human miRNAs, which might be specific for nasopharyngeal tissues. We further show that a number of different cellular miRNAs are upor down-regulated in NPC tissues compared to control tissue including miR-15a and miR-16. We find that the tumor suppressor BRCA-1 is a target of miR-15a as well as miR-16 suggesting a miRNA role in NPC pathogenesis. 2 pairs of NPC and control tissues from 2 patients (4 samples in total) were examined.

2009-02-07 | E-GEOD-14738 | biostudies-arrayexpress

NCI-H1299 lung cancer cell line transfected with miR-34a and ghR-34a

Project description:Analysis NCI-H1299 lung cancer cells transfected with synthetic oligo mimics for microRNAs (miRNAs) miR-34a and ghR-34a. We developed a 30-nucleotide single-strand RNA (ssRNA), termed “guide hairpin RNA (ghR),” that has a physiological function similar to that of miRNA and siRNA. The ghR caused no innate cytokine response either in vitro or in vivo. In addition, its structure does not contain a passenger strand seed sequence, reducing the potential for off-target effects relative to existing short RNA reagents. Systemic injection of ghR-form miR-34a (ghR-34a) suppressed tumor growth in a mouse model of RAS-induced lung cancer. Furthermore, ghR-34a functioned in a Dicer- and Ago2-independent manner. This novel RNAi technology may provide a novel, safe, and effective nucleic acid drug platform that will increase the clinical usefulness of nucleic acid therapy. MiR-34a–targeted mRNAs regulated by mRNA degradation rather than translational inhibition were identified using microarray data from miR-34 and ghR-34a transfectants.

2015-07-29 | E-GEOD-71423 | biostudies-arrayexpress

EBV BART MicroRNAs Target Multiple Pro-apoptotic Cellular Genes to Promote Epithelial Cell Survival

Project description:Here, we report a systematic effort to identify pro-apoptotic mRNA targets for the EBV miR-BART miRNAs. We demonstrate that at least five of the 22 miR-BART pre-miRNAs have anti-apoptotic activity and we identify seven pro-apoptotic cellular mRNA targets, six of them novel, that contribute significantly to the observed anti-apoptotic phenotype. Together, these data represent a substantial increase in our understanding of the role of the miR-BART miRNAs in promoting EBV infection and latency. Use of deep sequencing to identify all the miRNAs expressed in C666 cells and PAR-CLIP to comprehensively profile EBV miRNA targets in C666 cells.

2015-06-16 | E-GEOD-67990 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data