Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA91523 | ENA |
REPOSITORIES: ENA
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Project description:Latent infection with Epstein-Barr virus (EBV) is recognised as a factor in the pathogenesis of nasopharyngeal carcinoma (NPC). We found that EBV encoded Latent membrane protein 2A (LMP2A) enhances lipid accumulation significantly in NPC cells. We used microarrays to identify differential genes regulated by LMP2A in NPC cell lines.
2018-08-21 | GSE118807 | GEO
Project description:Comprehensive Profiling of Epstein-Barr Virus-Encoded miRNAome Associated with Specific Latent Type in Tumor Cells Epstein-Barr virus (EBV) is an etiological cause of many human lymphocytic and epithelial malignancies. EBV expressed different genes associated with three latent types. So far as many as 44 EBV-encoded miRNA species have been found but their comprehensive and comparative profiling is not well documented in three latent infection states linked to various tumor cells. In this study, we utilized the polyA-tailed quantitative real time RT-PCR procedure to measure the relative abundance of viral miRNA species that linked to individual viral genome locations in combination with microarray evaluation in a subset of representative lymphoid and epithelial tumor cells undergoing various types of EBV latent infection. The results showed that miR-BHRF1 family and miR-BART family are expressed differentially in a tissue-dependent and latency-dependent manner. In particular, in NPC tissue and the only EBV consistently harboring cell line C666-1 with latency type II, there were highly abundant miR-BART family but not miR-BHRF1 family members that accounted for more than 10% of the whole known human miRNA library, implicating their important roles in maintaining EBV latent infection and driving NPC tumorigenesis. In addition, EBV miRNAome-based clustering analysis could classify three distinct EBV latency types, meanwhile, for the first time, we found and subsequently evaluated a novel secret latent switch in BL cell line Daudi from type I to III, which was unable to be identified by traditional latent biomarkers. Together, our data provided an in-depth and comparative profiling of EBV miRNA transcriptome in correspondence with three EBV latent infections, suggesting that different viral miRNA species were involved in divergent host cell carcinogenesis. Finally, EBV miRNAome, as a cluster of novel latency biomarkers expressed variedly in tumor cells, greatly complements and improves the classical typing criteria in conjunction with other latently expressed marker genes. 2 NPC tissue samples and 2 NPC cell lines and 5 lymphocytic cell lines
2012-07-06 | E-GEOD-33225 | biostudies-arrayexpress
Project description:ATAC-seq samples from 2 species and 2 cell types were generated to study cis-regulatory element evolution. Briefly, previously generated urinary stem cell derived iPS-cells (Homo sapiens) of 2 human individuals and fibroblast derived cynomolgus macaque iPSCs (Macaca fascicularis) of 2 individuals (Geuder et al. 2021) were differentiated to neural progenitor cells via dual-SMAD inhibition as three-dimensional aggregation culture (Chambers et al. 2009; Ohnuki et al. 2014). The NPC lines were cultured in NPC proliferation medium and passaged 2 - 4 times until they were dissociated and subjected to ATAC-seq together with the respective iPSC clones. ATAC-seq libraries were generated using the Omni-ATAC protocol (Corces et al. 2017) with minor modifications.
2023-10-25 | E-MTAB-13373 | biostudies-arrayexpress
Project description:<p>Nasopharyngeal carcinoma (NPC) is an aggressive head and neck cancer characterized by Epstein-Barr virus (EBV) infection and dense lymphocyte infiltration. The scarcity of NPC genomic data hinders the understanding of NPC biology, disease progression, and rational therapy design. Here, we performed whole-exome sequencing (WES) on 111 micro-dissected EBV-positive NPCs, with 15 cases subjected to further whole-genome sequencing (WGS), to determine its mutational landscape. We identified enrichment for genomic aberrations of multiple negative regulators of the NF-kB pathway in a total of 41% of cases including CYLD, TRAF3, NFKBIA and NLRC5. Functional analysis confirmed novel inactivating CYLD mutations as drivers for NPC cell growth. The EBV oncoprotein latent member protein 1 (LMP1) functions to constitutively activate NF-kB signaling, and we observed mutual exclusivity among somatic NF-kB pathway aberrations and LMP1-overexpression, suggesting that NF-kB activation is selected for by both somatic and viral events during NPC pathogenesis.</p>
| phs001244 | dbGaP
Project description:Nasopharyngeal carcinoma (NPC), a cancer that is etiologically associated with the Epstein-Barr virus (EBV), is endemic in Southern China and Southeast Asia. The scarcity of representative NPC cell lines owing to the frequent loss of EBV episomes following prolonged propagation and compromised authenticity of previous models underscores the critical need for new EBV-positive NPC models. Herein, we describe the establishment of a new EBV-positive NPC cell line, designated NPC268 from a primary non-keratinizing, differentiated NPC tissue. NPC268 can undergo productive lytic reactivation of EBV and is highly tumorigenic in immunodeficient mice. Whole-genome sequencing (WGS) revealed close similarities with the tissue of origin, including large chromosomal rearrangements, while whole-genome bisulfite sequencing (WGBS) and RNA sequencing demonstrated a hypomethylated genome and enrichment in immune-related pathways, respectively. Drug screening of NPC268 together with six other NPC cell lines using 339 compounds, representing the largest high-throughput drug testing in NPC, revealed biomarkers associated with specific drug classes. NPC268 represents the first and only available EBV-positive non-keratinizing differentiated NPC model, and extensive genomic, methylomic, transcriptomic, and drug response data should facilitate research in EBV and NPC, where current models are limited.
2024-03-13 | GSE233426 | GEO
Project description:Unlike other EBV-associated human tumors, nearly 100% wild-type p53 gene is found in NPC, p53 protein is also frequently found to accumulate in NPC biopsies. However, the role of p53 in EBV-positive nasopharyngeal carcinoma is unclear. The expression profiles of mRNAs and miRNAs of EBV-positive NPC cells are unknown. To elucidate the function of p53 in EBV-positive NPC, we used the CRISPR-Cas9 gene editing system to p53 knockout C666-1 cells with Epstein-Barr virus and performed mRNA and miRNA sequencing in p53 KO C666-1 and their control cells. Gene Ontology (GO), KEGG and STRING analyses were implemented to identify significant functions, pathways of differentially expressed mRNAs. Through comparative analysis of p53-regulated genes from EBV-positive C666-1 cells and EBV-negative HONE2 cells with p53 target genes from 16 high throughput data sets, we found that the number of target genes and KEGG pathways downregulated by p53 in EBV-positive C666-1 cells were much less than in EBV-negative HONE2 cells, but “p53 signaling pathway” and related cell cycle arrest and apoptosis genes were significantly downregulated after knockout of p53 gene in C666-1 cells. To explore the effect of p53 on cell cycle and apoptosis, we established stable p53 C666-1-KO cell lines with stable expression of exogenous p53-WT and their control cell lines. Using the established cell lines, we observed that stable expression of p53 repressed cell proliferation, increased cell apoptosis and blocked G1/S phase progression. In conclusion, our results show that the accumulated p53 protein in EBV-positive C666-1 cells still has some tumour suppressor functions such as blocking cell-cycle progression and promoting apoptosis, but the ability of p53 to downregulate gene expression is inhibited.
2021-03-01 | GSE138257 | GEO
Project description:Nasopharyngeal carcinoma (NPC) is endemic in Southeast Asia and southern China. The primary treatment for NPC is radiotherapy. Despite of the encouraging results of radiotherapy, local recurrence or distant metastases of NPC after the initial therapy is frequently found due to radioresistance. Therefore, there is an urgent need to identify genes that control radiosensitivty, aiming to reduce disease recurrence. Epstein-Barr virus (EBV) infection was closely associated with undifferentiated NPC. EBV-encoded microRNAs (miRNAs) played crucial roles in the pathogenesis of NPC. Ebv-miR-BART7 belongs to the 44 EBV BART miRNAs and was found to be up-regulated in NPC tissues and plasma. Forced expression of ebv-miR-BART7 enhanced the radiosensitivity of NPC cells. However, the mechanisms underlying the sensitizing effect of ebv-miR-BART7 on radiation remain largely unknown. Given that miRNA exerts biological functions by regulating its targets, we used microarray to identify the targets of ebv-miR-BART7 that regulate radiosensitivity of NPC cells.
2017-03-31 | GSE79571 | GEO
Project description:ABBERANT GENE EXPRESSION BY EBERs IN EBV-NEGATIVE NPC HK1 CELL LINE
| PRJNA140389 | ENA
Project description:We proposed that the frequency of EBV reactivation may be crucial for its pathogenic role and highly recurrent EBV reactivations exert a profound influence on genome instability. Recurrent reactivations were induced in the EBV-latently infected NPC cells (NA cells) by treating with 12-o-tetradecanoylphorbol-13-acetate (TPA) and sodium n-butyrate (SB) once per passage periodically. Genome-wild oligoarray-based comparative genomic hybridization (CGH) technology was applied to investigate the copy-number aberrations in response for different frequencies of EBV reactivation. The results showed that the NR15 cells, NA cells with the highest frequency (15 times) of reactivation, exhibit extensive genomic copy-number alterations (CNAs) mostly involving chromosome 3p, 3q, 8p, 8q, 9p and 9q, whereas limited number of CNAs were observed both in NR1 cells where only the initial reactivation take place and NP15 cells which were culture in parallel with NR15 cells without EBV-reactivation. We concluded that it is the highly recurrent reactivations of EBV, but neither just a primary reactivation nor EBV-latent infection, may intimately involve in carcinogenesis of nasopharyngeal epithelial cells with the progressive genome instabilities and the accumulation of genetic mutations. Keywords: array-based comparative genomic hybridization, reactivation of EBV, incidence, frequency, recurrent, genome instability, copy-number alterations, carcinogenesis, and nasopharyngeal carcinoma (NPC).
2007-05-30 | GSE6472 | GEO