Expression analysis of Epstein-Barr virus–transformed human lymphoblastoid cell lines (LCLs) between male and female.
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE35207 | GEO | 2012/01/20
SECONDARY ACCESSION(S): PRJNA150699
REPOSITORIES: GEO
Similar Datasets
Project description:Investigation of human X-linked imprinted gene. Comparing pooled RNA of lymphoblastoid cell lines from normal human male and female, identify the genes expressed with sex spesific manner. Expression array study with total RNA extracted from pooled male and female LCLs with eight 60-mer probe per gene. 47633 exemplar genes representing a total of 63780 transcripts/variants.
2012-01-20 | E-GEOD-35207 | biostudies-arrayexpress
Project description:Epstein-Barr virus (EBV) can infect human B cells and is associated with various types of B cell lymphomas. Studies on the global alterations of the cellular pathways mediated by EBV-induced B cell transformation are limited. In the present study, microarray analysis was performed following generation of two EBV-infected B-lymphoblastoid cell lines (BLCL), in which normal B cells obtained from two healthy Thai individuals and transcriptomic profiles were compared with their respective normal B cells. The two EBV-transformed BLCL datasets exhibited a high degree of similarity between their RNA expression profiles, whereas the two normal B-cell datasets did not exhibit the same degree of similarity in their RNA expression profiles. Differential gene expression analysis was performed, and the results showed that EBV infection was able to dysregulate several cellular pathways in the human B-cell genes involved in cancer and cell activation, such as the MAPK, WNT and PI3K-Akt signaling pathways, which were upregulated in the BLCL and were associated with increased cellular proliferation and immortalization of EBV-infected B cells. Expression of proteins located in the plasma membrane, which initiate a biological response to ligand binding, were also notably upregulated. Expression of genes involved in cell cycle control, the p53 signaling pathway and cellular senescence were downregulated. In conclusion, genes that were markedly upregulated by EBV included those involved in the acquisition of a tumorigenic phenotype of BLCL, which was positively correlated with several hallmarks of cancer.
| S-EPMC7469576 | biostudies-literature
Project description:Epstein-Barr virus (EBV) is one of the common human herpesvirus types in the world. EBV is known to infect more than 95% of adults in the world. The virus mainly infects B lymphocytes and could immortalize and transform the cells into EBV-bearing lymphoblastoid cell lines (LCLs). Limited studies have been focused on characterizing the surface marker expression of the immortalized LCLs. This study demonstrates the generation of 15 LCLs from sixteen rheumatoid arthritis (RA) patients and a healthy volunteer using B95-8 marmoset-derived EBV. The success rate of LCL generation was 88.23%. All CD19+ LCLs expressed CD23 (16.94-58.9%) and CD27 (15.74-80.89%) on cell surface. Our data demonstrated two distinct categories of LCLs (fast- and slow-growing) (p<0.05) based on their doubling time. The slow-growing LCLs showed lower CD23 level (35.28%) compared to fast-growing LCLs (42.39%). In contrast, the slow-growing LCLs showed higher percentage in both CD27 alone and CD23+CD27+ in combination. Overall, these findings may suggest the correlations of cellular CD23 and CD27 expression with the proliferation rate of the generated LCLs. Increase expression of CD23 may play a role in EBV immortalization of B-cells and the growth and maintenance of the EBV-transformed LCLs while CD27 expression might have inhibitory effects on LCL proliferation. Further investigations are warranted to these speculations.
| S-EPMC6458955 | biostudies-literature
Project description:BackgroundEpstein-Barr virus (EBV) infection immortalizes primary B cells in vitro and generates lymphoblastoid cell lines (LCLs), which are used for several purposes in immunological and genetic studies. Purinergic receptors, consisting of P2X and P2Y, are activated by extracellular nucleotides in most tissues and exert various physiological effects. In B cells, especially EBV-induced LCLs, their expression and function have not been well studied. We investigated the expression of P2 receptors on primary human B cells and LCLs using the quantitative reverse transcriptase-polymerase chain reaction (RT-PCR) method for revealing the gene expression profile of the P2 receptor subtypes and their changes during transformation.ResultsThe mRNA transcripts of most P2 receptors were detected in primary B cells; the expression of P2X3 and P2X7 receptors was the lowest of all the P2 receptors. By contrast, LCLs expressed several dominant P2 receptors--P2X4, P2X5, and P2Y11--in amounts similar to those seen in B cells infected with EBV for 2 weeks. The amount of most P2 subtypes in LCLs or EBV-infected B cells was lower than in normal B cells. However, the amount of P2X7 receptor expressed in LCLs was higher. Protein expression was studied using Western blotting to confirm the mRNA findings for P2X1, P2X4, P2X7, P2Y1, and P2Y11 receptors. ATP increased the intracellular free Ca2+ concentration ([Ca2+]i) by enhancing the Ca2+ influx in both B cells and LCLs in a dose-dependent manner.ConclusionThese findings describe P2 receptor expression profiles and the effects of purinergic stimuli on B cells and suggest some plasticity in the expression of the P2 receptor phenotype. This may help explain the nature and effect of P2 receptors on B cells and their role in altering the characteristics of LCLs.
| S-EPMC1609185 | biostudies-literature
Project description:Simvastatin and pravastatin are inhibitors of 3-hydroxy-3-methylglutaryl CoA reductase, and are used as antihypercholesterolemia drugs. Simvastatin, but not pravastatin, binds to the inserted domain of leukocyte function antigen (LFA)-1 and inhibits the function of LFA-1, including adhesion and costimulation of lymphocytes. Epstein-Barr virus (EBV)-transformed lymphoblastoid cell lines (LCLs) express high levels of LFA-1 on their surface and grow in tight clumps. Here we show that simvastatin (2 microM) inhibits clump formation and induces apoptosis of EBV-transformed LCLs. The apoptosis-inducing effect of simvastatin depends on binding to the inserted domain of LFA-1. Simvastatin, but not pravastatin, dissociates EBV latent membrane protein 1 from lipid rafts of LCLs, resulting in down-regulation of nuclear factor kappaB activity and induction of apoptosis. Analysis of multiple EBV-positive and -negative cell lines indicated that both LFA-1 and EBV latent membrane protein 1 expression were required for simvastatin's effects. Administration of simvastatin to severe combined immunodeficiency mice followed by inoculation with LCLs resulted in delayed development of EBV lymphomas and prolonged survival of animals. To our knowledge, this is the first report in which a drug that targets LFA-1 has been used to treat B cell lymphoma. These data suggest that simvastatin may have promise for treatment or prevention of EBV-associated lymphomas that occur in immunocompromised persons.
| S-EPMC387356 | biostudies-literature
Project description:Investigation of 5-aza-2'-cytidine and trichostatin A effect to gene expression of human LCLs. LCLs estabulished from patients with genetic dissease are commonly used for mRNA or protein analysis of disease related genes. However, ofen times the gene of interset is not expressed in LCL. Epigenetic modification could be overcome this problem.
2012-01-27 | GSE35359 | GEO
Project description:Epstein-Barr virus (EBV) transforms B cells to continuously proliferating lymphoblastoid cell lines (LCLs), which represent an experimental model for EBV-associated cancers. EBV nuclear antigens (EBNAs) and LMP1 are EBV transcriptional regulators that are essential for LCL establishment, proliferation, and survival. Starting with the 3D genome organization map of LCL, we constructed a comprehensive EBV regulome encompassing 1,992 viral/cellular genes and enhancers. Approximately 30% of genes essential for LCL growth were linked to EBV enhancers. Deleting EBNA2 sites significantly reduced their target gene expression. Additional EBV super-enhancer (ESE) targets included MCL1, IRF4, and EBF. MYC ESE looping to the transcriptional stat site of MYC was dependent on EBNAs. Deleting MYC ESEs greatly reduced MYC expression and LCL growth. EBNA3A/3C altered CDKN2A/B spatial organization to suppress senescence. EZH2 inhibition decreased the looping at the CDKN2A/B loci and reduced LCL growth. This study provides a comprehensive view of the spatial organization of chromatin during EBV-driven cellular transformation.
| S-EPMC5662195 | biostudies-literature
Project description:While human lymphoblastoid cell lines represent a valuable resource for population genetic studies, they have usually been regarded as difficult for CRISPR-mediated genomic editing because of very inefficient DNA transfection and retroviral or lentiviral transduction in these cells, which becomes a substantial problem when multiple constructs need to be co-expressed. Here we describe a protocol using a single-stranded donor oligonucleotide strategy for 'scarless' editing in lymphoblastoid cells, yielding 12/60 (20%) of clones with homology-directed recombination, when rates of <5-10% are frequently typical for many other cell types. The protocol does not require the use of lentiviruses or stable transfection, permitting lymphoblastoid cell lines to be used for CRISPR-mediated genomic targeting and screening in population genetic studies.
| S-EPMC6694121 | biostudies-literature
Project description:Investigation of 5-aza-2'-cytidine and trichostatin A effect to gene expression of human LCLs. LCLs estabulished from patients with genetic dissease are commonly used for mRNA or protein analysis of disease related genes. However, ofen times the gene of interset is not expressed in LCL. Epigenetic modification could be overcome this problem. Expression array study with total RNA extracted from normal male derived LCLs with eight 60-mer probe per gene. 47633 exemplar genes representing a total of 63780 transcripts variants.
2012-01-27 | E-GEOD-35359 | biostudies-arrayexpress
Project description:Epstein-Barr virus (EBV) episome is known to interact with the three-dimensional structure of human genome in infected cells. However, the exact locations of these interactions and their potential functional consequences remain unclear. Recently the high-resolution chromatin interaction capture (Hi-C) assays in lymphoblastoid cells have become available enabling us to precisely map the contacts between the EBV episome(s) and the human host genome. Using available Hi-C data at 10kb resolution, we have identified nearly 15000 reproducible contacts between EBV episome and human genome. These contacts are highly enriched in chromatin regions denoted by typical or super enhancers and active marks including histone H3 K27ac, K4me1, K79me2 and K4me2. Additionally, these contacts are highly enriched at loci bound by host transcription factors that regulate B cell growth (e.g. IKZF1 and RUNX3), factors that enhance cell proliferation (e.g. HDGF) or factors that promote viral replication (e.g. NBS1 and NFIC). EBV contacts show nearly two-fold enrichment in host regions bound by EBV EBNA2 and EBNA3B transcription factors. Chromosome conformation capture coupled with sequencing (4C-seq) using the EBV oriP as a “bait” loci in lymphoblastoid cells further confirmed contact with active chromatin regions. Collectively, our analysis supports the interaction between EBV episome(s) and active regions of human genome in lymphoblastoid cells.
2020-09-23 | GSE154052 | GEO