Project description:Cellular targets for most of EBV miRNAs are not known. In our study, we aimed at identifying genes that are regulated by individual EBV mature miRNA, particularly BART 18-5p We used microarrays to explore the global gene expression (particularly the downregulated genes) targeted by EBV miRNA mimics. Burkitt's lymphoma cell lines, BL2 and BJAB, were transfected with miRNA mimic control (MC) and EBV miRNA mimics BART 18-5p, 10 and 14* for 24 hour prior to RNA extraction and hybridization on Affymetrix human HGU133 plus 2.0 microarrays.
Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are using transcriptome profiling (RNA-seq) to evaluate the effects of EBV infection or (and) EBV BART6-3p mimics on the global transcriptome of the BJAB cells. Methods: BJAB cells were transfected with negative control mimics or BART6-3p mimics for 48 h and then infected with EBV virons for 2h. RNAs were extracted by Trizol and sequenced by Solexa high-throughput sequencing service (Oebiotech, Shanghai, China). Data were extracted and normalized according to the manufacturer’s standard protocol. Results: Log-fold changes of up- or down-regulated mRNAs between the control and experiment group were selected with a significance threshold of p<0.05. There are 408 mRNAs were up-regulated and 263 were down-regulated in “EBV infection” group cells comparing to “Mock” group cells. There are 385 mRNAs were up-regulated and 246 were down-regulated in “EBV infection + Bart6-3p mimics” group cells comparing to “EBV infection + negative control mimics” group cells. Conclusions: Our study describes the global transciptome changes of BJAB cells induced by EBV infection or (and) EBV 6-3p mimics.
Project description:Genome-Scale draft model for Human Peripheral Blood Mononuclear Cells (PBMCs). A GEM for PBMCs was developed by applying the INIT
algorithm on Human Metabolic Reconstruction (HMR 2.0) as a template model. GEMs were contextualised/ constrained for different conditions using expression datasets. The gene/transcript expression data obtained from PBMCs of Type 1 Diabetes progressors, non-progressors, and healthy controls were employed to score each reaction of HMR 2.0. For further detail please refer to Electronic Supplementary Information of Sen et.al, Metabolic alterations in immune cells associate with progression to type 1 diabetes, Diabetologia, 15/01/2020, (https://doi.org/10.1007/s00125-020-05107-6).
Project description:Epstein-Barr virus (EBV) is highly successful virus infecting the majority of the human population worldwide. During the latent infection period, there are only a few of EBV-encoded proteins can be detected, whereas EBV-encoded non-coding RNAs are highly activated, especially microRNAs. Recent studies found that those BART microRNAs not only disturb EBV genes expression, but also interfere many host genes expression, thus modulating cellular proliferation and immune regulation. In the present study, we investigate the effect of EBV BART6-3p on gene expression profile of the human PBMCs.
Project description:EBV encodes 44 mature miRNAs, a number of which have been found to promote carcinogenesis by targeting host genes. To determine the biological functions of the BART cluster miRNAs, we singly transfected these miRNAs into HEK293T cells. Interestingly, we found that overexpression of EBV-miR-BART6-3p in HEK293T cells dramatically altered HEK293T cell shape. To explore the mechanism of EBV-miR-BART6-3p-mediated inhibition of cell migration and invasion, we attempted to identify its downstream host cellular genes by whole genome microarray, which contains probes to all known human protein coding genes (mRNAs) and long non-coding RNA genes (lncRNAs).
Project description:Application of Systems Genetics analysis for systematic evaluation of candidate causal genes associated with risk of Type 1 Diabetes along with follow-up bioinformatics pathway analysis. Total RNA obtained from whole blood (for EBV-B cells) and Peripheral blood mononuclear cells (PBMCs) (for T-cells)
Project description:To investigate differential protein and phospho-protein changes in the signaling cascades related to mutant G2019S LRRK2 using peripheral blood mononuclear cells (PBMCs)
Project description:Cellular targets for most of EBV miRNAs are not known. In our study, we aimed at identifying genes that are regulated by individual EBV mature miRNA, particularly BART 18-5p We used microarrays to explore the global gene expression (particularly the downregulated genes) targeted by EBV miRNA mimics.
Project description:To examine the effect of DNA from the Epstein-Barr Virus (EBV) on the transcriptional profile of mouse peripheral blood mononuclear cells (PBMCs), BALB/c mouse cells were isolated and cultured in the presence or absence of EBV DNA. RNA was extracted from these cells and then subjected to sequencing. We observed significantly enhanced expression of genes that play roles in proinflammatory processes including ones involved in autoimmune diseases such as rheumatoid arthritis.
