Journal Article

Epstein-Barr virus nuclear antigen 3C regulated genes in lymphoblastoid cell lines

Gewurz, Benjamin E, Holton, Kristina, Zhao, Bo, Kieff, Elliott, Takada, Kenzo, Maruo, Seiji, Lee, Sungwook, Johannsen, Eric, Quackenbush, John, Rubio, Renee, Mar, Jessica C

2011

Overview

EBV nuclear antigen 3C (EBNA3C) is an essential transcription factor for EBV transformed lymphoblast cell line (LCL) growth. To identify EBNA3C-regulated genes in LCLs, microarrays were used to measure RNA abundances in each of three different LCLs that conditionally express EBNA3C fused to a 4-OH-Tamoxifen-dependent estrogen receptor hormone binding domain (EBNA3CHT). At least three RNAs were assayed for each EBNA3CHT LCL under nonpermissive conditions, permissive conditions, and nonpermissive conditions with wild-type EBNA3C transcomplementation. Using a two-way ANOVA model of EBNA3C levels, we identified 550 regulated genes that were at least 1.5-fold up- or down-regulated with false discovery rates < 0.01. EBNA3C-regulated genes overlapped significantly with genes regulated by EBNA2 and EBNA3A consistent with coordinated effects on cell gene transcription. Of the 550 EBNA3C-regulated genes, 106 could be placed in protein networks. A seeded Bayesian network analysis of the 80 most significant EBNA3C-regulated genes suggests that RAC1, LYN, and TNF are upstream of other EBNA3C-regulated genes. Gene set enrichment analysis found enrichment for MAP kinase signaling, cytokine-cytokine receptor interactions, JAK-STAT signaling, and cell adhesion molecules, implicating these pathways in EBNA3C effects on LCL growth or survival. EBNA3C significantly up-regulated the CXCL12 ligand and its CXCR4 receptor and increased LCL migration. CXCL12 up-regulation depended on EBNA3C's interaction with the cell transcription factor, RBPJ, which is essential for LCL growth. EBNA3C also up-regulated MYC 1.3-fold and down-regulated CDKN2A exons 2 and 3, shared by p16 and p14, 1.4-fold, with false discovery rates < 5 x 10⁻⁴.

• Publisher: National Academy of Sciences,National Acad Sciences
• Subject: Analysis of Variance / Antigens / Antigens, Viral - metabolism / B lymphocytes / Bayes Theorem / Bayesian analysis / Bayesian theory / Biological Sciences / cell adhesion / Cell adhesion molecules / Cell growth / Cell Line, Tumor / Cell lines / Cell migration / Cell survival / Cells / chemokine CXCL12 / Cluster Analysis / CXCL12 protein / CXCR4 protein / CXCR4 receptor / DNA microarrays / EBNA-3C protein / Epstein Barr virus infections / Epstein-Barr virus / Epstein-Barr Virus Nuclear Antigens / Estrogen receptors / Estrogens / Exons / Gene Expression Profiling / gene expression regulation / Gene Expression Regulation, Neoplastic - genetics / Genes / Genes - genetics / Hormones / Human gammaherpesvirus 4 / Human herpesvirus 4 / Humans / Immunoglobulin J Recombination Signal Sequence-Binding Protein - metabolism / Lymphoblastoid cell lines / Lymphoblasts / Lymphocyte Activation / Lymphoma / Lyn protein / MAP kinase / Mathematical models / Microarray Analysis / microarray technology / mitogen-activated protein kinase / Myc protein / Nuclear antigens / Rac1 protein / Receptors / Receptors, Estrogen - metabolism / Reverse Transcriptase Polymerase Chain Reaction / Ribonucleic acid / RNA / Signal transduction / transcription (genetics) / Transcription factors / Transcription Factors - metabolism / Tumor necrosis factor / tumor necrosis factors / Up regulation / Variance analysis / Viruses