In Epstein-Barr virus (EBV)
latent infection, the EBV-encoded RNAs
EBER1 and
EBER2 accumulate in the host cell nucleus to ~10(6) copies. While the expression of EBERs in cell lines is associated with transformation, a mechanistic explanation of their roles in EBV latency remains elusive. To identify EBER-specific gene expression features, we compared the
proteome and
mRNA transcriptome from BJAB cells (an EBV-negative B
lymphoma cell line) stably transfected with an empty plasmid or with one carrying both EBER genes. We identified ~1800
proteins with at least 2 SILAC pair measurements, of which only 8 and 12 were up- and downregulated ≥ 2-fold, respectively. One upregulated
protein was PIK3AP1, a B-cell specific
protein adapter known to activate the PI3K-AKT signaling pathway, which regulates alternative splicing and translation in addition to its pro-survival effects. In the
mRNA-seq data, the
mRNA levels for some of the
proteins changing in the SILAC data did not change. We instead observed
isoform switch events. We validated the most relevant findings with biochemical assays. These corroborated the upregulation of PIK3AP1 and AKT activation in BJAB cells expressing high levels of both EBERs and EBNA1 (a surrogate of
Burkitt's lymphoma EBV latency I) relative to those expressing only EBNA1. The
mRNA-seq data in these cells showed multiple upregulated oncogenes whose mRNAs are enriched for 3´-UTR AU-rich elements (AREs), such as ccl3, ccr7,
il10, vegfa and zeb1. The CCL3, CCR7,
IL10 and VEGFA
proteins promote cell proliferation and are associated with EBV-mediated
lymphomas. In EBV latency, ZEB1 represses the transcription of ZEBRA, an EBV lytic phase activation factor. We previously found that
EBER1 interacts with AUF1 in vivo and proposed stabilization of ARE-containing mRNAs. Thus, the ~10(6) copies of
EBER1 may promote not only cell proliferation due to an increase in the levels of ARE-containing genes like ccl3, ccr7,
il10, and vegfa, but also the maintenance of latency, through higher levels of zeb1.