Epstein-barr virus-induced changes in B-lymphocyte gene expression

Abstract

To elucidate the mechanisms by which Epstein-Barr virus (EBV) latency III gene expression transforms primary B lymphocytes to lymphoblastoid cell lines (LCLs), the associated alterations in cell gene expression were assessed by using 4,146 cellular cDNAs arrayed on nitrocellulose filters and real-time reverse transcription-PCR (RT-PCR). A total of 1,405 of the 4,146 cDNAs were detected using cDNA probes from poly(A)(+) RNA of IB4 LCLs, a non-EBV-infected Burkitt's lymphoma (BL) cell line, BL41, or EBV latency III-converted BL41 cells (BL41EBV). Thirty-eight RNAs were consistently twofold more abundant in the IB4 LCL and BL41EBV than in BL41 by microarray analysis. Ten of these are known to be EBV induced. A total of 23 of 28 newly identified EBV-induced genes were confirmed by real-time RT-PCR. In addition, nine newly identified genes and CD10 were EBV repressed. These EBV-regulated genes encode proteins involved in signal transduction, transcription, protein biosynthesis and degradation, and cell motility, shape, or adhesion. Seven of seven newly identified EBV-induced RNAs were more abundant in newly established LCLs than in resting B lymphocytes. Surveys of eight promoters of newly identified genes implicate NF-kappaB or PU.1 as potentially important mediators of EBV-induced effects through LMP1 or EBNA2, respectively. Thus, examination of the transcriptional effects of EBV infection can elucidate the molecular mechanisms by which EBV latency III alters B lymphocytes.

FIG. 1.

(A) Effect of latency III EBV infection on cellular gene expression. Vertical columns represent hybridization to a single filter; a row represents a single cDNA array element. Values are displayed as fold changes (normalized counts detected from ³³P-labeled first-strand cDNAs generated from BL41EBV or IB4 divided by those from BL41). Red bar, genes highly expressed in both BL41EBV and IB4. Green bar, genes suppressed by EBV in BL41EBV and IB4. Group a genes are highly expressed in IB4 but unaffected by EBV in BL41; group b genes are highly induced by EBV in BL41EBV but not highly expressed in IB4; and group c genes are unaffected by EBV in BL41 but expressed at a low level in IB4; group d genes are repressed by EBV in BL41EBV and are unaffected in IB4. (B) Intersection of genes induced by EBV twofold or greater in both BL41EBV and IB4, including known and newly identified genes. (C) Intersection of genes repressed by EBV twofold or greater in both BL41EBV and IB4. Scales are indicated.

FIG. 2.

Effect of latency III EBV infection on activated and germinal center signature genes. Fold changes are displayed as described in the legend for Fig. 1.