Figure 1.
Similarities in the transcriptomes of blasts induced by EBV infection or by CD40L/IL4 treatment of resting peripheral blood B cells.
Significant changes in transcript expression were identified by paired LIMMA (p<0.01; FC>1.5) and complete gene-lists are available in Data-File S2. (A) Venn diagram indicating the overlap of the 4197 genes changed by EBV and the 1666 genes changed by CD40L/IL4, irrespective of the direction of the change. (B) Venn diagram showing the 3519 genes that were up-regulated by EBV, and the overlap with the 1394 genes up-regulated by CD40L/IL4 and the 272 down-regulated by CD40L/IL4. (C) Venn diagram showing the 679 genes that were down-regulated by EBV, and the overlap with the 1394 genes up-regulated by CD40L/IL4 and the 272 down-regulated by CD40L/IL4.
Table 1.
Similarities in gene-expression changes induced by EBV and CD40L/IL4.
Table 2.
Ontology analysis of genes differentially expressed between EBV blasts and CD40L/IL-4 blasts.
Table 3.
Expression of Interferon-regulated genes by EBV and CD40L/IL4 blasts.
Figure 2.
Relationships between genes regulated by Interferon, IRF-1, and IL-4.
Venn diagrams showing the overlaps of 370 ISGs and 113 IRF-1 up-regulated genes defined by Schoggins et al. [31] with IL-4-regulated genes (567 up-regulated and 452 down-regulated) identified by Elo et al [35]. Only genes that were annotated and common to both U133 plus 2 and Human Exon 1.0 ST Affymetrix array platforms (i.e. 16420 genes) were analysed here. Complete gene-lists are available in Data-File S2.
Table 4.
Expression of IL4-regulated genes by EBV-infected B blasts.
Figure 3.
Effect of IL4 on transcription in B cells.
Quantitative RT-qPCR assays for selected cellular gene transcripts in peripheral blood B cell cultures in normal medium or containing IL-4 (assayed at 6 hrs), or infected with EBV in normal medium or containing IL-4 (assayed at 7 days). The results are expressed as mean ± SEM of three replicate experiments using B cells from different donors. An established LCL was used as a reference for all assays, and all values are shown relative to LCL transcript expression = 1, except for SPINT2 and DUSP6 whose expression in the reference LCL was extremely low (ddCt<12) and where expression is shown relative to control B cell cultures. The six cellular genes shown in (A) were reported by Elo et al [35] to be down-regulated by IL4 in T cells, whilst the 2 genes shown in (B) were reported to be up-regulated by IL-4 in T cells.
Figure 4.
Effect of IL4 on EBV-induced B cell transformation.
Purified B cells were infected with EBV at a series of multiplicities of infection (m.o.i.) in the absence or presence of added IL-4. For each infection dose, 103 B cells were seeded into each of the 96-wells of a microtest plate. The cultures were maintained in the presence or absence of IL-4 for 6 weeks, at which point the number of wells containing viable transformed colonies was counted. The data points and error bars represent the mean ± s.d for replicate experiments performed on B cells from three separate donors. Transformation efficiency, defined as the M.O.I. at which 50% of the cultures were transformed, was 23.8±3.2 for EBV alone and 56.5±10.2 for EBV plus IL-4.
Table 5.
Expression of IL-4 regulated genes in GC-B cell LCL.
Table 6.
Expression of IL-4 regulated genes in HRS malignant cells.
Figure 5.
Discordant expression of IL-4 regulated transcripts by EBV and in malignant HRS cells.
Gene-sets regulated by IL-4, in EBV-infected GC B cells, and in micro-dissected HRS cells were identified as described in Tables 5 and 6. To facilitate analysis of statistical significance, equal sized gene-sets were compared by ranking probe-sets according to the magnitude of FC of the HRS cells, and selecting the top 640 or 484 unique genes. Complete gene-lists are available in Data-File S2.
Table 7.
Regulation by LMP1 and LMP2A of EBV/HRS/IL-4 signature genes.