Figure 2: 3q27.2 gain targets BCL6 but does not alter its expression or target-gene repression.

(a) GISTIC Q values are shown for DNA copy number loss (blue) and gain (red) on chromosome 3. The peak of 3q27.2 gain included the BCL6 oncogene, but not the previously described target FOXP1. (b) Significance of 3q27.2 gain was contributed to by broad gains of chromosome 3 or the 3q arm in 76 tumours, as well as focal gains of 3q27 in 52 tumours. These gains were mutually exclusive to BCL6 translocation in the 21 tumours for which matching DNA copy number and fluorescence in situ hybridization data were available. Grey bars represent data not available. (c) Increased DNA copy number of BCL6 was not associated with increased transcript abundance compared with cases with no gain. Box plots represent the mean ± the interquartile range with whiskers extending to the minimum and maximum value. (d) GSEA of BCL6 target genes showed no significant repression within cases possessing BCL6 DNA copy number gain (GSEA FDR =0.509). (e) For the 58 tumours with matching BCL6 translocation status and gene expression profiling data, BCL6 transcript abundance was not increased in tumours with BCL6 translocation compared with tumours without BCL6 translocation. Box plots represent the mean ± the interquartile range with whiskers extending to the minimum and maximum value. (f) Tumours with BCL6 translocation (Trans. pos.) showed no significant repression of BCL6 target genes by GSEA (GSEA FDR=0.642) compared with tumours without BCL6 translocation (Trans. neg.).