Figure 5
From: Spontaneous loss of B lineage transcription factors leads to pre-B leukemia in Ebf1+/–Bcl-xLTg mice
Loss of Ebf1 expression does not occur through loss of heterozygosity in most EB tumors. (a) One EB tumor (4606) expressed B220 but not CD19, suggesting loss of Ebf1 expression and/or function in this tumor as CD19 is positively regulated by EBF1. Flow cytometric analysis of peripheral blood leukocytes (PBL) from aged controls and an affected EB mouse is shown. Tumor cells are B220lo/CD244+/CD19–. CD19 is a positive target and CD244 is a negative target of EBF1 transcriptional regulation. Histograms in this figure are representative of one affected EB, five Bcl-xLTg and five wild-type control mice analyzed. (b) High-throughput sequencing of Ebf1 genes was performed on paired normal tissue (tail or ear clip) and tumor (lymph node or spleen) DNA from eight different mice bearing EB tumors. The table lists copy number variations in the samples found by the control-FREEC application and verified by visual inspection of aligned reads using normalized counts. One tumor (EB54) displayed ~50% loss of coverage inside four regions in introns 7, 8 and 10. (c) Histograms depicting depth of sequence coverage for two regions with loss in EB54 tumor compared to tail DNA are shown. Boxes highlight the areas of sequence coverage loss. ChIP-seq data show monomethyl H3K4 density across Ebf1 in the CH12 murine B lymphoma cell line (Hardison PSU, UCSC accession wgEncodeEM002370). Boxes correspond to the locations of EB54 sequence coverage loss shown above. (d) Correlation of gene expression data for EBF1, TCF3, RUNX1, BCL2L1, BCL2 and MCL1 from N=177 high-risk pediatric B-cell-acute lymphoblastic leukemia (B-ALL) patient samples.8 The significance of each correlation is shown in the legend for each graph (*P<0.05; **P<0.01; ***P<0.001; ****P<0.0001, ns=not significant.) Data accessed from Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo), accession GSE11877.
