Fig. 2: t(6;9) AML differs from NPM1-mutated AML in the HOX/MEIS axis.
A. Scatterplot of gene expression as log2 FPKM in t(6;9) vs PBSCs. Genes shown in red are at least 4-fold upregulated in blue at least 4-fold downregulated in NPM1 AML compared to PBSCs. Dashed lines de-lineate 4-fold up and downregulated in t(6;9) vs PBSCs. Heatmap with hierarchical clustering showing the log2 motif score for footprinted motifs identified in t(6;9) and NPM1 DNase1 datasets and not found in PBSCs. B Tag counts of the DNaseI distal peaks were ranked by the fold change between the average of two NPM1-only patients and two t(6;9)-only patients. Density plots show the tag counts across a 2 kb window, with enriched motifs plotted on the same axis. LSC17 scores were calculated from the normalised FPKM values of the RNA-seq for these patients, the horizontal bar indicates the mean of the two patients which are shown by individual points. C UCSC Genome Browser screenshot of the HOXA and HOXB loci showing normalised DNaseI read coverage, boxes indicate sites which display less accessible chromatin in both t(6;9) patients as compared to all FLT3-ITD and NPM1 patients, average 1.94-fold less accessible across all peaks in each patient compared to each FLT3-ITD/NPM1 patient (range 1.17–5.49-fold), top. Normalised counts of key HOX genes and MEIS1 shown for cells from t(6;9) patients and a t(6;9) cell line, healthy PBSCs and patient cells from other AML backgrounds. Horizontal line indicates the mean, individual patients/cell line are shown by circles. *indicates p < 0.05, **p < 0.01 with green asterisks showing the significance between t(6;9) and FLT3-ITD only expression and orange asterisks showing significance between t(6;9) and NPM1 only expression by Student’s T-test.
