CNS ALL cells are characterized by high VEGF expression and a profile associated with hypoxia adaptation. (A) Signature of 27 differentially regulated genes (33 probe sets; shrinkage t statistic; false-discovery rate [FDR] < 5%; fold change [FC] < −2 or FC > +2) comparing ALL sample pairs (n = 9) retrieved from CNS and BM identifying VEGF as a highly differentially regulated gene (red box; FC = 9.18; q = 9.68 × 10⁻¹³). Unsupervised cluster analysis according to this signature showing 2 clusters of CNS- and BM-derived ALL. (B) Gene-set enrichment analysis of CNS and BM signatures identified hypoxia-annotated gene sets (FDR q < 0.05). Enrichment score is shown as a green line, which reflects members of the annotated gene sets (black vertical lines) appearing along the gene list ranked from CNS (red) to BM (blue). (C) Differential VEGF expression (qPCR) in ALL sample pairs isolated from CNS and BM (BM CNS⁺; n = 9; P = .002) of CNS⁺ and BM samples derived from CNS⁻ primografts (BM CNS⁻; n = 6; P = .0176). (D) qPCR analysis of VEGF expression in CNS and BM sample pairs of an independent cohort of CNS⁺ primografts (n = 8; P = .0009). Bars indicate median; significance by 2-tailed Mann-Whitney U test.