Gene expression profiling of AML cells derived from patients and engrafted in the humanized or murine hematopoietic niche of huBM-sc mice. (A) Unsupervised hierarchical cluster analysis (Pearson uncentered absolute distance, average linkage) on gene expression profiles of murine BM- or human scaffold (SC) –engrafted huCD45⁺ cells or patient-derived (MNCs or CD34⁺) leukemic cells from 6 different AMLs. (B) Supervised cluster with Euclidean distance and ward linkage analyses per AML using genes that were differentially expressed between huBM-sc– and murine BM–retrieved cells (fold change [FC] ≥3). (C) Gene ontology (GO) analyses on genes that were differentially expressed between huBM-sc– and murine BM–retrieved cells (FC ≥3). (D) Gene set enrichment analyses on genes that were differentially expressed between cells retrieved from huBM-sc and murine BM (FC ≥3). (E) Expression of individual stem cell–related genes in the diagnostic patient sample and in cells retrieved from huBM-sc and murine BM. LSC, leukemic stem cell; Pt, patient.