Figure 3.

Human AML impact on the functional identity of the BM niche

(A) Schematic representation of the experimental setup. Depicted stromal components were isolated from the BM of NSG mice carrying specific fluorescent reporters and non-transplanted (ctrl) or xenografted with healthy hematopoietic cells (CB) or patient-derived AML samples (AML; see Table 1 for details). FACS-sorted populations were analyzed by RNA-seq. CD31: ctrl n = 7, CB = 4, AML = 15; Col^high: ctrl n = 5, CB = 2, AML = 9; Col^low: ctrl n = 4, CB = 3, AML = 13; Nes^high: ctrl n = 4, CB = 2, AML = 11; Nes^low: ctrl n = 5, CB = 2, AML = 11; Ng2: ctrl n = 3, CB = 3, AML = 12; Osx: ctrl n = 5, CB = 4, AML = 10.

(B) Comparison of within-cluster averages of Z-scored expression profiles between control samples (black) and leukemic samples (red).

(C–G) Deregulation (mean log2FC) of genes in depicted clusters in the presence of AML (^∗means FDR <0.1).

See also Figures S3 and S4 and Table S3.