Figure 6.

Identification of AML patient subsets by hierarchical clustering analysis of constitutive leukemic cell protein release. The AML cells were derived from 40 patients, and the cells were cultured alone for 48 h in serum-free medium before supernatants were analyzed. The number of quantified proteins varied from 557 to 2380 proteins (average 1699 proteins), and the proteomic analysis was based on the 1770 proteins detected in 50% or more of the AML-CM samples. This clustering analysis is presented in Figure 4; two main clusters each with two subclusters were identified (left and right part, respectively, of the present Figure 6), and the patients are listed from the upper part to the bottom of the present figure according to the results from this clustering analysis (patient identity columns). For 33 patients we also analyzed their release of 19 selected soluble mediators for AML cells cultured alone using antibody-based methodology (Figure S3); a hierarchical clustering analysis based on these mediator levels classified the patients into three main subsets with generally low, intermediate and high constitutive mediator release (see upper right). The column Cytokine release cluster refers to this classification, and the color codes are explained in the lower left part of the figure. Finally, we also did a hierarchical clustering analysis based on the protein release profile of all 40 patients when MSCs were cultured with AML-CM for all 40 patients (Figure S4). The subclusters/subclassification of patients based on this last analysis is summarized in the column referred to as MSC/AML-CM cluster (color code explanation, see lower left). The right part of the figure presents the number of quantified proteins and the number of viable AML cells after 48 h of in vitro culture for each patient sample. The median and range of quantified proteins/viability for each of the four patient subsets are presented to the right in each part of the figure.