To investigate bone marrow stromal abnormalities in AML patients, long-term bone marrow cultures from 21 untreated patients with acute myeloid leukemia (AML) and 28 controls were established. The ability of stroma to support hematopoiesis was compared by the number of colony-forming cells in the adherent layer and the supernatant after 5 weeks of culture (W5 CFC), and gene expression profiles of purified stroma macrophages and fibroblasts were established by Affymetrix microarray analysis. Unfractionated stroma which was irradiated to eliminate endogenous blood cell formation showed no statistically significant difference in W5 CFC numbers between the AML group and the control group. Stroma fibroblasts fractionated from confluent stroma by magnetic cell separation, showed a significantly lower capacity in the AML group to support the growth of CD34+ cells than in the controls. By contrast, purified stroma macrophages cocultured with irradiated murine M2-10B4 cells, showed a significantly higher supportive capacity in the AML group compared to the controls. Although the results were statistically significant, considerable overlap was observed in the range of activities of stroma cells from controls and patients, suggesting that the occurrence of functionally abnormal cells was limited to a subfraction of AML patients. Unsupervised hierarchical cluster analysis of gene expression profiles of stroma macrophages from four AML and four control patients revealed two major subgroups composed exclusively of AML patients and controls, respectively, and gene clustering of purified stroma fibroblasts also showed two subgroups, but with three AML patients plus one control patient in the first and three controls and one AML patient in the second group. The results suggest that the function of stroma fibroblasts and macrophages is markedly perturbed in a substantial proportion of AML patients. Work is in progress to identify candidate genes which may be responsible for the observed functional differences.