GSE138340
Differential expression analysis of primary AML cells treated with AC220 vs DMSO in endothelial cell co-culture.
Although chemotherapy can successfully induce remission in FLT3/ITD positive acute myeloid leukemia (AML) patients, many, especially those with a high ratio of the FLT3/ITD versus wild type allele (FLT3-AR), exhibit a high relapse rate, requiring hematopoietic stem cell (HSC) transplantation to increase the chance of long-term remission. As the bone marrow tumor microenvironment (TME) has been implicated in drug resistance, we reasoned that AML-TME interactions might be critical for leukemic precursor survival and drug resistance, and that targeting AML-TME interactions might be crucial to improving survival in FLT3/ITD AML patients. In this study, we demonstrate that endothelial cells (ECs), a component of the TME, and the Notch pathway plays a critical role in the protection of FLT3/ITD positive progenitors against AC220 in AML patient samples with high FLT3-AR.  We have previously shown that high FLT3-AR disease is distinguished by the presence of the mutation in the least mature CD34+CD33- precursors, where leukemic stem cells (LSCs) reside. Here, we demonstrate that inhibiting Notch signaling overcomes the TME-mediated drug resistance of the LSC-enriched CD34+CD33- precursors, raising the possibility that Notch may serve as a therapeutic target for eradicating LSCs that are thought to be responsible for relapse in this high-risk AML subset. Overall design: A total of 3 primary AML samples were analyzed. Each sample was treated with either AC220 or DMSO control in endothelial cell co-culture in duplicate prior to RNA-seq analysis. Reads from technical duplicates were pooled before edgeR analysis consisting of 3 AML samples as biological replicates per treatment group.