Leukemias are cancers of the blood cells that cause serious illness and death in children and adults. Even patients who are successfully cured of their disease often suffer from long-term deleterious health effects of their curative treatment. Thus, there is a need for more targeted, less toxic, and more effective treatments. Our studies focus on the defects and mechanisms that induce leukemia by disrupting the normal growth controls that regulate blood-forming stem cells. Using a comparative genomics approach we have identified genes that are differentially expressed in leukemia stem cells. These genes have been the focus of our studies to establish better biomarkers and treatment targets. One candidate gene codes for an enzyme with a previously unknown, non-canonical causal role in a specific genetic subtype of leukemia caused by abnormalities of the MLL oncogene. To characterize its molecular contributions, we are identifying and characterizing protein partners that may assist and interact with the enzyme in its oncogenic role. Candidate interaction partners have been identified using proteomic techniques, and are being investigated for their possible mechanistic roles in leukemia stem cell functions. Another promising candidate that we identified in the comparative gene expression approach encodes a cell surface protein that is preferentially expressed on leukemia stem cells. We have exploited this cell surface protein as a marker to isolate the rare population of cells in human leukemias with stem cell properties. This technical approach has resulted in the isolation of leukemia stem cell populations that are more highly enriched than those obtained using previous techniques. The highly enriched sub-population of leukemia stem cells has been used for comparative gene expression profiling to define a dataset of genes that are differentially expressed between highly matched populations of leukemia cells that are enriched or depleted of leukemia stem cells. Bioinformatics analysis of the dataset has further suggested specific cellular processes and transcriptional regulatory factors that distinguish human leukemia stem cells caused by abnormalities of the MLL oncogene. These newly identified factors will be studied using in vitro and in vivo assays for their specific contributions to leukemia stem cell function and leukemia pathogenesis. Continued characterization of crucial growth controls that go awry in blood stem cells to cause leukemia will identify new drug targets for more effective and less toxic treatments against these devastating, life-threatening diseases.