IntroductionSeveral studies have demonstrated that normal hematopoietic stem cells (HSCs) exist in 2 functional states that can be distinguished based on CD34 expression. 1 CD34 Ϫ cells represent a kinetically and functionally resting stem cell subset that needs to be activated to generate a CD34 ϩ cell population with high proliferative and engraftment potential. 2,3 Acquisition of CD34 expression on human HSCs is associated with in vitro hematopoietic activity and cell-cycle recruitment. 4 CD34 Ϫ /CD34 ϩ transition results in metabolic activation and down-regulation of growth-inhibitory pathways, and CD34 ϩ stem cells show a significant up-regulation of self-renewal-, commitment-, and engraftment-related genes. 5 No data are presently available on the existence of a stem cell population devoid of CD34 expression in leukemic hematopoiesis.Chronic myelogenous leukemia (CML) is a clonal myeloproliferative disorder of HSCs that have acquired a BCR-ABL fusion gene. The encoded 210-kDa protein has constitutively elevated tyrosine kinase activity that results in a large variety of biochemical changes in leukemic stem cells (LSCs) mainly inducing growth factor-independent proliferation, inhibition of apoptosis, and alteration of adhesive properties. 6 There is an increasing body of evidence indicating that, similar to normal hematopoiesis, a kinetically quiescent stem cell population can be isolated within the CD34 ϩ LSC compartment. 7 These G 0 CML cells are able to repopulate immunodeficient mice 8 and show a different transcriptional profile from dividing CD34 ϩ cells. 9 More importantly, the dissection of the stem cell pool in CML has allowed the characterization of subsets of CD34 ϩ LSCs resistant, in vitro and in vivo, to targeted therapies with BCR-ABL inhibitors. [10][11][12] Multiple mechanisms of drug resistance have been described, including kinetic quiescence per se, 10 increased expression level of BCR-ABL, and altered expression of ABCB1, ABCG2, and OCT1 cell membrane drug transporter genes in the most primitive CD34 ϩ /CD38 Ϫ LSCs. 13 Taken together, these findings stress the importance of gaining further understanding of the molecular and functional properties of the stem cell compartment in CML, in view of the development of more effective therapies.To this end, in the present study, we assessed the gene expression profile and the functional characteristics of a novel Lin Ϫ CD34 Ϫ stem cell population in CML patients at diagnosis. Our data demonstrate that approximately one-third of Lin Ϫ CD34 Ϫ cells are leukemic and capable of engraftment in immunodeficient mice. Overall, molecular analysis showed 1827 transcripts differentially expressed in CML HSC subpopulations compared with normal counterparts, genes affecting many cellular functions associated with the neoplastic phenotype. Microarray data also highlighted the highest transcriptome differences between CML Lin Ϫ CD34 Ϫ cells and their normal counterparts. Functional The online version of this article contains a data supplement.The publication co...