Abstract Chronic myeloid leukemia (CML) is a myeloproliferative disorder by BCR-ABL, which can transform hematopoietic stem cells (HSCs) into leukemic stem cells (LSCs) with a limitless capacity for self-renewal. Despite substantial prognostic improvement of CML by a specific debulking of tumor burden with a tyrosine kinase inhibitor (TKI) targeting ABL kinase, imatinib-treated CML patients in chronic phase can relapse and progress to blast phase due to the remnant CML stem cells. Ecotropic viral integration site 1 (EVI1), a key transcription factor in HSC regulation, is known to predict poor outcomes in myeloid malignancies, however, incapability of prospective isolation of EVI1-high leukemic cells precludes the functional evaluation of intra-individual EVI1-high cells. In this study, we hypothesized that EVI1 is a valuable marker of CML stem cells as well as HSCs and aimed to cover in depth the regulation of CML stem cells by Evi1. Introduction of CML into Evi1-IRES-GFP knock-in mice, a versatile HSC-reporter strain, enabled us to separate Evi1-high CML cells from the individual and revealed that Evi1 was predominantly enriched in the stem cell fraction and associated with an enhanced proliferative as well as a leukemia-initiating capacity. Comparison of gene expression profiles between Evi1-high and -low CML cells revealed that Evi1-high CML cells had a more quiescent feature and a less differentiated feature than Evi1-low CML cells, suggesting that Evi1-high CML LSK cells could keep self-renewal capacity. Furthermore, Evi1-high CML cells exhibited apparent resistance to TKIs in vivo. Given that Evi1 heterozygosity ameliorated CML development in vivo and that the combination of Evi1 and BCR-ABL caused acute myeloid leukemia (AML) in mice resembling blastic transformation of CML, Evi1 could regulate CML development as a potent driver. In accordance to our data of Evi1-trafficking CML mouse, our single-cell analysis of primitive or differentiated subsets from primary CML-CP samples show that EVI1 was highly expressed in stem cell-enriched CD34+CD38-CD90+ cells, which implied that EVI1 could mark CML stem cells as well as normal HSCs. This point can be translated to human CML cases like that high EVI1 means the increasing number of CML stem cells. As opposed to Evi1-reporter CML models, in AML model by MLL-ENL oncogene, Evi1-high MLL-ENL leukemic cells showed no advantage in leukemia initiation compared to Evi1-low cells. Other Evi1-reporter AML models by MOZ-TIF2 and TEL-PDGFR+AML1-ETO never generated Evi1-high fraction, suggesting the high affinity of Evi1 for stem cell disease such as CML. In conclusion, high Evi1 can define the population of CML stem cells which are resistant to nilotinib. Combinatorial analyses of Evi1-IRES-GFP allele CML animals and single cells from primary CML-CP patients also covered in depth the critical regulation of CML stem cells by Evi1. Citation Format: Tomohiko Sato, Susumu Goyama, Keisuke Kataoka, Ryo Nasu, Takako Tsuruta-Kishino, Yuki Kagoya, Arika Nukina, Katsuyoshi Kumagai, Naoto Kubota, Masahiro Nakagawa, Shunya Arai, Akihide Yoshimi, Hiroaki Honda, Takashi Kadowaki, Mineo Kurokawa. Evi1 defines leukemia-initiating capacity and tyrosine kinase inhibitor resistance in chronic myeloid leukemia. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3901. doi:10.1158/1538-7445.AM2014-3901