BCR-ABL - LSK BCR-ABL + LKS - (%)

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1 Marker Clone BCR-ABL + LSK (%) BCR-ABL + LKS - (%) BCR-ABL - LSK (%) P value vs. BCR-ABL + LKS - P value vs. BCR-ABL - LSK CD2 RM ± ± ± CD ± ± ± CD9 KMC ± ± ± CD11b M1/ ± ± ± CD13 R ± ± ± CD19 ID ± ± ± CD24 M1/ ± ± ± CD25 3C ± ± ± CD31 MEC ± ± ± CD34 RAM ± ± ± CD40 3/ ± ± ± CD41 MWReg ± ± ± CD43 S ± ± ± CD44 IM ± ± ± CD47 Miap ± ± ± CD48 HM ± ± ± CD49e 5H ± ± ± CD51 RMV ± ± ± CD52 BTG-2G 11.1 ± ± ± CD62L MEL ± ± ± CD69 H1.2F ± ± ± CD71 C ± ± ± CD90 30-H ± ± ± Fas Jo ± ± ± CD105 MJ7/ ± ± ± Mpl AMM ± ± ± M-CSFR AFS ± ± ± CD127 SB/ ± ± ± CD133 13A ± ± ± Flt3 A2F ± ± ± CD144 BV ± ± ±

2 CD150 TC15-12F ± ± ± Alcam ALC ± ± ± CXCR4 2B11/CXCR ± ± ± EPCR RCR ± ± ± Tie2 TEK ± ± ± PD-L1 10F.9G ± ± ± Flk1 Avas 12alpha ± ± ± Jam1 H ± ± ± 1.2 < N-cad D ± ± ± EpCAM G ± ± ± PCLP-1 10B ± ± ± PLVAP MECA ± ± ± Supplemental Table 1. Screen for markers specifically expressed on CML LSK cells. Bone-marrow cells from CML mice were collected, stained for various surface proteins using fluorphore- or biotin-conjugated antibodies, and then analyzed by FACS (n = 3 6). Shown are percentages of cells positive for the indicated markers in the BCR-ABL + LSK, BCR-ABL + LKS -, and BCR-ABL - LSK fractions. P values were calculated based on the twotailed Student s t-test comparing BCR-ABL + LSK vs BCR-ABL - LSK cells or BCR-ABL + LSK vs BCR-ABL + LKS - cells. Among the markers tested, only CD25 was specifically expressed on BCR-ABL + LSK cells. Supplemental Table 2. Gene sets used for GSEA. GSE3982_EOSINOPHIL_VS_BASOPHIL_UP GSE3982_EOSINOPHIL_VS_BASOPHIL_DN GSE3982_MAST_CELL_VS_BASOPHIL_UP GSE3982_MAST_CELL_VS_BASOPHIL_DN GSE3982_DC_VS_BASOPHIL_UP GSE3982_DC_VS_BASOPHIL_DN GSE3982_MAC_VS_BASOPHIL_UP GSE3982_MAC_VS_BASOPHIL_DN GSE3982_NEUTROPHIL_VS_BASOPHIL_UP

3 GSE3982_NEUTROPHIL_VS_BASOPHIL_DN GSE3982_BCELL_VS_BASOPHIL_UP GSE3982_BCELL_VS_BASOPHIL_DN GSE3982_BASOPHIL_VS_EFF_MEMORY_CD4_TCELL_UP GSE3982_BASOPHIL_VS_EFF_MEMORY_CD4_TCELL_DN GSE3982_BASOPHIL_VS_CENT_MEMORY_CD4_TCELL_UP GSE3982_BASOPHIL_VS_CENT_MEMORY_CD4_TCELL_DN GSE3982_BASOPHIL_VS_NKCELL_UP GSE3982_BASOPHIL_VS_NKCELL_DN GSE3982_BASOPHIL_VS_TH1_UP GSE3982_BASOPHIL_VS_TH1_DN GSE3982_BASOPHIL_VS_TH2_UP GSE3982_BASOPHIL_VS_TH2_DN GSE3982_CTRL_VS_IGE_STIM_MAST_CELL_UP GSE3982_CTRL_VS_IGE_STIM_MAST_CELL_DN GSE3982_EOSINOPHIL_VS_MAST_CELL_UP GSE3982_EOSINOPHIL_VS_MAST_CELL_DN GSE3982_MAST_CELL_VS_DC_UP GSE3982_MAST_CELL_VS_DC_DN GSE3982_MAST_CELL_VS_MAC_UP GSE3982_MAST_CELL_VS_MAC_DN GSE3982_MAST_CELL_VS_NEUTROPHIL_UP GSE3982_MAST_CELL_VS_NEUTROPHIL_DN GSE3982_MAST_CELL_VS_BCELL_UP GSE3982_MAST_CELL_VS_BCELL_DN GSE3982_MAST_CELL_VS_EFF_MEMORY_CD4_TCELL_UP GSE3982_MAST_CELL_VS_EFF_MEMORY_CD4_TCELL_DN GSE3982_MAST_CELL_VS_CENT_MEMORY_CD4_TCELL_UP GSE3982_MAST_CELL_VS_CENT_MEMORY_CD4_TCELL_DN GSE3982_MAST_CELL_VS_NKCELL_UP GSE3982_MAST_CELL_VS_NKCELL_DN GSE3982_MAST_CELL_VS_TH1_UP GSE3982_MAST_CELL_VS_TH1_DN GSE3982_MAST_CELL_VS_TH2_UP GSE3982_MAST_CELL_VS_TH2_DN

4 Supplemental References 1 Toyama, H., Arai, F., Hosokawa, K., Ikushima, Y. M. & Suda, T. N-cadherin + HSCs in fetal liver exhibit higher long-term bone marrow reconstitution activity than N-cadherin - HSCs. Biochem. Biophys. Res. Commun. 428, (2012).

5 Supplemental Figure 1. CD25 is highly expressed in the CD34 - Flt3 - LSK fraction of CML model mice. (A B) Flow-cytometric analysis of the frequency (A; means ± s.d.) and number (B; means ± s.d.) of CD25 + cells in the CD34 - Flt3 - LSK fraction of CML model mice (red histogram) and control mice (gray histogram) (CML, n = 4; GFP, n = 4). (C) Flow-cytometric analysis of the frequency of CD25 + cells in LSK, LSK -, LKS -, LS - K -, and Gr-1/Mac-1 + cells of CML model mice (means ± s.d., n = 7). *P < 0.05 and **P < Supplemental Figure 2. Mast-cell-related genes are highly expressed in CD25 + LSK cells. A set of genes with an expression pattern similar to that of CD25. Genes expressed in CD25 + LSK, CD25 - LSK, LKS -, and Gra-1 + Mac-1 + cells from BCR-ABL + spleens were analyzed by microarray. Supplemental Figure 3. Variations in Sca-1 staining among antibody clones. Frequencies of CML LSK, CD25 - F - LSK, CD25 + F - LSK, or CD25 + F + LSK fractions detected by the Sca-1 antibody (clone E ) used throughout this study and another Sca-1 antibody,

6 clone D7 (means ± s.d., n = 3). Supplemental Figure 4. CD25 + F - LSK cells exhibit higher colony-forming capacity and a predisposition to mast-cell differentiation. (A) Colony-forming capacity of CD25 + F + LSK, CD25 + F - LSK, or CD25 - F - LSK cells from CML model mice was examined in methyl cellulose supplemented with cytokines (means ± s.d., n = 3). (B) Single cell-derived colony counts and cellular morphology of CD25 + F + LSK, CD25 + F - LSK, or CD25 - F - LSK cells in liquid culture. Upper, Number of colonies derived from single CD25 + F + LSK, CD25 + F - LSK, or CD25 - F - LSK cells in the presence or absence of 100 ng/ml IL-2 or 50 ng/ml SCF plus 10 ng/ml of IL-3. Lower, cell morphology in liquid culture. Images were obtained and analyzed using a microscope (IX70; Olympus), UplanApo 20x/0.70 objective lens (Olympus), UPIanApo 40 /0.85 objective lens (Olympus) and DP Controller (Olympus). **P < Supplemental Figure 5. Apoptosis, homing capacity, and cell-cycle status of distinct subsets of cells in the CML LIC population. (A) Annexin V + cells in normal LSK, CML CD25 - F - LSK, CD25 + F - LSK, and CD25 + F + LSK

7 fractions (means ± s.d., n = 3). **P < (B C) Homing capacity of BCR-ABL transduced CD25 + LSK or CD25 - LSK cells ( per sample) to bone marrow (B) or spleen (C) 16 hr after BMT (n = 3; means ± SD). (D) Flow-cytometric analysis of the cell cycle in CML CD25 - F - LSK, CD25 + F - LSK, or CD25 + F + LSK fractions (means ± s.d., n = 4). *P < Supplemental Figure 6. TGF-β2 is highly expressed in CD25 + LSK cells and increases the number of CML LSK cells. (A) Quantitative PCR (qpcr) of TGF-β2 and TGF-βR1 expression in the indicated fractions from CML model mice. Each value was normalized to β-actin expression and is expressed as fold induction compared to the corresponding level in the control group (means ± s.d, n = 4). (B) Number of LSK cells after ex vivo culture of CD25 + F - LSK or CD25 - F - LSK cells with 10 ng/ml TGF-β1 or TGF-β2 for 8 days (means ± s.d., n = 4 5). *P < 0.05 and **P < Supplemental Figure 7. Expression of IL-2 receptor components in CML and normal primitive subpopulations. (A) Flow-cytometric analysis of CD122 (IL-2Rβ) and CD132 (common γ-chain) in the

8 indicated fractions (red histograms; means ± s.d., n = 4). Gray histograms are isotype controls. (B) Flow-cytometric analysis of CD122 (IL-2R ) and CD132 (common -chain) expression in normal bone-marrow fractions, including LT-HSC (CD34 - Flt3 - LSK), LSK, and GMP (Lin - c- Kit + Sca-1 - CD34 + FcγRII/III + ) (orange histograms). Gray histograms indicate isotype control staining. Numbers indicate the CD122- or CD132-positive fraction (means ± s.d., n = 3). Supplemental Figure 8. Surface marker profiles of IL-2 + cells in CML mice. Intracellular flow-cytometric analysis of IL-2 + cells in CML spleen (red histogram: IL-2 PE staining, gray histogram: isotype control) in combination with anti-cd8a, anti-b220, and anti- Gr-1 antibodies (mean ± s.d., n = 3). Supplemental Figure 9. Acceleration of leukemia by IL-2. (A) Survival of CML mice injected with vehicle or IL-2 (n = 7). (B) CD25 + F - LSK or CD25 - F - LSK cells from CML model mice ( cells per sample) were cultured for 16 days. Calculated cell number in LSK fractions (means ± s.d.) are shown (n = 5). *P < 0.05 and **P < (C) Colony numbers from CFU-C assay of three independent human CML samples with or

9 without human IL-2 (100U/ml) or anti-human CD25 neutralizing antibody (10 g/ml) (means ± s.d., n = 3). *P < Supplemental Figure 10. Peripheral blood parameters of Il2ra -/- LSK derived CML mice after transplantation. Blood parameters were examined 11 days after transplantation (n = 6). Supplemental Figure 11. Characterization of Il2Ra -/- CML mice and Il2Ra -/- mice. (A C) BCR-ABL + myeloid cell number in bone marrow (BM) or spleen (Sp) (A), BCR-ABL + cell frequency (B) and number (C) in Il2Ra +/+ or Il2Ra -/- CML mice (11 days after transplantation) (means ± s.d., n = 7). **P < (D) LSK frequency in Il2Ra +/+ or Il2Ra -/- BM (means ± s.d., n = 4 5). Supplemental Figure 12. Characterization of CML model mice treated with anti IL-2 monoclonal antibody. Peripheral blood status (A), BCR-ABL + myeloid cell number in bone marrow (BM) or spleen (Sp) (B), BCR-ABL + myeloid cell frequency in peripheral blood (PB) (C), spleen weight (D), BCR-ABL + cell frequency (E) and number (F) in bone marrow or spleen, and number of bone-

10 marrow LSK cells (G) in CML model mice treated with isotype antibody (n = 4) or anti-il-2 monoclonal antibody (n = 7) (11 days after transplantation) (means ± s.d.). *P < 0.05, **P < Supplemental Figure 13. Effect of anti-cd25 monoclonal antibody on CML model mice treated with nilotinib. Spleen weight (A), BCR-ABL + cell frequency in bone marrow (B) and spleen (C), and number of bone-marrow LSK cells in bone marrow (D) and spleen (E) in CML model mice treated with either vehicle or nilotinib in conjunction with either isotype antibody or anti-cd25 monoclonal antibody (11 days after transplantation) (n = 5; means ± s.d.). *P < 0.05, **P < Supplemental Figure 14. CD25 expression in untreated CML or normal human hematopoietic stem/progenitor cells. (A) Another pair of representative profiles for CD25 expression in freshly isolated bonemarrow CD34 + CD38 - (red histogram) and CD34 + CD38 + (blue histogram) fractions from an untreated CML CP patient or a lymphoma patient without bone-marrow involvement (related to Figure 6D).

11 (B) Flow-cytometric profiles for CD25 expression in the frozen bone-marrow CD34 + CD38 - (red histogram) and CD34 + CD38 + (blue histogram) fractions from untreated CML CP patients (n = 3). Numbers indicate CD25 + cells in CD34 + CD38 - fractions. Supplemental Figure 15. Gene set enrichment analysis on human CML and B-ALL samples. (A B) Gene set enrichment analysis was applied to human leukemia samples. CML BC (n = 33) was compared to CML CP (n = 57) (A), and CD25 + B-ALL (n = 43) was compared to CD25-low or -negative B-ALL (n = 151) (B). Supplemental Figure 16. Revised model of CML LIC formation. Proposed model indicating distinct roles for IL-2 and CD25 + LSK cell-derived TGF-β in maintaining the leukemia-initiating capacity of CML LSK cells.

12 Supplemental Figure 1 A BCR-ABL + CD34 - Flt3 - LSK gated B Count CD ±16.2%* Number of cells (x10 3 ) GFP * CML C ** CD25 positive cells (%) LSK LSK - LKS - LS - K - Gr-1 /Mac-1 +

13 Supplemental Figure 2

14 Supplemental Figure 3 LSK CD25 - F - LSK CD25 + F - LSK CD25 + F + LSK P=0.51 P=0.49 P=0.30 P=0.85 Frequency (%) Frequency (%) Frequency (%) Frequency (%)

15 Supplemental Figure 4 A B

16 Supplemental Figure 5 A ** B P=0.45 C P=0.22 Annexin V + (%) Number of cells Number of cells Normal LSK CD25 - F - LSK CD25 + F - LSK CD25 + F + LSK CD25 - LSK CD25 + LSK CD25 - LSK CD25 + LSK D Normal LSK CD25 - F - LSK CD25 + F - LSK CD25 + F + LSK Ki ±9.1% ±11.3% G1 S/G2/M 26.9 ±5.0% 55.5 ±4.1% 36.4 ±8.6% 53.8 ±8.2% 67.1 ±9.3% 15.1 ±5.8% G ± 3.1% 17.6 ± 4.6% 9.7 ± 2.7%* 17.8 ± 6.7% Hoechst 33342

17 Supplemental Figure 6 A B

18 Supplemental Figure 7 A B

19 Supplemental Figure 8 Splenic MNCs Cell number 1.4±1.1% CD8a 58.5±10.2% Cell number 87.6±5.1% IL-2-PE B220 Gr-1

20 Supplemental Figure 9 A Survival rate (%) Vehicle IL-2 P=0.029 B Cell number ** ** * ** CD25 + F + LSK CD25 + F - LSK CD25 - F - LSK Time post BMT (days) Vehicle IL-2 CD25 - F - LSK Vehicle IL-2 CD25 + F - LSK C * Colony number * *

21 Supplemental Figure 10 WBC (x10 3 / l) RBC (x10 4 / l) Hb (g/dl) HCT (%) WBC (x10 3 / l) P = RBC (x10 4 / l) P = Hb (g/dl) P = HCT (%) P = Il2ra +/+ Il2ra -/- Il2ra +/+ Il2ra -/- Il2ra +/+ Il2ra -/- Il2ra +/+ Il2ra -/ MCV (fl) P = MCH (pg) P = MCHC (g/dl) P = Plt (x10 4 / l) P = MCV (fl) MCH (pg) MCHC (g/dl) Plt (x10 4 / l) Il2ra +/+ Il2ra -/- Il2ra +/+ Il2ra -/- Il2ra +/+ Il2ra -/- Il2ra +/+ Il2ra -/- 0

22 Supplemental Figure 11 A Number of cells (x10 7 ) P= P= P= P= Il2Ra +/+ Il2Ra -/- BCR-ABL + BM granulocyte Il2Ra +/+ Il2Ra -/- BCR-ABL + BM monocyte Il2Ra +/+ Il2Ra -/- Il2Ra +/+ Il2Ra -/- BCR-ABL + Sp granulocyte BCR-ABL + Sp monocyte B Frequency (%) ** ** C Number of cells (x10 7 ) ** ** D Frequency (%) LSK P=0.069 Il2Ra +/+ Il2Ra -/- Bone marrow Il2Ra +/+ Il2Ra -/- Spleen Il2Ra +/+ Il2Ra -/- Bone marrow Il2Ra +/+ Il2Ra -/- Spleen Il2Ra +/+ Il2Ra -/-

A Number of cells (x10 7 ) Supplemental Figure 12 anti-il-2 P value WBC (/ul) 28750±9946 27167±1657 0.854 RBC (x10 4 /ul) 838±102 1032±26 0.031 Hb (g/dl) 12.5±1.7 16.2±0.8 0.002 HCT (%) 40.0±7.0 52.

23 A Number of cells (x10 7 ) Supplemental Figure 12 anti-il-2 P value WBC (/ul) 28750± ± RBC (x10 4 /ul) 838± ± Hb (g/dl) 12.5± ± HCT (%) 40.0± ± MCV (fl) 47.6± ± MCH (pg) 14.9± ± Plt (x10 4 /ul) 33.0± ± B P=0.96 P=0.038 P=0.38 P=0.012 C Frequency in PB (%) * anti IL-2 BCR-ABL + granulocyte * anti IL-2 BCR-ABL + monocyte D Spleen weight (mg) P=0.19 anti IL-2 anti IL-2 anti IL-2 BCR-ABL + BM granulocyte BCR-ABL + BM monocyte E Frequency (%) ** ** BCR-ABL + Sp granulocyte anti IL-2 F anti IL-2 BCR-ABL + Sp monocyte Number of cells (x10 7 ) * * G Number of cells (x10 3 ) * * CD25 + F + LSK CD25 + F - LSK CD25 - F - LSK anti IL-2 anti IL-2 Bone marrow Spleen anti IL-2 Bone marrow anti IL-2 Spleen anti IL-2

+Nilo +Nilo D CD25 + F + LSK CD25 + F - LSK CD25 - F - LSK E CD25 + F + LSK CD25 + F - LSK CD25 - F

24 Supplemental Figure 13 A ** B * C ** * * Spleen weight (mg) GFP + frequency in BM (%) GFP + frequency in Sp (%) +vehicle +Nilo Anti CD25 +Nilo +vehicle Anti CD25 +Nilo +Nilo Anti CD25 +vehicle +Nilo +Nilo D CD25 + F + LSK CD25 + F - LSK CD25 - F - LSK E CD25 + F + LSK CD25 + F - LSK CD25 - F - LSK Number of cells (BM) Number of cells (Sp) +vehicle +Nilo Anti CD25 +Nilo +vehicle +Nilo Anti CD25 +Nilo

25 Supplemental Figure 14 A CD38 Count Count B CD34 CD25 CML Case 3 CML Case 4 CML Case % 0.88% 0 % Count CD25

26 Supplemental Figure 15 A CML BC vs CML CP B B-ALL CD25 positive vs B-ALL CD25 low or negative

27 Supplemental Figure 16

sequences of a styx mutant reveals a T to A transversion in the donor splice site of intron 5

sfigure 1 Styx mutant mice recapitulate the phenotype of SHIP -/- mice. (A) Analysis of the genomic sequences of a styx mutant reveals a T to A transversion in the donor splice site of intron 5 (GTAAC