Supplemental Figure 1 A B panobinostat

Supplemental Figure 2 A Control 20 50 nM BC2059, 24 hr OCI-AML3 B

C D E Supplemental Figure 2 Control 20 50 100 nM BC2059, 48 hr OCI-AML3 TO-PRO-3 iodide Annexin V-FITC D Control 50 100 nM BC2059, 48 hr HL-60 TO-PRO-3 iodide Annexin V-FITC E Control 20 50 100 nM BC2059, 48 hr Primary FLT3-ITD AML Propidium iodide

A B C D OCI-AML3 MV4-11 Primary FLT3-ITD AML Supplemental Figure 3 0 20 50 100 nM, BC2059, 24 h 0 20 50 100 nM, BC2059, 24 h BIMEL BIMEL BIML BIML BIMS BIMS p27 p27 MCL1 β-Actin β-Actin D Primary FLT3-ITD AML 0 20 50 100 nM, BC2059, 24 h β-Catenin BIMEL BIML BIMS p27 β-Actin

β Catenin Merge DAPI 100 nM BC2059 20 nM Control DAPI TBL1 β-Catenin Merge TBL1/β-Catenin MV4-11 cells Supplemental Figure 4 A β-catenin DAPI Merge CD34+ Primary FLT3-ITD AML cells Control 50 nM BC2059 B Primary AML cells TBL1 β Catenin Merge DAPI Control 100 nM BC2059 20 nM D β-catenin DAPI Merge CD34+ FLT3 WT Primary AML cells Control 100 nM BC2059, 16 hours C

Supplemental Figure 5 A B C D

tryptophan 2,3-dioxygenase TDO2 204103_at 10.6149 Supplemental Table 1: Genes with greater than 3 fold induction in OCI-AML3 cells following treatment with 100 nM of BC-2059 for 8 hours. Probe Set ID Fold-Change Gene Title Gene Symbol 205943_at 10.8824 tryptophan 2,3-dioxygenase TDO2 204103_at 10.6149 chemokine (C-C motif) ligand 4 CCL4 216834_at 10.3006 regulator of G-protein signaling 1 RGS1 201739_at 9.68812 serum/glucocorticoid regulated kinase 1 SGK1 215078_at 7.01567 superoxide dismutase 2, mitochondrial SOD2 205114_s_at 6.90463 chemokine (C-C motif) ligand 3 CCL3 204472_at 6.23896 GTP binding protein overexpressed in skeletal muscle GEM 205476_at 5.13516 chemokine (C-C motif) ligand 20 CCL20 212724_at 4.6973 Rho family GTPase 3 RND3 201041_s_at 4.671 dual specificity phosphatase 1 DUSP1 220054_at 4.66513 interleukin 23, alpha subunit p19 IL23A 243296_at 4.53019 Nicotinamide phosphoribosyltransferase NAMPT 212099_at 4.39901 ras homolog gene family, member B RHOB 206025_s_at 4.19698 tumor necrosis factor, alpha-induced protein 6 TNFAIP6 1554997_a_at 4.16341 prostaglandin-endoperoxide synthase 2 PTGS2 214038_at 3.89781 chemokine (C-C motif) ligand 8 CCL8 207433_at 3.84862 interleukin 10 IL10 230170_at 3.71956 oncostatin M OSM 216598_s_at 3.60761 chemokine (C-C motif) ligand 2 CCL2 201466_s_at 3.53626 jun proto-oncogene JUN 227697_at 3.51644 suppressor of cytokine signaling 3 SOCS3 219371_s_at 3.40553 Kruppel-like factor 2 (lung) KLF2 206115_at 3.37739 early growth response 3 EGR3 207850_at 3.32973 chemokine (C-X-C motif) ligand 3 CXCL3 204533_at 3.30282 chemokine (C-X-C motif) ligand 10 CXCL10 203665_at 3.2795 heme oxygenase (decycling) 1 HMOX1 209774_x_at 3.20119 chemokine (C-X-C motif) ligand 2 CXCL2 204748_at 3.15079

solute carrier family 40 (iron-regulated transporter), member 1 Supplemental Table 2: Genes with greater than 2 fold depletion in OCI-AML3 cells following treatment with 100 nM of BC-2059 for 8 hours Probe Set ID Fold-Change Gene Title Gene Symbol 220184_at -3.31242 Nanog homeobox NANOG 204834_at -2.8117 fibrinogen-like 2 FGL2 223044_at -2.80649 solute carrier family 40 (iron-regulated transporter), member 1 SLC40A1 213436_at -2.74949 cannabinoid receptor 1 (brain) CNR1 207063_at -2.47669 non-protein coding RNA 185 NCRNA00185 204301_at -2.33592 kelch repeat and BTB (POZ) domain containing 11 KBTBD11 238900_at -2.32845 major histocompatibility complex, class II, DR beta 1 HLA-DRB1 240429_at -2.28028 zinc finger protein 546 ZNF546 206978_at -2.27337 chemokine (C-C motif) receptor 2 CCR2 228055_at -2.21045 napsin B aspartic peptidase pseudogene NAPSB 217047_s_at -2.21015 family with sequence similarity 13, member A FAM13A 233555_s_at -2.20734 sulfatase 2 SULF2 207794_at -2.13184 227804_at -2.12735 TLC domain containing 1 TLCD1 219714_s_at -2.11454 calcium channel, voltage-dependent, alpha 2/delta subunit 3 CACNA2D3 217546_at -2.11094 metallothionein 1M MT1M 229545_at -2.10518 fermitin family member 1 FERMT1 211341_at -2.09286 POU class 4 homeobox 1 POU4F1 207761_s_at -2.06641 methyltransferase like 7A METTL7A 218858_at -2.06145 DEP domain containing 6 DEPDC6 207728_at -2.03694 activating transcription factor 7 interacting protein ATF7IP 213725_x_at -2.02015 xylosyltransferase I XYLT1

Associated Network Functions Score Supplemental Table 3: Ingenuity Pathway Analysis of the 4 most perturbed networks in OCI-AML3 cells following treatment with 100 nM of BC-2059 for 8 hours. Network Associated Network Functions Score 1 Cellular Movement, Hematological System Development and Function, Immune Cell Trafficking 31 2 Cell Morphology, Endocrine System Disorders, Gastrointestinal Disease 24 3 Neurological Disease, Organismal Injury and Abnormalities, Molecular Transport 21 4 Cellular Development, Cellular Growth and Proliferation, Hematological System Development and Function

* * C A B Supplemental Figure 6 OCI-AML3 BC2059 PS Fa CI (nM) (nM) 60 6 0.566 1.043 70 7 0.701 0.961 75 7.5 0.811 0.812 80 8 0.836 0.811 90 9 0.9 0.735 A HL-60 BC2059 PS Fa CI (nM) (nM) 60 6 0.52 1.027 70 7 0.66 0.792 75 7.5 0.771 0.578 80 8 0.756 0.653 90 9 0.867 0.442 MV4-11 BC2059 PS Fa CI (nM) (nM) 30 3 0.474 0.963 35 3.5 0.641 0.612 40 4 0.746 0.452 50 5 0.942 0.128 B * *

A B Control 10 nM PS, 16 h 20 nM PS, 16 h 50 nM PS, 16h OCI-AML3 Supplemental Figure 7 OCI-AML3 cells A TBL1 DAPI Merge Control 10 nM PS, 16 h 20 nM PS, 16 h 50 nM PS, 16h β-Actin TBL1 OCI-AML3 0 10 20 50 nM, PS, 16 h B

AML #1 AML #2 BC2059 (nM) PS (nM) Fa CI 50 25 0.391 0.545 60 30 0.44 Supplemental Figure 8 AML #1 AML #2 BC2059 (nM) PS (nM) Fa CI 50 25 0.391 0.545 60 30 0.44 0.453 70 35 0.441 0.525 75 37.5 0.515 80 40 0.527 0.322 90 45 0.498 0.446 100 0.512 0.449 BC2059 (nM) PS (nM) Fa CI 50 25 0.47 0.993 60 30 0.625 0.624 70 35 0.611 0.773 75 37.5 0.668 0.644 80 40 0.653 0.735 90 45 0.694 0.761 100 0.512 0.449