Supplemental Figure 1

A

B

panobinostat

OCI-AML3

Supplemental Figure 2

Control 20 50 nM BC2059, 24 hrA

B

OCI-AML3

Control 20 50 100 nM BC2059, 48 hr

Annexin V-FITC

TO-PRO-3 iodide

HL-60

Control 50 100 nM BC2059, 48 hr

Annexin V-FITC

TO-PRO-3 iodide

C

D

Primary FLT3-ITD

AML

Propidium iodide

Control 20 50 100 nM BC2059, 48 hrE

Supplemental Figure 2

Supplemental Figure 3

A

D

β-Actin

MCL1

p27

OCI-AML3

0 20 50 100 nM, BC2059, 24 h

BIMEL

BIML

BIMS

B

β-Actin

p27

BIMEL

BIML

BIMS

MV4-11

0 20 50 100 nM, BC2059, 24 h

C

Primary FLT3-ITD AML

0 20 50 100 nM, BC2059, 24 h

β-Actin

p27

BIMEL

BIML

BIMS

β-Catenin

20 nMBC2059

100 nMBC2059

Control

DAPITBL1 β-CateninMerge TBL1/β-Catenin

MV4-11 cells

β-catenin DAPI Merge

CD34+ Primary FLT3-ITD AML cells

Control

50 nM BC2059

B

A

C

β-catenin DAPI Merge

CD34+ FLT3 WT Primary AML cells

Control

100 nM BC2059,16 hours

Primary AML cells

TBL1 β Catenin Merge DAPI

Control

100 nM BC2059

20 nM BC2059

D

Supplemental Figure 4

Supplemental Figure 5

A B

C D

Probe Set ID Fold-Change Gene Title Gene Symbol205943_at 10.8824 tryptophan 2,3-dioxygenase TDO2204103_at 10.6149 chemokine (C-C motif) ligand 4 CCL4216834_at 10.3006 regulator of G-protein signaling 1 RGS1201739_at 9.68812 serum/glucocorticoid regulated kinase 1 SGK1215078_at 7.01567 superoxide dismutase 2, mitochondrial SOD2205114_s_at 6.90463 chemokine (C-C motif) ligand 3 CCL3

204472_at 6.23896GTP binding protein overexpressed in skeletal muscle GEM

205476_at 5.13516 chemokine (C-C motif) ligand 20 CCL20212724_at 4.6973 Rho family GTPase 3 RND3201041_s_at 4.671 dual specificity phosphatase 1 DUSP1220054_at 4.66513 interleukin 23, alpha subunit p19 IL23A243296_at 4.53019 Nicotinamide phosphoribosyltransferase NAMPT212099_at 4.39901 ras homolog gene family, member B RHOB206025_s_at 4.19698 tumor necrosis factor, alpha-induced protein 6 TNFAIP61554997_a_at 4.16341 prostaglandin-endoperoxide synthase 2 PTGS2214038_at 3.89781 chemokine (C-C motif) ligand 8 CCL8207433_at 3.84862 interleukin 10 IL10230170_at 3.71956 oncostatin M OSM216598_s_at 3.60761 chemokine (C-C motif) ligand 2 CCL2201466_s_at 3.53626 jun proto-oncogene JUN227697_at 3.51644 suppressor of cytokine signaling 3 SOCS3219371_s_at 3.40553 Kruppel-like factor 2 (lung) KLF2206115_at 3.37739 early growth response 3 EGR3207850_at 3.32973 chemokine (C-X-C motif) ligand 3 CXCL3204533_at 3.30282 chemokine (C-X-C motif) ligand 10 CXCL10203665_at 3.2795 heme oxygenase (decycling) 1 HMOX1209774_x_at 3.20119 chemokine (C-X-C motif) ligand 2 CXCL2204748_at 3.15079 prostaglandin-endoperoxide synthase 2 PTGS2

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 IDFold-

Change Gene Title Gene Symbol

220184_at -3.31242 Nanog homeobox NANOG

204834_at -2.8117 fibrinogen-like 2 FGL2

223044_at -2.80649solute 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 -2.33592kelch repeat and BTB (POZ) domain containing 11 KBTBD11

238900_at -2.32845major 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 chemokine (C-C motif) receptor 2 CCR2

227804_at -2.12735 TLC domain containing 1 TLCD1

219714_s_at -2.11454calcium 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

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

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

21

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.

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

CA

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

B

Supplemental Figure 6

MV4-11

BC2059 PS Fa CI(nM) (nM)30 3 0.474 0.96335 3.5 0.641 0.61240 4 0.746 0.45250 5 0.942 0.128

*

*

Control

DAPI Merge

10 nM PS, 16 h

OCI-AML3 cells

TBL1

20 nM PS, 16 h

50 nM PS, 16h

A

β-Actin

TBL1

OCI-AML3

0 10 20 50 nM, PS, 16 h

B

Supplemental Figure 7

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 0.453 0.515

80 40 0.527 0.322

90 45 0.498 0.446

100 50 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 50 0.512 0.449

AML #1 AML #2

Supplemental Figure 8