Figure S1

HDAC1 KD

HDAC2 KD

HDAC3 KD

HDAC4 KD

HDAC5 KD

HDAC6 KD

HDAC7 KD

HDAC8 KD

HDAC9 KD

HDAC10 KD

HDAC11 KD

0

20

40

60

80

100

120

140

160

Rela

tive

LSD

1 m

RNA

(%)

(HDA

C si

RNA

vs. S

cram

ble)

MDA-MB-231 cells

Vasilatos et al.

mRN

A le

vel (

Fold

)Re

lativ

e to

MD

A-M

B-23

1 NR4A1

MDA-MB-436

HS 578T

MDA-MB-231

HCC1419

BT-474

ZR-75-30

MDA-MB-157

HCC202

HCC1599

HCC1187

BT 549

MDA-MB-453

MCF-7

DU4475

HCC1428

HCC1569

HCC38

UACC-812

CAMA-1

HCC1395

HCC70T-4

7D

SK-BR-3

ZR-75-1

HCC1500

HCC1806

MDA-MB-361

HCC2218BT-2

0

AU565

HCC1954

UACC-893

BT-483

HCC1937

MDA-MB-415

MDA-MB-134-VI

0

100

200

300

400

500

600

mRN

A le

vel (

Fold

)Re

lativ

e to

MD

A-M

B-23

1

PCDH1

HS 578T

MDA-MB-231

BT 549

HCC70

HCC38BT-2

0

BT-474

HCC1954

HCC1395

HCC202

HCC1806

HCC1428

HCC1937

MDA-MB-436

HCC1569T-4

7D

MDA-MB-134-VI

BT-483

CAMA-1

MDA-MB-361

MDA-MB-453

MDA-MB-157

DU4475

ZR-75-30

HCC1187

MDA-MB-415

HCC1500

HCC1419

HCC1599

UACC-893

AU565

SK-BR-3

UACC-812

ZR-75-1

HCC2218MCF-7

0

100

200

300

400

500

600

RGS16

mRN

A le

vel (

Fold

)Re

lativ

e to

MD

A-M

B-23

1

HS 578T

BT 549

MDA-MB-231

MDA-MB-157

MDA-MB-436

BT-20

HCC1569

HCC38

HCC1395MCF-7

T-47D

HCC1954

HCC1806

HCC1937

HCC70

AU565

HCC1187

HCC1428

HCC1419

UACC-893

ZR-75-1

HCC1599

SK-BR-3

ZR-75-30

MDA-MB-361

HCC2218

HCC202

HCC1500

UACC-812

BT-483

MDA-MB-453

BT-474

CAMA-1

DU4475

MDA-MB-134-VI

MDA-MB-415

020406080

100120140160180200

mRN

A le

vel (

Fold

)Re

lativ

e to

MD

A-M

B-23

1

BIK

Figure S2

Vasilatos et al.

HCC1806

MDA-MB-231

MDA-MB-157

HCC70

BT 549

MCF10F

HS 578T

HCC1187

MDA-MB-436

HCC1954

MDA-MB-453

BT-20

HCC38

DU4475

CAMA-1MCF-7

MDA-MB-134-VI

HCC1419

HCC1937

MCF12A

T-47D

MCF10A

HCC1428

UACC-893

HCC202

ZR-75-30

BT-483

BT-474

ZR-75-1

HCC1500

MDA-MB-361

HCC1599

HCC1395

UACC-812

MDA-MB-415

AU565

HCC1569

SK-BR-3

HCC2218

0102030405060708090

100

A LSD1

HDAC5

P=0.189

LSD1

P=0.677HDAC5

B

Figure S3

Vasilatos et al.

CDKN1A

b-Actin

Cytoplasmic

Nuclear

SAHA - +

CDKN1A

PCNA

A

Figure S4

SAHAPargyline

- - + + - + - +

NR4A1

b-actin

B

NR4A1

PCNA

Cytoplasmic

Nuclear

MDA-MB-231

MDA-MB-468

Cell Line ER PR HER2Gene

ClusterClinical Subtype

ZR-75-30 + - + Lu HERUACC-812 + - + Lu HERUACC-893 - - + Lu HERHCC202 - - + Lu HERHCC1419 - - + Lu HERHCC1569 - - + BaA HERHCC1954 - - + BaA HERHCC2218 - - + Lu HERAU565 - - + Lu HERBT-474 + + + Lu HERMDA-MB-361 + - + Lu HERSK-BR-3 - - + Lu HERMDA-MB-453 - - + Lu HERZR-75-1 + - - Lu HRHCC1428 + + - Lu HRHCC1500 + + - Lu HRCAMA-1 + + - Lu HRMCF-7 + + - Lu HR

MDA-MB-134-VI + - - Lu HRBT-483 + + - Lu HRMDA-MB-415 + + - Lu HRT-47D + + - Lu HRHCC38 - - - BaB TNHCC70 - - - BaA TNHCC1187 - - - BaA TNHCC1395 - - - BaB TNHCC1599 - - - BaA TNHCC1806 - - - BaA TNHCC1937 - - - BaA TNBT-20 - - - BaA TNMDA-MB-157 - - - BaB TNMDA-MB-231 - - - BaB TNBT 549 - - - BaB TNDU4475 - - - BaA TNHS 578T - - - BaB TNMDA-MB-436 - - - BaB TN

Supplemental Table 1. Thirty-six breast cancer cell lines used in this study. ER-estrogen receptor; PR-progesterone receptor; Lu-luminal; BaA-Basal A; BaB-Basal B; HER2-human epidermal growth receptor 2; HR-hormone receptor positive; TN-triple negative.

Vasilatos et al.

ID Gene Symbol Gene Title Fold Induction SD209460_at ABAT 4-aminobutyrate aminotransferase 5.215 0.100219671_at HPCAL4 hippocalcin like 4 4.681 0.131209083_at CORO1A coronin, actin binding protein, 1A 3.879 0.477203980_at FABP4 fatty acid binding protein 4, adipocyte 3.841 0.113214657_s_at NEAT1 nuclear paraspeckle assembly transcript 1 (non-protein coding) 3.610 0.587210015_s_at MAP2 microtubule-associated protein 2 3.492 0.112203841_x_at MAPRE3 microtubule-associated protein, RP/EB family, member 3 3.458 0.055206463_s_at DHRS2 dehydrogenase/reductase (SDR family) member 2 3.350 0.753210839_s_at ENPP2 ectonucleotide pyrophosphatase/phosphodiesterase 2 3.317 0.117203498_at RCAN2 regulator of calcineurin 2 3.284 0.082206118_at STAT4 signal transducer and activator of transcription 4 3.275 0.092204596_s_at STC1 stanniocalcin 1 3.233 0.755221035_s_at TEX14 testis expressed 14 3.153 0.189209683_at FAM49A family with sequence similarity 49, member A 3.111 0.310221185_s_at IQCG IQ motif containing G 3.076 0.046209198_s_at SYT11 synaptotagmin XI 3.050 0.076209159_s_at NDRG4 NDRG family member 4 3.027 0.345203932_at HLA-DMB major histocompatibility complex, class II, DM beta 3.023 0.245206076_at LRRC23 leucine rich repeat containing 23 2.959 0.157212664_at TUBB4 tubulin, beta 4 2.942 0.271204199_at RALGPS1 Ral GEF with PH domain and SH3 binding motif 1 2.920 0.178220468_at ARL14 ADP-ribosylation factor-like 14 2.917 0.203204749_at NAP1L3 nucleosome assembly protein 1-like 3 2.894 0.151213050_at COBL cordon-bleu homolog (mouse) 2.854 0.606210657_s_at SEPT4 septin 4 2.835 0.281205934_at PLCL1 phospholipase C-like 1 2.815 0.255204687_at PARM1 prostate androgen-regulated mucin-like protein 1 2.814 0.536211237_s_at FGFR4 fibroblast growth factor receptor 4 2.807 0.380218087_s_at SORBS1 sorbin and SH3 domain containing 1 2.792 0.141209392_at ENPP2 ectonucleotide pyrophosphatase/phosphodiesterase 2 2.778 0.525220999_s_at CYFIP2 cytoplasmic FMR1 interacting protein 2 2.759 0.069209839_at DNM3 dynamin 3 2.746 0.153209189_at FOS FBJ murine osteosarcoma viral oncogene homolog 2.729 0.257205249_at EGR2 early growth response 2 2.706 0.11337547_at BBS9 Bardet-Biedl syndrome 9 2.684 0.212209848_s_at SILV silver homolog (mouse) 2.677 0.126202454_s_at ERBB3 v-erb-b2 erythroblastic leukemia viral oncogene homolog 3 (avian) 2.652 0.140211990_at HLA-DPA1 major histocompatibility complex, class II, DP alpha 1 2.650 0.151214040_s_at GSN gelsolin 2.650 0.222202708_s_at HIST2H2BE histone cluster 2, H2be 2.626 0.246221541_at CRISPLD2 cysteine-rich secretory protein LCCL domain containing 2 2.620 0.177204217_s_at RTN2 reticulon 2 2.617 0.225220150_s_at FAM184A family with sequence similarity 184, member A 2.598 0.076204321_at NEO1 neogenin homolog 1 (chicken) 2.596 0.121214823_at ZNF204P zinc finger protein 204 (pseudogene) 2.578 0.128203151_at MAP1A microtubule-associated protein 1A 2.559 0.075210102_at VWA5A von Willebrand factor A domain containing 5A 2.551 0.093210675_s_at PTPRR protein tyrosine phosphatase, receptor type, R 2.537 0.110205259_at NR3C2 nuclear receptor subfamily 3, group C, member 2 2.495 0.523209504_s_at PLEKHB1 pleckstrin homology domain containing, family B (evectins) member 1 2.484 0.022206518_s_at RGS9 regulator of G-protein signaling 9 2.475 0.210203961_at NEBL nebulette 2.431 0.289204035_at SCG2 secretogranin II 2.430 0.041210090_at ARC activity-regulated cytoskeleton-associated protein 2.421 0.043208300_at PTPRH protein tyrosine phosphatase, receptor type, H 2.406 0.147204622_x_at NR4A2 nuclear receptor subfamily 4, group A, member 2 2.395 0.213204437_s_at FOLR1 folate receptor 1 (adult) 2.376 0.160205489_at CRYM crystallin, mu 2.331 0.073218839_at HEY1 hairy/enhancer-of-split related with YRPW motif 1 2.319 0.219213106_at ATP8A1 ATPase, aminophospholipid transporter (APLT), class I, type 8A, member 1 2.315 0.386202575_at CRABP2 cellular retinoic acid binding protein 2 2.280 0.043209462_at APLP1 amyloid beta (A4) precursor-like protein 1 2.275 0.255213096_at TMCC2 transmembrane and coiled-coil domain family 2 2.264 0.235218789_s_at C11orf71 chromosome 11 open reading frame 71 2.243 0.009201107_s_at THBS1 thrombospondin 1 2.227 0.149205125_at PLCD1 phospholipase C, delta 1 2.224 0.173

Table S2. Gene expression induced by treatment with SAHA in MDA-MB-231 cellsVasilatos et al.

ID Gene Symbol Gene Title Fold Induction SD210130_s_at TM7SF2 transmembrane 7 superfamily member 2 2.214 0.315219747_at C4orf31 chromosome 4 open reading frame 31 2.198 0.190207536_s_at TNFRSF9 tumor necrosis factor receptor superfamily, member 9 2.179 0.227219529_at CLIC3 chloride intracellular channel 3 2.173 0.059211506_s_at IL8 interleukin 8 2.171 0.233218976_at DNAJC12 DnaJ (Hsp40) homolog, subfamily C, member 12 2.165 0.248213679_at TTC30A tetratricopeptide repeat domain 30A 2.162 0.135201566_x_at ID2 inhibitor of DNA binding 2, dominant negative helix-loop-helix protein 2.160 0.052220361_at IQCH IQ motif containing H 2.155 0.195208216_at DLX4 distal-less homeobox 4 2.148 0.164205676_at CYP27B1 cytochrome P450, family 27, subfamily B, polypeptide 1 2.138 0.167203388_at ARRB2 arrestin, beta 2 2.111 0.083213045_at MAST3 microtubule associated serine/threonine kinase 3 2.105 0.153205239_at AREG amphiregulin 2.093 0.045211348_s_at CDC14B CDC14 cell division cycle 14 homolog B (S. cerevisiae) 2.079 0.137221986_s_at KLHL24 kelch-like 24 (Drosophila) 2.078 0.353203798_s_at VSNL1 visinin-like 1 2.061 0.162206176_at BMP6 bone morphogenetic protein 6 2.054 0.106206448_at ZNF365 zinc finger protein 365 2.037 0.305204966_at BAI2 brain-specific angiogenesis inhibitor 2 2.036 0.209215321_at RUNDC3B RUN domain containing 3B 2.035 0.11033646_g_at GM2A GM2 ganglioside activator 2.011 0.055204546_at KIAA0513 KIAA0513 2.007 0.145210078_s_at KCNAB1 potassium voltage-gated channel, shaker-related subfamily, beta member 1 1.985 0.16159437_at C9orf116 chromosome 9 open reading frame 116 1.968 0.176212701_at TLN2 talin 2 1.964 0.132202455_at HDAC5 histone deacetylase 5 1.964 0.112209002_s_at CALCOCO1 calcium binding and coiled-coil domain 1 1.964 0.131209737_at MAGI2 membrane associated guanylate kinase, WW and PDZ domain containing 2 1.962 0.116219268_at ETNK2 ethanolamine kinase 2 1.933 0.149214130_s_at PDE4DIP phosphodiesterase 4D interacting protein 1.923 0.076212706_at RASA4 RAS p21 protein activator 4 1.917 0.215220244_at LOH3CR2A loss of heterozygosity, 3, chromosomal region 2, gene A 1.906 0.024215364_s_at KIAA0467 KIAA0467 1.906 0.176214519_s_at RLN2 relaxin 2 1.905 0.23139248_at AQP3 aquaporin 3 (Gill blood group) 1.897 0.123205206_at KAL1 Kallmann syndrome 1 sequence 1.884 0.126221769_at SPSB3 splA/ryanodine receptor domain and SOCS box containing 3 1.881 0.027220673_s_at PPP4R4 protein phosphatase 4, regulatory subunit 4 1.875 0.059219689_at SEMA3G sema domain, immunoglobulin domain (Ig), short basic domain, secreted, 3G 1.867 0.229206218_at MAGEB2 melanoma antigen family B, 2 1.864 0.124218574_s_at LMCD1 LIM and cysteine-rich domains 1 1.853 0.085204567_s_at ABCG1 ATP-binding cassette, sub-family G (WHITE), member 1 1.847 0.077213847_at PRPH peripherin 1.843 0.246205749_at CYP1A1 cytochrome P450, family 1, subfamily A, polypeptide 1 1.821 0.165203488_at LPHN1 latrophilin 1 1.806 0.084219760_at LIN7B lin-7 homolog B (C. elegans) 1.805 0.133205709_s_at CDS1 CDP-diacylglycerol synthase (phosphatidate cytidylyltransferase) 1 1.805 0.050201141_at GPNMB glycoprotein (transmembrane) nmb 1.794 0.211208116_s_at MAN1A1 mannosidase, alpha, class 1A, member 1 1.790 0.176218780_at HOOK2 hook homolog 2 (Drosophila) 1.774 0.145210075_at MARCH2 membrane-associated ring finger (C3HC4) 2 1.768 0.203209962_at EPOR erythropoietin receptor 1.764 0.052215078_at SOD2 superoxide dismutase 2, mitochondrial 1.761 0.106205141_at ANG angiogenin, ribonuclease, RNase A family, 5 1.734 0.166209568_s_at RGL1 ral guanine nucleotide dissociation stimulator-like 1 1.728 0.084635_s_at PPP2R5B protein phosphatase 2, regulatory subunit B', beta 1.728 0.062203021_at SLPI secretory leukocyte peptidase inhibitor 1.725 0.084204979_s_at SH3BGR SH3 domain binding glutamic acid-rich protein 1.721 0.055202590_s_at PDK2 pyruvate dehydrogenase kinase, isozyme 2 1.721 0.065AFFX-HUMISGF3A/ M97935_MA_at

STAT1 signal transducer and activator of transcription 1, 91kDa 1.717 0.097

204279_at PSMB9 proteasome (prosome, macropain) subunit, beta type, 9 1.709 0.104210943_s_at LYST lysosomal trafficking regulator 1.706 0.061216234_s_at PRKACA protein kinase, cAMP-dependent, catalytic, alpha 1.703 0.123204303_s_at KIAA0427 KIAA0427 1.702 0.082209859_at TRIM9 tripartite motif-containing 9 1.689 0.080212259_s_at PBXIP1 pre-B-cell leukemia homeobox interacting protein 1 1.684 0.078221606_s_at HMGN5 high-mobility group nucleosome binding domain 5 1.683 0.194

Vasilatos et al.

ID Gene Symbol Gene Title Fold Induction SD211548_s_at HPGD hydroxyprostaglandin dehydrogenase 15-(NAD) 1.673 0.04965133_i_at INO80B INO80 complex subunit B 1.673 0.057221530_s_at BHLHE41 basic helix-loop-helix family, member e41 1.672 0.184206907_at TNFSF9 tumor necrosis factor (ligand) superfamily, member 9 1.670 0.017203516_at SNTA1 syntrophin, alpha 1 1.670 0.137213013_at MAPK8IP1 mitogen-activated protein kinase 8 interacting protein 1 pseudogene 1.669 0.181220372_at DNAJC28 DnaJ (Hsp40) homolog, subfamily C, member 28 1.669 0.022221868_at PAIP2B poly(A) binding protein interacting protein 2B 1.667 0.093205645_at REPS2 RALBP1 associated Eps domain containing 2 1.665 0.075220173_at C14orf45 chromosome 14 open reading frame 45 1.662 0.085211828_s_at TNIK TRAF2 and NCK interacting kinase 1.654 0.181218665_at FZD4 frizzled homolog 4 (Drosophila) 1.651 0.115214369_s_at RASGRP2 RAS guanyl releasing protein 2 (calcium and DAG-regulated) 1.648 0.080219956_at GALNT6 UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-

acetylgalactosaminyltransferase1.640 0.151

204415_at IFI6 interferon, alpha-inducible protein 6 1.636 0.074205728_at ODZ1 odz, odd Oz/ten-m homolog 1(Drosophila) 1.636 0.074215417_at EXOC6B exocyst complex component 6B 1.636 0.094202718_at IGFBP2 insulin-like growth factor binding protein 2, 36kDa 1.635 0.130219583_s_at SPATA7 spermatogenesis associated 7 1.632 0.115222088_s_at SLC2A14 /// SLC2A3 solute carrier family 2 (member 3) 1.629 0.077204340_at TMEM187 transmembrane protein 187 1.623 0.052219195_at PPARGC1A peroxisome proliferator-activated receptor gamma, coactivator 1 alpha 1.618 0.179213234_at KIAA1467 KIAA1467 1.618 0.158206401_s_at MAPT microtubule-associated protein tau 1.616 0.070218466_at TBC1D17 TBC1 domain family, member 17 1.610 0.122213463_s_at FAM149B1 family with sequence similarity 149, member B1 1.609 0.068204334_at KLF7 Kruppel-like factor 7 (ubiquitous) 1.602 0.046219313_at GRAMD1C GRAM domain containing 1C 1.599 0.015218489_s_at ALAD aminolevulinate dehydratase 1.599 0.063218858_at DEPDC6 DEP domain containing 6 1.596 0.089219147_s_at C9orf95 chromosome 9 open reading frame 95 1.594 0.04557540_at RBKS ribokinase 1.592 0.016209824_s_at ARNTL aryl hydrocarbon receptor nuclear translocator-like 1.578 0.043207125_at ZNF225 zinc finger protein 225 1.574 0.153220374_at KLHL28 kelch-like 28 (Drosophila) 1.574 0.106204284_at PPP1R3C protein phosphatase 1, regulatory (inhibitor) subunit 3C 1.570 0.066206204_at GRB14 growth factor receptor-bound protein 14 1.570 0.059212912_at RPS6KA2 ribosomal protein S6 kinase, 90kDa, polypeptide 2 1.569 0.035221560_at MARK4 MAP/microtubule affinity-regulating kinase 4 1.567 0.081202498_s_at SLC2A3 solute carrier family 2 (facilitated glucose transporter), member 3 1.565 0.072212143_s_at IGFBP3 insulin-like growth factor binding protein 3 1.564 0.125210132_at EFNA3 ephrin-A3 1.553 0.033221053_s_at TDRKH tudor and KH domain containing 1.553 0.047205750_at BPHL biphenyl hydrolase-like (serine hydrolase) 1.552 0.046205248_at DOPEY2 dopey family member 2 1.552 0.054211756_at PTHLH parathyroid hormone-like hormone 1.549 0.081203722_at ALDH4A1 aldehyde dehydrogenase 4 family, member A1 1.549 0.029219270_at CHAC1 ChaC, cation transport regulator homolog 1 (E. coli) 1.546 0.114215082_at ELOVL5 ELOVL family member 5, elongation of long chain fatty acids 1.546 0.053210954_s_at TSC22D2 TSC22 domain family, member 2 1.542 0.045202284_s_at CDKN1A cyclin-dependent kinase inhibitor 1A (p21, Cip1) 1.541 0.023203936_s_at MMP9 matrix metallopeptidase 9 1.538 0.064201044_x_at DUSP1 dual specificity phosphatase 1 1.536 0.052201452_at RHEB Ras homolog enriched in brain 1.533 0.151204796_at EML1 echinoderm microtubule associated protein like 1 1.531 0.111222043_at CLU clusterin 1.530 0.029266_s_at CD24 CD24 molecule 1.530 0.023218177_at CHMP1B chromatin modifying protein 1B 1.530 0.028219688_at BBS7 Bardet-Biedl syndrome 7 1.523 0.060205769_at SLC27A2 solute carrier family 27 (fatty acid transporter), member 2 1.522 0.037220444_at ZNF557 zinc finger protein 557 1.522 0.018208869_s_at GABARAPL1 GABA(A) receptor-associated protein like 1 1.518 0.028207981_s_at ESRRG estrogen-related receptor gamma 1.516 0.009219410_at TMEM45A transmembrane protein 45A 1.510 0.087205352_at SERPINI1 serpin peptidase inhibitor, clade I (neuroserpin), member 1 1.510 0.030206483_at LRRC6 leucine rich repeat containing 6 1.504 0.133203604_at ZNF516 zinc finger protein 516 1.503 0.038218631_at AVPI1 arginine vasopressin-induced 1 1.503 0.058

Vasilatos et al.

ID Gene Symbol Gene Title Fold Reduction SD219500_at CLCF1 cardiotrophin-like cytokine factor 1 -4.663 0.014204747_at IFIT3 interferon-induced protein with tetratricopeptide repeats 3 -4.283 0.017212776_s_at OBSL1 obscurin-like 1 -4.112 0.029219911_s_at SLCO4A1 solute carrier organic anion transporter family, member 4A1 -3.715 0.01360471_at RIN3 Ras and Rab interactor 3 -3.546 0.024207714_s_at SERPINH1 serpin peptidase inhibitor, clade H (heat shock protein 47), member 1, (collagen binding protein 1) -3.368 0.017209676_at TFPI tissue factor pathway inhibitor (lipoprotein-associated coagulation inhibitor) -3.205 0.026221270_s_at QTRT1 queuine tRNA-ribosyltransferase 1 -3.071 0.026202827_s_at MMP14 matrix metallopeptidase 14 (membrane-inserted) -3.048 0.030204999_s_at ATF5 activating transcription factor 5 -3.012 0.068201332_s_at STAT6 signal transducer and activator of transcription 6, interleukin-4 induced -2.970 0.044217502_at IFIT2 interferon-induced protein with tetratricopeptide repeats 2 -2.946 0.087221335_x_at C19orf61 chromosome 19 open reading frame 61 -2.923 0.031201809_s_at ENG endoglin -2.684 0.051213589_s_at B3GNTL1 UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase-like 1 -2.619 0.023219278_at MAP3K6 mitogen-activated protein kinase kinase kinase 6 -2.606 0.038207711_at C20orf117 chromosome 20 open reading frame 117 -2.574 0.019209873_s_at PKP3 plakophilin 3 -2.570 0.049204503_at EVPL envoplakin -2.453 0.028209834_at CHST3 carbohydrate (chondroitin 6) sulfotransferase 3 -2.399 0.039209417_s_at IFI35 interferon-induced protein 35 -2.383 0.003216250_s_at LPXN leupaxin -2.364 0.028208806_at CHD3 chromodomain helicase DNA binding protein 3 -2.340 0.035202958_at PTPN9 protein tyrosine phosphatase, non-receptor type 9 -2.328 0.054219441_s_at LRRK1 leucine-rich repeat kinase 1 -2.327 0.035218154_at GSDMD gasdermin D -2.307 0.057202240_at PLK1 polo-like kinase 1 (Drosophila) -2.248 0.025214927_at ITGBL1 integrin, beta-like 1 (with EGF-like repeat domains) -2.245 0.008222062_at IL27RA interleukin 27 receptor, alpha -2.238 0.001210510_s_at NRP1 neuropilin 1 -2.216 0.07241386_i_at KDM6B lysine (K)-specific demethylase 6B -2.172 0.045217937_s_at HDAC7 histone deacetylase 7 -2.171 0.013219594_at NINJ2 ninjurin 2 -2.168 0.050221519_at FBXW4 F-box and WD repeat domain containing 4 -2.137 0.01537793_r_at RAD51L3 RAD51-like 3 (S. cerevisiae) -2.134 0.033219080_s_at CTPS2 CTP synthase II -2.131 0.008215429_s_at ZNF428 zinc finger protein 428 -2.115 0.018213323_s_at ZC3H7B zinc finger CCCH-type containing 7B -2.102 0.067214881_s_at UBTF upstream binding transcription factor, RNA polymerase I -2.097 0.012203723_at ITPKB inositol 1,4,5-trisphosphate 3-kinase B -2.090 0.021219861_at DNAJC17 DnaJ (Hsp40) homolog, subfamily C, member 17 -2.070 0.016221566_s_at NOL3 nucleolar protein 3 (apoptosis repressor with CARD domain) -2.064 0.070211392_s_at PATZ1 POZ (BTB) and AT hook containing zinc finger 1 -2.060 0.024210340_s_at CSF2RA colony stimulating factor 2 receptor, alpha, low-affinity (granulocyte-macrophage) -2.046 0.044221610_s_at STAP2 signal transducing adaptor family member 2 -2.019 0.016206767_at RBMS3 RNA binding motif, single stranded interacting protein 3 -2.011 0.057203866_at NLE1 notchless homolog 1 (Drosophila) -2.010 0.043204038_s_at LPAR1 lysophosphatidic acid receptor 1 -2.008 0.037212427_at KIAA0368 KIAA0368 -2.003 0.00165517_at AP1M2 adaptor-related protein complex 1, mu 2 subunit -1.987 0.048220474_at SLC25A21 solute carrier family 25 (mitochondrial oxodicarboxylate carrier), member 21 -1.967 0.051220169_at TMEM156 transmembrane protein 156 -1.926 0.077212951_at GPR116 G protein-coupled receptor 116 -1.915 0.019205379_at CBR3 carbonyl reductase 3 -1.913 0.014210664_s_at TFPI tissue factor pathway inhibitor (lipoprotein-associated coagulation inhibitor) -1.909 0.039215982_s_at DOM3Z dom-3 homolog Z (C. elegans) -1.900 0.038213895_at EMP1 epithelial membrane protein 1 -1.895 0.005218266_s_at NCS1 neuronal calcium sensor 1 -1.894 0.042219342_at CASD1 CAS1 domain containing 1 -1.881 0.073221558_s_at LEF1 lymphoid enhancer-binding factor 1 -1.879 0.023205090_s_at NAGPA N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase -1.878 0.021212551_at CAP2 CAP, adenylate cyclase-associated protein, 2 (yeast) -1.874 0.049210892_s_at GTF2I general transcription factor IIi -1.873 0.035207247_s_at ZFX /// ZFY zinc finger protein, X-linked /// zinc finger protein, Y-linked -1.862 0.016207414_s_at PCSK6 proprotein convertase subtilisin/kexin type 6 -1.852 0.036209052_s_at WHSC1 Wolf-Hirschhorn syndrome candidate 1 -1.850 0.03591826_at EPS8L1 EPS8-like 1 -1.848 0.032219279_at DOCK10 dedicator of cytokinesis 10 -1.841 0.067204950_at CARD8 caspase recruitment domain family, member 8 -1.838 0.039219673_at MCM9 minichromosome maintenance complex component 9 -1.836 0.036218986_s_at DDX60 DEAD (Asp-Glu-Ala-Asp) box polypeptide 60 -1.828 0.033208719_s_at DDX17 DEAD (Asp-Glu-Ala-Asp) box polypeptide 17 -1.823 0.029207766_at CDKL1 cyclin-dependent kinase-like 1 (CDC2-related kinase) -1.813 0.038204123_at LIG3 ligase III, DNA, ATP-dependent -1.807 0.015

Table S3. Gene expression reduced by treatment with SAHA in MDA-MB-231 cells.Vasilatos et al.

ID Gene Symbol Gene Title Fold Induction SD214390_s_at BCAT1 branched chain amino-acid transaminase 1, cytosolic -1.801 0.039203964_at NMI N-myc (and STAT) interactor -1.787 0.044202269_x_at GBP1 guanylate binding protein 1, interferon-inducible, 67kDa -1.782 0.044211317_s_at CFLAR CASP8 and FADD-like apoptosis regulator -1.776 0.044207871_s_at ST7 suppression of tumorigenicity 7 -1.767 0.02938892_at KIAA0240 KIAA0240 -1.751 0.067201159_s_at NMT1 N-myristoyltransferase 1 -1.747 0.047211300_s_at TP53 tumor protein p53 -1.744 0.024206578_at NKX2-5 NK2 transcription factor related, locus 5 (Drosophila) -1.735 0.015215767_at ZNF804A zinc finger protein 804A -1.720 0.027204696_s_at CDC25A cell division cycle 25 homolog A (S. pombe) -1.718 0.043218552_at ECHDC2 enoyl CoA hydratase domain containing 2 -1.718 0.028202319_at SENP6 SUMO1/sentrin specific peptidase 6 -1.717 0.049204401_at KCNN4 potassium intermediate/small conductance calcium-activated channel, subfamily N, member 4 -1.707 0.069207375_s_at IL15RA interleukin 15 receptor, alpha -1.704 0.015219491_at LRFN4 leucine rich repeat and fibronectin type III domain containing 4 -1.697 0.044220643_s_at FAIM Fas apoptotic inhibitory molecule -1.694 0.036205726_at DIAPH2 diaphanous homolog 2 (Drosophila) -1.687 0.071221826_at ANGEL2 angel homolog 2 (Drosophila) -1.682 0.004218821_at NPEPL1 aminopeptidase-like 1 -1.672 0.033213030_s_at PLXNA2 plexin A2 -1.670 0.028221218_s_at TPK1 thiamin pyrophosphokinase 1 -1.667 0.021221435_x_at HYI hydroxypyruvate isomerase homolog (E. coli) -1.663 0.048204112_s_at HNMT histamine N-methyltransferase -1.657 0.044205463_s_at PDGFA platelet-derived growth factor alpha polypeptide -1.656 0.004212494_at TENC1 tensin like C1 domain containing phosphatase (tensin 2) -1.655 0.031203887_s_at THBD thrombomodulin -1.653 0.072211200_s_at EFCAB2 EF-hand calcium binding domain 2 -1.651 0.051201977_s_at KIAA0141 KIAA0141 -1.645 0.025205210_at TGFBRAP1 transforming growth factor, beta receptor associated protein 1 -1.641 0.015215489_x_at HOMER3 homer homolog 3 (Drosophila) -1.638 0.064201932_at LRRC41 leucine rich repeat containing 41 -1.637 0.025210916_s_at CD44 CD44 molecule (Indian blood group) -1.636 0.06546947_at GNL3L guanine nucleotide binding protein-like 3 (nucleolar)-like -1.630 0.036204493_at BID BH3 interacting domain death agonist -1.628 0.046205302_at IGFBP1 insulin-like growth factor binding protein 1 -1.616 0.015218898_at FAM57A family with sequence similarity 57, member A -1.616 0.047209938_at TADA2A transcriptional adaptor 2A -1.614 0.049203506_s_at MED12 mediator complex subunit 12 -1.600 0.009216836_s_at ERBB2 v-erb-b2 erythroblastic leukemia viral oncogene homolog 2 -1.596 0.029217076_s_at HOXD3 homeobox D3 -1.594 0.022202137_s_at ZMYND11 zinc finger, MYND domain containing 11 -1.592 0.060206377_at FOXF2 forkhead box F2 -1.592 0.009205349_at GNA15 guanine nucleotide binding protein (G protein), alpha 15 (Gq class) -1.591 0.055218457_s_at DNMT3A DNA (cytosine-5-)-methyltransferase 3 alpha -1.579 0.037203806_s_at FANCA Fanconi anemia, complementation group A -1.569 0.024215517_at PYGO1 pygopus homolog 1 (Drosophila) -1.557 0.025214496_x_at MYST4 MYST histone acetyltransferase (monocytic leukemia) 4 -1.557 0.014221849_s_at DCAF15 DDB1 and CUL4 associated factor 15 -1.552 0.038209040_s_at PSMB8 proteasome (prosome, macropain) subunit, beta type, 8 (large multifunctional peptidase 7) -1.549 0.053206805_at SEMA3A sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A -1.545 0.057217889_s_at CYBRD1 cytochrome b reductase 1 -1.539 0.032219749_at SH2D4A SH2 domain containing 4A -1.538 0.045207920_x_at ZFX zinc finger protein, X-linked -1.537 0.042217599_s_at MDFIC MyoD family inhibitor domain containing -1.537 0.041213437_at RUFY3 RUN and FYVE domain containing 3 -1.537 0.058212660_at PHF15 PHD finger protein 15 -1.537 0.048213010_at PRKCDBP protein kinase C, delta binding protein -1.531 0.021215022_x_at ZNF33B zinc finger protein 33B -1.529 0.032215617_at SPATS2L spermatogenesis associated, serine-rich 2-like -1.529 0.04948117_at CCDC101 coiled-coil domain containing 101 -1.526 0.018210278_s_at AP4S1 adaptor-related protein complex 4, sigma 1 subunit -1.521 0.012203269_at NSMAF neutral sphingomyelinase (N-SMase) activation associated factor -1.521 0.032213298_at NFIC nuclear factor I/C (CCAAT-binding transcription factor) -1.519 0.039219320_at MYO19 myosin XIX -1.519 0.020221029_s_at WNT5B wingless-type MMTV integration site family, member 5B -1.518 0.050218796_at FERMT1 fermitin family homolog 1 (Drosophila) -1.516 0.051203260_at HDDC2 HD domain containing 2 -1.502 0.044

Vasilatos et al.