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Figure S1 Relative LSD1 mRNA (%) (HDAC siRNA vs. Scramble) MDA-MB-231 cells Vasilatos et al.

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Presentation on theme: "Figure S1 Relative LSD1 mRNA (%) (HDAC siRNA vs. Scramble) MDA-MB-231 cells Vasilatos et al."— Presentation transcript:

1 Figure S1 Relative LSD1 mRNA (%) (HDAC siRNA vs. Scramble) MDA-MB-231 cells Vasilatos et al.

2 mRNA level (Fold) Relative to MDA-MB-231 NR4A1 mRNA level (Fold) Relative to MDA-MB-231 PCDH1 RGS16 mRNA level (Fold) Relative to MDA-MB-231 mRNA level (Fold) Relative to MDA-MB-231 BIK Figure S2 Vasilatos et al.

3 A LSD1 HDAC5 P=0.189 LSD1 P=0.677 HDAC5 B Figure S3 Vasilatos et al.

4 CDKN1A  -Actin Cytoplasmic Nuclear SAHA - + CDKN1A PCNA A Figure S4 SAHA Pargyline NR4A1  -actin B NR4A1 PCNA Cytoplasmic Nuclear MDA-MB-231 MDA-MB-468

5 Cell LineERPRHER2 Gene Cluster Clinical Subtype ZR LuHER UACC LuHER UACC LuHER HCC LuHER HCC LuHER HCC BaAHER HCC BaAHER HCC LuHER AU LuHER BT LuHER MDA-MB LuHER SK-BR LuHER MDA-MB LuHER ZR LuHR HCC LuHR HCC LuHR CAMA LuHR MCF LuHR MDA-MB-134-VI+- - LuHR BT LuHR MDA-MB LuHR T-47D++ - LuHR HCC BaBTN HCC BaATN HCC BaATN HCC BaBTN HCC BaATN HCC BaATN HCC BaATN BT BaATN MDA-MB BaBTN MDA-MB BaBTN BT BaBTN DU BaATN HS 578T --- BaBTN MDA-MB BaBTN 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.

6 IDGene SymbolGene TitleFold InductionSD _atABAT4-aminobutyrate aminotransferase _atHPCAL4hippocalcin like _atCORO1Acoronin, actin binding protein, 1A _atFABP4fatty acid binding protein 4, adipocyte _s_atNEAT1nuclear paraspeckle assembly transcript 1 (non-protein coding) _s_atMAP2microtubule-associated protein _x_atMAPRE3microtubule-associated protein, RP/EB family, member _s_atDHRS2dehydrogenase/reductase (SDR family) member _s_atENPP2ectonucleotide pyrophosphatase/phosphodiesterase _atRCAN2regulator of calcineurin _atSTAT4signal transducer and activator of transcription _s_atSTC1stanniocalcin _s_atTEX14testis expressed _atFAM49Afamily with sequence similarity 49, member A _s_atIQCGIQ motif containing G _s_atSYT11synaptotagmin XI _s_atNDRG4NDRG family member _atHLA-DMBmajor histocompatibility complex, class II, DM beta _atLRRC23leucine rich repeat containing _atTUBB4tubulin, beta _atRALGPS1Ral GEF with PH domain and SH3 binding motif _atARL14ADP-ribosylation factor-like _atNAP1L3nucleosome assembly protein 1-like _atCOBLcordon-bleu homolog (mouse) _s_atSEPT4septin _atPLCL1phospholipase C-like _atPARM1prostate androgen-regulated mucin-like protein _s_atFGFR4fibroblast growth factor receptor _s_atSORBS1sorbin and SH3 domain containing _atENPP2ectonucleotide pyrophosphatase/phosphodiesterase _s_atCYFIP2cytoplasmic FMR1 interacting protein _atDNM3dynamin _atFOSFBJ murine osteosarcoma viral oncogene homolog _atEGR2early growth response _atBBS9Bardet-Biedl syndrome _s_atSILVsilver homolog (mouse) _s_atERBB3v-erb-b2 erythroblastic leukemia viral oncogene homolog 3 (avian) _atHLA-DPA1major histocompatibility complex, class II, DP alpha _s_atGSNgelsolin _s_atHIST2H2BEhistone cluster 2, H2be _atCRISPLD2cysteine-rich secretory protein LCCL domain containing _s_atRTN2reticulon _s_atFAM184Afamily with sequence similarity 184, member A _atNEO1neogenin homolog 1 (chicken) _atZNF204Pzinc finger protein 204 (pseudogene) _atMAP1Amicrotubule-associated protein 1A _atVWA5Avon Willebrand factor A domain containing 5A _s_atPTPRRprotein tyrosine phosphatase, receptor type, R _atNR3C2nuclear receptor subfamily 3, group C, member _s_atPLEKHB1pleckstrin homology domain containing, family B (evectins) member _s_atRGS9regulator of G-protein signaling _atNEBLnebulette _atSCG2secretogranin II _atARCactivity-regulated cytoskeleton-associated protein _atPTPRHprotein tyrosine phosphatase, receptor type, H _x_atNR4A2nuclear receptor subfamily 4, group A, member _s_atFOLR1folate receptor 1 (adult) _atCRYMcrystallin, mu _atHEY1hairy/enhancer-of-split related with YRPW motif _atATP8A1ATPase, aminophospholipid transporter (APLT), class I, type 8A, member _atCRABP2cellular retinoic acid binding protein _atAPLP1amyloid beta (A4) precursor-like protein _atTMCC2transmembrane and coiled-coil domain family _s_atC11orf71chromosome 11 open reading frame _s_atTHBS1thrombospondin _atPLCD1phospholipase C, delta Table S2. Gene expression induced by treatment with SAHA in MDA-MB-231 cells Vasilatos et al.

7 IDGene SymbolGene TitleFold InductionSD _s_atTM7SF2transmembrane 7 superfamily member _atC4orf31chromosome 4 open reading frame _s_atTNFRSF9tumor necrosis factor receptor superfamily, member _atCLIC3chloride intracellular channel _s_atIL8interleukin _atDNAJC12DnaJ (Hsp40) homolog, subfamily C, member _atTTC30Atetratricopeptide repeat domain 30A _x_atID2inhibitor of DNA binding 2, dominant negative helix-loop-helix protein _atIQCHIQ motif containing H _atDLX4distal-less homeobox _atCYP27B1cytochrome P450, family 27, subfamily B, polypeptide _atARRB2arrestin, beta _atMAST3microtubule associated serine/threonine kinase _atAREGamphiregulin _s_atCDC14BCDC14 cell division cycle 14 homolog B (S. cerevisiae) _s_atKLHL24kelch-like 24 (Drosophila) _s_atVSNL1visinin-like _atBMP6bone morphogenetic protein _atZNF365zinc finger protein _atBAI2brain-specific angiogenesis inhibitor _atRUNDC3BRUN domain containing 3B _g_atGM2AGM2 ganglioside activator _atKIAA _s_atKCNAB1potassium voltage-gated channel, shaker-related subfamily, beta member _atC9orf116chromosome 9 open reading frame _atTLN2talin _atHDAC5histone deacetylase _s_atCALCOCO1calcium binding and coiled-coil domain _atMAGI2membrane associated guanylate kinase, WW and PDZ domain containing _atETNK2ethanolamine kinase _s_atPDE4DIPphosphodiesterase 4D interacting protein _atRASA4RAS p21 protein activator _atLOH3CR2Aloss of heterozygosity, 3, chromosomal region 2, gene A _s_atKIAA _s_atRLN2relaxin _atAQP3aquaporin 3 (Gill blood group) _atKAL1Kallmann syndrome 1 sequence _atSPSB3splA/ryanodine receptor domain and SOCS box containing _s_atPPP4R4protein phosphatase 4, regulatory subunit _atSEMA3Gsema domain, immunoglobulin domain (Ig), short basic domain, secreted, 3G _atMAGEB2melanoma antigen family B, _s_atLMCD1LIM and cysteine-rich domains _s_atABCG1ATP-binding cassette, sub-family G (WHITE), member _atPRPHperipherin _atCYP1A1cytochrome P450, family 1, subfamily A, polypeptide _atLPHN1latrophilin _atLIN7Blin-7 homolog B (C. elegans) _s_atCDS1CDP-diacylglycerol synthase (phosphatidate cytidylyltransferase) _atGPNMBglycoprotein (transmembrane) nmb _s_atMAN1A1mannosidase, alpha, class 1A, member _atHOOK2hook homolog 2 (Drosophila) _atMARCH2membrane-associated ring finger (C3HC4) _atEPORerythropoietin receptor _atSOD2superoxide dismutase 2, mitochondrial _atANGangiogenin, ribonuclease, RNase A family, _s_atRGL1ral guanine nucleotide dissociation stimulator-like _s_atPPP2R5Bprotein phosphatase 2, regulatory subunit B', beta _atSLPIsecretory leukocyte peptidase inhibitor _s_atSH3BGRSH3 domain binding glutamic acid-rich protein _s_atPDK2pyruvate dehydrogenase kinase, isozyme AFFX-HUMISGF3A/ M97935_MA_at STAT1signal transducer and activator of transcription 1, 91kDa _atPSMB9proteasome (prosome, macropain) subunit, beta type, _s_atLYSTlysosomal trafficking regulator _s_atPRKACAprotein kinase, cAMP-dependent, catalytic, alpha _s_atKIAA _atTRIM9tripartite motif-containing _s_atPBXIP1pre-B-cell leukemia homeobox interacting protein _s_atHMGN5high-mobility group nucleosome binding domain Vasilatos et al.

8 IDGene SymbolGene TitleFold InductionSD _s_atHPGDhydroxyprostaglandin dehydrogenase 15-(NAD) _i_atINO80BINO80 complex subunit B _s_atBHLHE41basic helix-loop-helix family, member e _atTNFSF9tumor necrosis factor (ligand) superfamily, member _atSNTA1syntrophin, alpha _atMAPK8IP1mitogen-activated protein kinase 8 interacting protein 1 pseudogene _atDNAJC28DnaJ (Hsp40) homolog, subfamily C, member _atPAIP2Bpoly(A) binding protein interacting protein 2B _atREPS2RALBP1 associated Eps domain containing _atC14orf45chromosome 14 open reading frame _s_atTNIKTRAF2 and NCK interacting kinase _atFZD4frizzled homolog 4 (Drosophila) _s_atRASGRP2RAS guanyl releasing protein 2 (calcium and DAG-regulated) _atGALNT6 UDP-N-acetyl-alpha-D-galactosamine:polypeptide N- acetylgalactosaminyltransferase _atIFI6interferon, alpha-inducible protein _atODZ1odz, odd Oz/ten-m homolog 1(Drosophila) _atEXOC6Bexocyst complex component 6B _atIGFBP2insulin-like growth factor binding protein 2, 36kDa _s_atSPATA7spermatogenesis associated _s_atSLC2A14 /// SLC2A3solute carrier family 2 (member 3) _atTMEM187transmembrane protein _atPPARGC1Aperoxisome proliferator-activated receptor gamma, coactivator 1 alpha _atKIAA _s_atMAPTmicrotubule-associated protein tau _atTBC1D17TBC1 domain family, member _s_atFAM149B1family with sequence similarity 149, member B _atKLF7Kruppel-like factor 7 (ubiquitous) _atGRAMD1CGRAM domain containing 1C _s_atALADaminolevulinate dehydratase _atDEPDC6DEP domain containing _s_atC9orf95chromosome 9 open reading frame _atRBKSribokinase _s_atARNTLaryl hydrocarbon receptor nuclear translocator-like _atZNF225zinc finger protein _atKLHL28kelch-like 28 (Drosophila) _atPPP1R3Cprotein phosphatase 1, regulatory (inhibitor) subunit 3C _atGRB14growth factor receptor-bound protein _atRPS6KA2ribosomal protein S6 kinase, 90kDa, polypeptide _atMARK4MAP/microtubule affinity-regulating kinase _s_atSLC2A3solute carrier family 2 (facilitated glucose transporter), member _s_atIGFBP3insulin-like growth factor binding protein _atEFNA3ephrin-A _s_atTDRKHtudor and KH domain containing _atBPHLbiphenyl hydrolase-like (serine hydrolase) _atDOPEY2dopey family member _atPTHLHparathyroid hormone-like hormone _atALDH4A1aldehyde dehydrogenase 4 family, member A _atCHAC1ChaC, cation transport regulator homolog 1 (E. coli) _atELOVL5ELOVL family member 5, elongation of long chain fatty acids _s_atTSC22D2TSC22 domain family, member _s_atCDKN1Acyclin-dependent kinase inhibitor 1A (p21, Cip1) _s_atMMP9matrix metallopeptidase _x_atDUSP1dual specificity phosphatase _atRHEBRas homolog enriched in brain _atEML1echinoderm microtubule associated protein like _atCLUclusterin _s_atCD24CD24 molecule _atCHMP1Bchromatin modifying protein 1B _atBBS7Bardet-Biedl syndrome _atSLC27A2solute carrier family 27 (fatty acid transporter), member _atZNF557zinc finger protein _s_atGABARAPL1GABA(A) receptor-associated protein like _s_atESRRGestrogen-related receptor gamma _atTMEM45Atransmembrane protein 45A _atSERPINI1serpin peptidase inhibitor, clade I (neuroserpin), member _atLRRC6leucine rich repeat containing _atZNF516zinc finger protein _atAVPI1arginine vasopressin-induced Vasilatos et al.

9 IDGene SymbolGene TitleFold ReductionSD _atCLCF1cardiotrophin-like cytokine factor _atIFIT3interferon-induced protein with tetratricopeptide repeats _s_atOBSL1obscurin-like _s_atSLCO4A1solute carrier organic anion transporter family, member 4A _atRIN3Ras and Rab interactor _s_atSERPINH1serpin peptidase inhibitor, clade H (heat shock protein 47), member 1, (collagen binding protein 1) _atTFPItissue factor pathway inhibitor (lipoprotein-associated coagulation inhibitor) _s_atQTRT1queuine tRNA-ribosyltransferase _s_atMMP14matrix metallopeptidase 14 (membrane-inserted) _s_atATF5activating transcription factor _s_atSTAT6signal transducer and activator of transcription 6, interleukin-4 induced _atIFIT2interferon-induced protein with tetratricopeptide repeats _x_atC19orf61chromosome 19 open reading frame _s_atENGendoglin _s_atB3GNTL1UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase-like _atMAP3K6mitogen-activated protein kinase kinase kinase _atC20orf117chromosome 20 open reading frame _s_atPKP3plakophilin _atEVPLenvoplakin _atCHST3carbohydrate (chondroitin 6) sulfotransferase _s_atIFI35interferon-induced protein _s_atLPXNleupaxin _atCHD3chromodomain helicase DNA binding protein _atPTPN9protein tyrosine phosphatase, non-receptor type _s_atLRRK1leucine-rich repeat kinase _atGSDMDgasdermin D _atPLK1polo-like kinase 1 (Drosophila) _atITGBL1integrin, beta-like 1 (with EGF-like repeat domains) _atIL27RAinterleukin 27 receptor, alpha _s_atNRP1neuropilin _i_atKDM6Blysine (K)-specific demethylase 6B _s_atHDAC7histone deacetylase _atNINJ2ninjurin _atFBXW4F-box and WD repeat domain containing _r_atRAD51L3RAD51-like 3 (S. cerevisiae) _s_atCTPS2CTP synthase II _s_atZNF428zinc finger protein _s_atZC3H7Bzinc finger CCCH-type containing 7B _s_atUBTFupstream binding transcription factor, RNA polymerase I _atITPKBinositol 1,4,5-trisphosphate 3-kinase B _atDNAJC17DnaJ (Hsp40) homolog, subfamily C, member _s_atNOL3nucleolar protein 3 (apoptosis repressor with CARD domain) _s_atPATZ1POZ (BTB) and AT hook containing zinc finger _s_atCSF2RAcolony stimulating factor 2 receptor, alpha, low-affinity (granulocyte-macrophage) _s_atSTAP2signal transducing adaptor family member _atRBMS3RNA binding motif, single stranded interacting protein _atNLE1notchless homolog 1 (Drosophila) _s_atLPAR1lysophosphatidic acid receptor _atKIAA _atAP1M2adaptor-related protein complex 1, mu 2 subunit _atSLC25A21solute carrier family 25 (mitochondrial oxodicarboxylate carrier), member _atTMEM156transmembrane protein _atGPR116G protein-coupled receptor _atCBR3carbonyl reductase _s_atTFPItissue factor pathway inhibitor (lipoprotein-associated coagulation inhibitor) _s_atDOM3Zdom-3 homolog Z (C. elegans) _atEMP1epithelial membrane protein _s_atNCS1neuronal calcium sensor _atCASD1CAS1 domain containing _s_atLEF1lymphoid enhancer-binding factor _s_atNAGPAN-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase _atCAP2CAP, adenylate cyclase-associated protein, 2 (yeast) _s_atGTF2Igeneral transcription factor IIi _s_atZFX /// ZFYzinc finger protein, X-linked /// zinc finger protein, Y-linked _s_atPCSK6proprotein convertase subtilisin/kexin type _s_atWHSC1Wolf-Hirschhorn syndrome candidate _atEPS8L1EPS8-like _atDOCK10dedicator of cytokinesis _atCARD8caspase recruitment domain family, member _atMCM9minichromosome maintenance complex component _s_atDDX60DEAD (Asp-Glu-Ala-Asp) box polypeptide _s_atDDX17DEAD (Asp-Glu-Ala-Asp) box polypeptide _atCDKL1cyclin-dependent kinase-like 1 (CDC2-related kinase) _atLIG3ligase III, DNA, ATP-dependent Table S3. Gene expression reduced by treatment with SAHA in MDA-MB-231 cells. Vasilatos et al.

10 IDGene SymbolGene TitleFold InductionSD _s_atBCAT1branched chain amino-acid transaminase 1, cytosolic _atNMIN-myc (and STAT) interactor _x_atGBP1guanylate binding protein 1, interferon-inducible, 67kDa _s_atCFLARCASP8 and FADD-like apoptosis regulator _s_atST7suppression of tumorigenicity _atKIAA _s_atNMT1N-myristoyltransferase _s_atTP53tumor protein p _atNKX2-5NK2 transcription factor related, locus 5 (Drosophila) _atZNF804Azinc finger protein 804A _s_atCDC25Acell division cycle 25 homolog A (S. pombe) _atECHDC2enoyl CoA hydratase domain containing _atSENP6SUMO1/sentrin specific peptidase _atKCNN4potassium intermediate/small conductance calcium-activated channel, subfamily N, member _s_atIL15RAinterleukin 15 receptor, alpha _atLRFN4leucine rich repeat and fibronectin type III domain containing _s_atFAIMFas apoptotic inhibitory molecule _atDIAPH2diaphanous homolog 2 (Drosophila) _atANGEL2angel homolog 2 (Drosophila) _atNPEPL1aminopeptidase-like _s_atPLXNA2plexin A _s_atTPK1thiamin pyrophosphokinase _x_atHYIhydroxypyruvate isomerase homolog (E. coli) _s_atHNMThistamine N-methyltransferase _s_atPDGFAplatelet-derived growth factor alpha polypeptide _atTENC1tensin like C1 domain containing phosphatase (tensin 2) _s_atTHBDthrombomodulin _s_atEFCAB2EF-hand calcium binding domain _s_atKIAA _atTGFBRAP1transforming growth factor, beta receptor associated protein _x_atHOMER3homer homolog 3 (Drosophila) _atLRRC41leucine rich repeat containing _s_atCD44CD44 molecule (Indian blood group) _atGNL3Lguanine nucleotide binding protein-like 3 (nucleolar)-like _atBIDBH3 interacting domain death agonist _atIGFBP1insulin-like growth factor binding protein _atFAM57Afamily with sequence similarity 57, member A _atTADA2Atranscriptional adaptor 2A _s_atMED12mediator complex subunit _s_atERBB2v-erb-b2 erythroblastic leukemia viral oncogene homolog _s_atHOXD3homeobox D _s_atZMYND11zinc finger, MYND domain containing _atFOXF2forkhead box F _atGNA15guanine nucleotide binding protein (G protein), alpha 15 (Gq class) _s_atDNMT3ADNA (cytosine-5-)-methyltransferase 3 alpha _s_atFANCAFanconi anemia, complementation group A _atPYGO1pygopus homolog 1 (Drosophila) _x_atMYST4MYST histone acetyltransferase (monocytic leukemia) _s_atDCAF15DDB1 and CUL4 associated factor _s_atPSMB8proteasome (prosome, macropain) subunit, beta type, 8 (large multifunctional peptidase 7) _atSEMA3Asema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A _s_atCYBRD1cytochrome b reductase _atSH2D4ASH2 domain containing 4A _x_atZFXzinc finger protein, X-linked _s_atMDFICMyoD family inhibitor domain containing _atRUFY3RUN and FYVE domain containing _atPHF15PHD finger protein _atPRKCDBPprotein kinase C, delta binding protein _x_atZNF33Bzinc finger protein 33B _atSPATS2Lspermatogenesis associated, serine-rich 2-like _atCCDC101coiled-coil domain containing _s_atAP4S1adaptor-related protein complex 4, sigma 1 subunit _atNSMAFneutral sphingomyelinase (N-SMase) activation associated factor _atNFICnuclear factor I/C (CCAAT-binding transcription factor) _atMYO19myosin XIX _s_atWNT5Bwingless-type MMTV integration site family, member 5B _atFERMT1fermitin family homolog 1 (Drosophila) _atHDDC2HD domain containing Vasilatos et al.


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