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1 Supplementary Table S1. Histological And Supplementary Table S1. Histological and immunocytochemestry of the bcMCF clones. Clones Tumor type AE1 CAM5.2 EMA Vimentin bcMCF-1 Invasive poorly - - - +++ bcMCF-4 differentiated spindle cell type bcMCF-2 Invasive poorly +/- +/- +/- ++ bcMCF-6 differentiated bcMCF-7 epithelial cell type bcMCF-3 Invasive poorly - +/- +/- ++ bcMCF-5 differentiated with mix features of spindle and epithelial type The mouse monoclonal antibodies anti- human cytokeratin of low molecular weight (AE1, Biogenex, San Ramon, CA), cytokeratin peptides 7 and 8 (CAM5.2, Ventana, Tucson, AZ), epithelial membrane antigen (EMA) clone E29 and vimentin, clone V9, both from DakoCytomation Inc. (Fort Collins, CO) were used. Negative (-), weak (+/-), moderate (++) or strong (+++). 1 Supplementary Table S2. Differentially expressed apoptosis genes (GO:00009165) in tumorigenic bcMCF cells. Fold change Symbol Gene name trMCF bcMC caMCF AHR aryl hydrocarbon receptor Ns* -2.1 Ns APP amyloid beta (A4) precursor protein Ns -1.7 -1.7 BAG1 BCL2-associated athanogene Ns -7.6 -9.2 BAG5 BCL2-associated athanogene 5 Ns -1.8 Ns BIRC4 baculoviral IAP repeat-containing 4 Ns -2.0 -2.7 BNIP3L BCL2/adenovirus E1B interacting protein 3-like Ns -2 -1.9 CASP14 caspase 14, apoptosis-related cysteine peptidase Ns -12 -12.3 CASP3 caspase 3, apoptosis-related cysteine peptidase Ns -2.4 Ns CASP6 caspase 6, apoptosis-related cysteine peptidase Ns -4.1 -4.1 CD14 CD14 antigen Ns -4.7 Ns DAPK1 death-associated protein kinase 1 Ns -4.1 -13.4 ELMO3 engulfment and cell motility 3 Ns -9.9 -10.8 ELMOD2 ELMO domain containing 2 Ns -2.5 -2.2 GADD45A growth arrest and DNA-damage-inducible, alpha Ns 2.1 Ns GADD45B growth arrest and DNA-damage-inducible, beta Ns 2.7 Ns HIPK2 homeodomain interacting protein kinase 2 Ns 3.2 2.6 HIPK3 homeodomain interacting protein kinase 3 Ns -3.1 -2.4 MAEA macrophage erythroblast attacher Ns -2.2 Ns NGFRAP1 nerve growth factor receptor associated protein 1 Ns 2.1 2.0 PPP1R13L protein phosphatase 1, inhibitory subunit 13 like Ns -2.1 -2.8 SGPL1 sphingosine-1-phosphate lyase 1 Ns -2.9 -2.7 STK17A serine/threonine kinase 17a (apoptosis-inducing) Ns -1.7 Ns STK3 serine/threonine kinase 3 (STE20 homolog, yeast) Ns -3.5 Ns TNFSF7 tumor necrosis factor superfamily, member 7 -2.0 -7.6 -4.1 TNFSF9 tumor necrosis factor superfamily, member 9 -2.0 -8.1 -4.5 TP73L tumor protein p73-like Ns -4.7 -11.4 TRAF4 TNF receptor-associated factor 4 Ns -2.6 -2.5 TTC11 tetratricopeptide repeat domain 11 Ns -1.9 -1.9 * Non-significant gene; Genes were identified by Gene Ontology tool, Onto-Express. 2 Supplementary Table S3. Canonical pathways enriched with dysregulated genes Fold change Symbol Gene name trMCF bcMCF caMCF TGFβ signaling pathway BMP2 bone morphogenetic protein 2 Ns* Ns -4.3 BMPR2 bone morphogenetic protein receptor, type II 2.0 3.0 2.5 HRAS v-Ha-ras Harvey rat sarcoma viral oncogene homolog Ns 6.0 7.4 INHBA inhibin, beta A (activin A, activin AB alpha polypeptide) Ns Ns -14.9 KRAS v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog Ns -2.7 Ns SERPINE1 serpin peptidase inhibitor, clade E, member 1 -5.1 Ns Ns SMAD2 SMAD, mothers against DPP homolog 2 Ns Ns -1.8 SMAD5 SMAD, mothers against DPP homolog 5 Ns Ns 2.1 SMURF2 SMAD specific E3 ubiquitin protein ligase 2 Ns Ns 2 TGFB1 transforming growth factor, beta 1 Ns 3.1 3.1 TGFB2 transforming growth factor, beta 2 -3.6 -9.4 -9.9 TGFBR2 transforming growth factor, beta receptor II -2.2 -1.8 Ns Pyrimidine metabolism pathway CANT1 calcium activated nucleotidase 1 Ns -1.9 Ns CDA cytidine deaminase -6.1 Ns Ns DCTD dCMP deaminase Ns -2.1 -2.1 DPYSL3 dihydropyrimidinase-like 3 Ns 24.1 26.9 ECGF1 endothelial cell growth factor 1 (platelet-derived) Ns -3.2 -3.4 ENTPD4 ectonucleoside triphosphate diphosphohydrolase 4 Ns -4.4 -2.9 NME4 non-metastatic cells 4, protein expressed in -2 -5.1 -4.7 NME7 non-metastatic cells 7, protein expressed in Ns -2.6 Ns NT5C2 5'-nucleotidase, cytosolic II Ns -2.6 -2.2 NT5E 5'-nucleotidase, ecto (CD73) -3.3 1.9 2.1 POLB polymerase (DNA directed), beta Ns -2.2 Ns POLE2 Polymerase (DNA directed), epsilon 2 (p59 subunit) 2.7 Ns Ns POLR1D polymerase (RNA) I polypeptide D, 16kDa Ns -1.8 Ns POLR2B polymerase (RNA) II (DNA directed) polypeptide B Ns -1.8 Ns RFC3 replication factor C (activator 1) 3, 38kDa 2.1 Ns Ns RRM2 ribonucleotide reductase M2 polypeptide 1.7 Ns Ns RRM2B ribonucleotide reductase M2 B (TP53 inducible) -2.9 -3.6 -3 UPP1 uridine phosphorylase 1 Ns -2.1 -1.8 Amyloid processing pathway APP amyloid beta (A4) precursor protein Ns -1.7 -1.7 CAPN1 calpain 1, (mu/I) large subunit Ns -2.6 -2.4 CSNK1E casein kinase 1, epsilon Ns -3.3 -2.2 GSK3B glycogen synthase kinase 3 beta Ns -2.2 -1.9 PRKAR1A protein kinase, cAMP-dependent, regulatory, type I, α Ns -1.9 Ns PSEN1 presenilin 1 (Alzheimer disease 3) Ns -1.8 -1.9 3 Supplementary Table S3. Continuation Fold change Symbol Gene name trMCF bcMCF caMCF Glutathione metabolism GCLC glutamate cysteine ligase, catalytic subunit Ns -2.9 -2.7 GPX1 glutathione peroxidase 1 Ns Ns -1.7 GSR glutathione reductase 2.2 NS Ns GSTK1 glutathione S-transferase kappa 1 -1.8 -2.3 -2.1 GSTO2 glutathione S-transferase omega 2 Ns -5.6 -6.6 GSTP1 glutathione S-transferase pi Ns -2.0 -2.3 GSTT2 glutathione S-transferase theta 2 Ns Ns 2.1 IDH1 isocitrate dehydrogenase 1 (NADP+), soluble Ns -2.2 -2.2 IDH2 isocitrate dehydrogenase 2 (NADP+) Ns -3.3 -2.3 MGST2 microsomal glutathione S-transferase 2 Ns -2.4 -2.4 MGST3 microsomal glutathione S-transferase 3 Ns Ns -2.2 RAB15 RAB15, member RA oncogene family Ns -2.8 -2.5 ERK/MAPK signaling pathway DUSP1 dual specificity phosphatase 1 3.0 2.7 Ns DUSP4 dual specificity phosphatase 4 Ns* -2.2 -2.4 DUSP6 dual specificity phosphatase 6 Ns 2.3 2.4 EIF4E eukaryotic translation initiation factor 4E Ns -2.4 -2.3 EIF4EBP1 (Eu) translation initiation factor 4E binding protein 1 Ns Ns -1.9 FOS v-fos FBJ murine osteosarcoma viral oncogene Ns Ns -11.5 FYN FYN oncogene related to SRC, FGR, YES Ns Ns 2.2 HRAS v-Ha-ras Harvey rat sarcoma viral oncogene Ns 6.0 7.4 HSPB1 heat shock 27kDa protein 1 Ns -1.9 -2.8 KRAS v-Ki-ras2 Kirsten rat sarcoma viral oncogene Ns -2.7 Ns MAP2K1IP1 MAP kinase kinase 1 interacting protein 1 Ns -3.6 -3.4 MKNK2 MAP kinase interacting serine/threonin kinase 2 Ns Ns -1.9 PPP1CB protein phosphatase 1, catalytic subunit, β Ns -2.2 -1.9 PPP1R14C protein phosphatase 1, inhibitory subunit 14C Ns -20.2 -9.7 PPP2CB protein phosphatase 2, catalytic subunit, β Ns Ns -2.0 PPP2R5C protein phosphatase 2, regulatory subunit B, γ Ns -2.0 Ns PRKAR1A Protein kinase cAMP-dependant regulatory type I α Ns -1.9 Ns PRKCI protein kinase C, iota Ns -2.0 -2.6 RAC1 ras-related C3 botulinum toxin substrate 1 Ns -1.9 Ns RAC2 ras-related C3 botulinum toxin substrate 2 Ns -1.9 Ns STAT3 signal transducer and activator of transcription 3 Ns Ns -2.1 YWHAZ tyrosine 3-monooxygenase zeta polypeptide Ns Ns -1.9 * Non-significant gene Genes were identified by Ingenuity Pathway Analysis (see Fig. 2C). 4 Supplementary Table S4. Dysregulated genes in intermediate filament (GO:0005882) Fold change Symbol Gene name trMCF bcMCF caMCF KRT5 keratin 5 Ns* -2.2 -17.2 KRT7 keratin 7 Ns -2.5 -5.3 KRT8 keratin 8 Ns -2.6 -4.4 KRT16 keratin 16 Ns -11.7 -50.4 KRT17 keratin 17 Ns -37.4 -50.6 KRT18 keratin 18 Ns -2.1 -1.9 KRT6B keratin 6B -1.7 -102.9 -114.9 KRTHB1 keratin, hair, basic, 1 Ns -6.1 -5.0 DSP desmoplakin Ns -8.7 -135.7 RSN restin Ns -2.8 -2.0 SPRR1B small proline-rich protein 1B (cornifin) Ns -14.2 -15.6 PLEC1 plectin 1 Ns Ns 4.3 VIM Vimentin Ns 7.0 8.1 * Non-significant gene; Genes were identified by Gene Ontology tool, Onto-Express for cellular component. 5 Supplementary Table S5: Epithelia-mesenchymal transition markers and their regulators reported in literature Symbol Gene Title Reference * JAG1 jagged 1 (Alagille syndrome) (Zavadil et al., 2004) HEY1 hairy/enhancer-of-split related with YRPW motif 1 (Zavadil et al., 2004) S100A4 S100 calcium binding protein A4 (Xue et al., 2003) SIP1 survival of motor neuron protein interacting protein 1 (Vandewalle et al., 2005) HMGA2 high mobility group AT-hook 2 (Thuault et al., 2006) TGFB1 Transforming growth factor, beta 1 (Janda et al., 2002) HRAS v-Ha-ras Harvey rat sarcoma viral oncogene (Janda et al., 2002) SERPINE2 serpin peptidase inhibitor, clade E (Buchholz et al., 2003) TWIST1 twist homolog 1 (Lee et al., 2006) TWIST2 twist homolog 2 (Drosophila) (Lee et al., 2006) SNAI2 snail homolog 2 (Drosophila) (Lee et al., 2006) (Lee et al., 2006) SNAI1 snail homolog 1 (Drosophila) GSK3B Glycogen synthase kinase 3 beta (Lee et al., 2006) CDH1 cadherin 1, type 1, E-cadherin (epithelial) (Lee et al., 2006) FN1 fibronectin 1 (Lee et al., 2006) CDH2 cadherin 2, type 1, N-cadherin (neuronal) (Lee et al., 2006) OCLN occludin (Lee et al., 2006) SOX10 SRY (sex determining region Y)-box 10 (Lee et al., 2006) FOXC2 forkhead box C2 (MFH-1, mesenchyme forkhead 1) (Lee et al., 2006) GSC goosecoid (Lee et al., 2006) MMP2 matrix metallopeptidase 2 (Lee et al., 2006) MMP3 matrix metallopeptidase 3 (Lee et al., 2006) MMP9 matrix metallopeptidase 9 (Lee et al., 2006) DSP desmoplakin (Lee et al., 2006) (Lee et al., 2006) KRIT1 KRIT1, ankyrin repeat containing KRT10 keratin 10 (Lee et al., 2006) KRT12 keratin 12 (Meesmann corneal dystrophy) (Lee et al., 2006) KRT13 keratin 13 (Lee et al., 2006) KRT14 keratin 14 (Lee et al., 2006) KRT15 keratin 15 (Lee et al., 2006) KRT16 keratin 16 (Lee et al., 2006) KRT17 keratin 17 (Lee et al., 2006) 6 Supplementary Table S5.
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