Supplemental Data

TABLE 1

Primer sequences for QRT-PCR Sense Primer Anti-sense Primer ABLIM3 5’-ATCAGCAAGGATGGTGTTCC-3’ 5’-CAGGTTGGGTGGTAGTGCTT-3’ ASPA 5’-TGGCTCCACTACCCTGCTAC-3’ 5’-TTGAGGCTGAGGACCAACTT-3’ BACTIN 5’-GGACTTCGAGCAAGAGATGG-3’ 5’-ACATCTGCTGGAAGGTGGAC-3’ BUB1 5’-CCTTTGGAGAACGCTCTGTC-3’ 5’-GGAAGCTTGTGGAATGGTGT-3’ CDH19 5’-TGATTCCCTCCAGACCTACG-3’ 5’-AGCGAGGTCCCAACTCATTA-3’ CRYAB 5’-TGATTGAGGTGCATGGAAAAA-3’ 5’-AGGACCCCATCAGATGACAG-3’ DDR1 5’-GAGCTCTATGGCTGCCTCTG-3’ 5’-CCGTCATAGGTGGAGTCGTT-3’ DTR 5’-CTTGCCTAGGCGATTTTGTC-3’ 5’-ATGGAAGCCCAACCTCTTCT-3’ ECM1 5’-AACCGTAACAGCCACCAGAC-3’ 5’-AGCAGAAGCAACAGCCAAAT-3’ EEF1A1 5’-AATGGTGACAACATGCTGGA-3’ 5’-ACGAGTTGGTGGTAGGATGC-3’ FLRT2 5’-CCTGCTTGTTTGGGGAGATA-3’ 5’-AGGCAGGGGATACATTCCTC-3’ FOLH1 5’-ACCAGGTTACCCAGCAAATG-3’ 5’-TGCTATCTGGTGGTGCTGAG-3’ FOXD1 5’-TGCGGGTCCCTCTATTTATG-3’ 5’-TTCATCTGCCAAACGTCAAG-3’ HLADMA 5’-TCCCTGAAGCTCCTACTCCA-3’ 5’-AAAAGCTGGTCCTCGTCGTA-3’ HLAF 5’-GGCAGAGGAATATGCAGAGG-3’ 5’-TGTAGCGTCTCCTTCCCATT-3’ KCNS3 5’-GGGTGTTTGTGCCTGTTTCT-3’ 5’-GGCTGAAAGGTACACCCTGA-3’ NGFR 5’-CAGGTGACCTTCTGGGAAAT-3’ 5’-CTAGGCAAGCATCCCATCTC-3’ PMP22 5’-GCCTTCATCACTCCCACATT-3’ 5’-GGCACAGAACAGCCTAGACC-3’ RDX 5’-TGCCAAAGCACTTACACCAG-3’ 5’-CATTCCCTGGACCAAAAGAA-3’ RUNX1 5’-AGTGAGTAGCTCACGCAGCA-3’ 5’-GCCTGGCAGAAAATTCCATA-3’ SAP18 5’-AAGAAAGCCACGGGATTGTA-3’ 5’- CGTCCAACACAGCTTCTTCA-3’ SEMA3B 5’-ATGCACCAGTGGGTGTCATA-3’ 5’-TTGTACATGAGGGGGTGGTT-3’ SEMA3C 5’-CTGTTGTGACGGACAAATGG-3’ 5’- ATCTCCCTGCTGATGTTGCT-3’ STARD13 5’-CTGTATGCCAGCACAGGAGA-3’ 5’-CTCTTGGAGCCCATTGACAT-3’ TCN1 5’-GAACTACTCAACCGCCGAAG-3’ 5’-ACACAGGTCAGAGCCAGGAC-3’ TRIM58 5’-GGACTATGAAGCCGGTGAAA-3’ 5’-TAAGGCCGAAGAAGACCAGA-3’ TWIST1 5’-TGTCCGCGTCCCACTAGC-3’ 5’-TGTCCATTTTCTCCTTCTCTGGA-3’

Supplemental Data Table 1.

Primer sequences used for QRT-PCR of TWIST1 and potential TWIST1 transcriptional targets.

Common name for are listed in alphabetical order. Primer sequences were obtained using

Primer3 software (http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www.cgi) and oligonucleotides were purchased from Integrated DNA Technologies.

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TABLE 2

(A) Genes over-expressed in MPNST cell lines and under-expressed in primary MPNSTs Genbank Gene Description NM_005242 F2RL1 coagulation factor II (thrombin) receptor-like 1 NM_001338 CXADR coxsackie virus and adenovirus receptor NM_004815 PARG1 PTPL1-associated RhoGAP 1 NM_004817 TJP2 tight junction 2 (zona occludens 2) NM_001451 FOXF1 forkhead box F1 NM_004336 BUB1 BUB1 budding uninhibited by benzimidazoles 1 homolog NM_002417 MKI67 ESTs, Moderately similar to KI67_HUMAN Antigen KI-67 NM_002916 RFC4 replication factor C (activator 1) 4 NM_002358 MAD2L1 MAD2 mitotic arrest deficient-like 1 NM_005496 SMC4L1 SMC4 structural maintenance of 4-like 1

(B) Genes over-expressed in MPNST cell lines and primary MPNSTs Genbank Gene Description NM_014220 TM4SF1 transmembrane 4 superfamily member 1 NM_002923 RGS2 regulator of G-protein signalling 2 NM_004956 ETV1 ets variant gene 1 NM_013231 FLRT2 leucine rich transmembrane protein 2 NM_000474 TWIST1 twist NM_004573 PLCB2 C, beta 2 NM_000022 ADA adenosine deaminase AJ011712 TNNT1 troponin T1 NM_006317 BASP1 brain abundant, membrane attached signal protein 1 NM_000346 SOX9 SRY (sex determining region Y)-box 9 NM_004472 FOXD1 forkhead box D1 NM_003483 HMGA2 high mobility group AT-hook 2 NM_006451 PAIP1 polyadenylate binding protein-interacting protein 1

(C) Genes under-expressed in MPNST cell lines and primary MPNSTs Genbank Gene Description NM_005860 FSTL3 follistatin-like 3 NM_175617 MT2A metallothionein 2A XM_034905 KIAA0256 KIAA0256 gene product AK128571 EST cDNA DKFZp564J0323 NM_002292 LAMB2 laminin, beta 2 (laminin S) NM_001998 FBLN2 fibulin 2 NM_015103 PLXND1 KIAA0620 protein NM_005253 FOSL2 FOS-like antigen 2 NM_033554 HLA-DPA1 major histocompatibility complex, class II, DP alpha 1 NM_004355 CD74 CD74 antigen NM_000582 SPP1 secreted phosphoprotein 1 (osteopontin, sialoprotein I)

2 (C) Genes under-expressed in MPNST cell lines and primary MPNSTs (continued) Genbank Gene Description NM_002510 GPNMB glycoprotein (transmembrane) nmb NM_007115 TNFAIP6 tumor necrosis factor, alpha-induced protein 6 NM_001321 CSRP2 cysteine and glycine-rich protein 2 NM_012098 ANGPTL2 angiopoietin-like 2 NM_001845 COL4A1 , type IV, alpha 1 NM_001846 COL4A2 collagen, type IV, alpha 2 NM_003118 SPARC secreted protein, acidic, cysteine-rich () NM_000089 COL1A2 collagen, type I, alpha 2 NM_015278 SASH1 KIAA0790 protein NM_004844 SH3BP5 SH3-domain binding protein 5 (BTK-associated) NM_000426 LAMA2 Homo sapiens cDNA: FLJ23176 fis, clone LNG10452 NM_002933 RNASE1 , RNase A family, 1 NM_018950 HLA-F major histocompatibility complex, class I, F M80469 HLA-J major histocompatibility complex, class I, J NM_005658 TRAF1 TNF receptor-associated factor 1 NM_001541 HSPB2 heat shock 27kDa protein 2 NM_006019 TCIRG1 T-cell, immune regulator 1 NM_001909 CTSD cathepsin D (lysosomal aspartyl protease) NM_002778 PSAP prosaposin NM_006120 HLA-DMA major histocompatibility complex, class II, DM alpha NM_002124 HLA-DRB3 major histocompatibility complex, class II, DR beta 4 NM_003670 BHLHB2 basic helix-loop-helix domain containing, class B, 2 NM_002045 GAP43 growth associated protein 43 NM_006533 MIA melanoma inhibitory activity NM_000210 ITGA6 integrin, alpha 6 NM_005878 SERPINE2 serine/cysteine proteinase inhibitor 2 (nexin) NM_000425 L1CAM L1 cell adhesion molecule NM_004696 SLC16A4 solute carrier family 16 (monocarboxylic acid transporters), member 4 NM_182643 DLC1 deleted in liver cancer 1 NM_004476 FOLH1 folate (prostate-specific membrane antigen) 1 NM_006186 NR4A2 nuclear receptor subfamily 4, group A, member 2 NM_006186 NR4A2 nuclear receptor subfamily 4, group A, member 2 NM_004448 ERBB2 v-erb-b2 erythroblastic leukemia viral oncogene homolog 2 NM_001185 AZGP1 alpha-2-glycoprotein 1, zinc NM_005384 NFIL3 nuclear factor, interleukin 3 regulated NM_004199 P4HA2 proline 4-hydroxylase alpha 2 NM_020250 GSN NM_194327 LGALS3 lectin, galactoside-binding, soluble, 3 (galectin 3) NM_006379 SEMA3C semaphorin 3C NM_014945 KIAA0843 KIAA0843 protein NM_002252 KCNS3 potassium voltage-gated channel, delayed-rectifier, subfamily S, member 3 NM_006398 UBD ubiquitin D NM_013994 DDR1 discoidin domain receptor family, member 1 NM_013994 DDR1 discoidin domain receptor family, member 1 NM_001402 EEF1A1 major histocompatibility complex, class I, A NM_002127 HLA-G HLA-G histocompatibility antigen, class I, G NM_002127 HLA-G HLA-G histocompatibility antigen, class I, G BC018925 HLA-F major histocompatibility complex, class I, F

3 (C) Genes under-expressed in MPNST cell lines and primary MPNSTs (continued) Genbank Gene Description NM_006410 HTATIP2 HIV-1 Tat interactive protein 2 NM_015431 BIA2 BIA2 NM_021980 OPTN optineurin NM_006769 LMO4 LIM domain only 4 NM_000611 CD59 CD59 antigen D50683 TGFBR2 transforming growth factor, beta receptor II NM_014937 INPP5F Sac domain-containing inositol 2 NM_007069 HRASLS3 HRAS-like suppressor 3 NM_002224 ITPR3 inositol 1,4,5-triphosphate receptor, type 3 NM_004393 DAG1 dystroglycan 1 (dystrophin-associated glycoprotein 1) NM_004414 DSCR1 Down syndrome critical region gene 1 NM_000081 CHS1 Chediak-Higashi syndrome 1 NM_022549 FEZ1 fasciculation and elongation protein zeta 1 (zygin I) NM_052851 STARD13 START domain containing 13 NM_014795 ZFHX1B zinc finger homeobox 1b NM_005890 GAS7 growth arrest-specific 7 NM_000049 ASPA aspartoacylase (aminoacylase 2) NM_015252 KIAA0903 KIAA0903 protein AL355532 GRIK2 glutamate receptor, ionotropic, kainate 2 NM_003128 SPTBN1 Beta II spectrin BC044915 EST 24405 Homo sapiens clone 24405 NM_013280 FLRT1 fibronectin leucine rich transmembrane protein 1 BC015055 FYN FYN oncogene related to SRC, FGR, YES NM_006339 HMG20B high-mobility group 20B NM_014467 SRPUL sushi-repeat protein NM_000543 SMPD1 sphingomyelin 1, acid lysosomal () NM_003255 TIMP2 tissue inhibitor of metalloproteinase 2 NM_182487 LOC169611 cDNA DKFZp564O222 NM_005529 HSPG2 heparan sulfate proteoglycan 2 (perlecan) NM_015254 KIF13B kinesin family member 13B NM_001945 DTR diphtheria toxin receptor (heparin-binding epidermal growth factor-like) NM_004273 CHST3 carbohydrate (chondroitin 6) sulfotransferase 3 NM_002380 MATN2 matrilin 2 NM_001754 RUNX1 runt-related transcription factor 1 NM_004024 ATF3 activating transcription factor 3 NM_152495 FLJ38993 hypothetical protein FLJ38993 NM_002514 NOV nephroblastoma overexpressed gene NM_014903 NAV3 neuron navigator 3 NM_001062 TCN1 transcobalamin I NM_002567 PBP prostatic binding protein AK026295 FLJ22642 Homo sapiens cDNA: FLJ22642 fis, clone HSI06970 NM_012413 QPCT glutaminyl-peptide cyclotransferase (glutaminyl cyclase) NM_013995 LAMP2 lysosomal-associated membrane protein 2 NM_003272 TM7SF1 transmembrane 7 superfamily member 1 NM_002396 ME2 malic 2 NM_006561 CUGBP2 CUG triplet repeat, RNA binding protein 2 NM_014717 KIAA0390 KIAA0390 gene product NM_152280 SYT11 synaptotagmin XI

4 (C) Genes under-expressed in MPNST cell lines and primary MPNSTs (continued) Genbank Gene Description NM_014733 ZFYVE16 endosome-associated FYVE-domain protein NM_007106 UBL3 ubiquitin-like 3 NM_002906 RDX radixin NM_004476 FOLH1 Prostate-specific membrane antigen PSM NM_005870 SAP18 sin3-associated polypeptide NM_000285 PEPD peptidase D NM_018534 NRP2 neuropilin 2 NM_004425 ECM1 extracellular matrix protein 1 NM_002373 MAP1A microtubule-associated protein 1A NM_033133 CNP 2',3'-cyclic nucleotide 3' phosphodiesterase AB023151 KIAA0934 KIAA0934 protein AB018258 ATP10B ATPase, Class V, type 10B NM_006674 HCP5 MHC class I region ORF NM_007312 HYAL1 hyaluronoglucosaminidase 1 XM_041018 KIAA0367 KIAA0367 protein NM_018849 ABCB4 ATP-binding cassette, sub-family B (MDR/TAP), member 4 NM_001495 GFRA2 GDNF family receptor alpha 2 NM_003687 RIL LIM domain protein NM_000930 PLAT plasminogen activator, tissue NM_014745 KIAA0233 KIAA0233 gene product NM_002507 NGFR nerve growth factor receptor (TNFR superfamily, member 16) NM_005682 GPR56 G protein-coupled receptor 56 NM_014550 CARD10 caspase recruitment domain family, member 10 NM_003706 PLA2G4C , group IVC NM_000362 TIMP3 tissue inhibitor of metalloproteinase 3 NM_002081 GPC1 glypican 1 NM_004750 CRLF1 cytokine receptor-like factor 1 NM_004998 MYO1E myosin IE NM_000304 PMP22 peripheral myelin protein 22 NM_006493 CLN5 ceroid-lipofuscinosis, neuronal 5 NM_144565 FLJ32334 ESTs, Weakly similar to neuronal thread protein AB011542 EGFL5 EGF-like-domain, multiple 5 NM_015529 MOXD1 DKFZP564G202 protein NM_004315 ASAH1 N-acylsphingosine amidohydrolase (acid ceramidase) 1 NM_014216 ITPK1 inositol 1,3,4-triphosphate 5/6 kinase AB067801 QKI quaking isoform NM_005278 GPM6B glycoprotein M6B NM_021153 CDH19 cadherin 19, type 2 NM_006941 SOX10 SRY (sex determining region Y)-box 10 NM_001885 CRYAB crystallin, alpha B NM_004636 SEMA3B semaphorin 3B NM_000313 PROS1 protein S (alpha)

Supplemental Data Table 2. Over-expression and under-expression of genes is relative to normal human Schwann cell as determined by microarray analysis. GenBank

5 accession number, common gene name, and gene description are given for each gene. Genes are arranged in order determined by cluster analysis of microarray data based upon gene expression value. Genes in the table are arranged in order from top to bottom as presented in the dendogram in Figure 3B. (A) Cluster of genes presented in Figures 3BI (B) Cluster of genes presented in

Figures 3BII (C) Cluster of genes presented in Figures 3BIII.

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