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Supplementary Table S1: Clinical and Histological Characteristics of the 10 Patients with MPNST

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Supplementary Table S1: Clinical and Histological Characteristics of the 10 Patients with MPNST Supplementary table S1: Clinical and histological characteristics of the 10 patients with MPNST Enlargement Neurological Tumor Tumor Histoprognostic Patient N° Sex/Age Pain of mass signs location size (cm) grade MPNST-1 M/31 - + - Face 15 III MPNST-2 M/24 + + + Abdomen 20 III MPNST-3 F/19 + + - Lower limb 27 III MPNST-4 M/34 + + + Lumbar spine 7 III MPNST-5 M/18 - + - Head 15 III MPNST-6 F/18 + - - Upper limb 20 III MPNST-7 M/53 + + + Upper limb 13 III MPNST-8 F/24 + + + Lumbar spine 7 I MPNST-9 M/35 + + + Abdomen 20 III MPNST-10 M/33 + + - Face 10 III F indicates female; M, male Plus sign indicates present; minus sign, absent Supplementary table S2: Oligonucleotide primer sequences PCR Genes Oligonucleotide Sequence product size (bp) TNR Upper primer 5' – AAG AAA GTG CTG CCA CAG GAC AA - 3' 88 Lower primer 5' – CAG ATG CAG CCA CAG GAC TCA A - 3' TNN Upper primer 5' – AGC ATC TAC TTG CCA CCA CAG ACC - 3' 80 Lower primer 5' – CAC GTC AAG GGA GTT CTC AGT CTC A - 3' TNXB Upper primer 5' – GCT TCC TCA CCA CGG TTC CT - 3' 67 Lower primer 5' – GCG AAT CCC TCG GTC AAG TT - 3' TNC Upper primer 5' – GAG GGT GAC CAC CAC ACG CTT - 3' 73 Lower primer 5' – CAA GGC AGT GGT GTC TGT GAC ATC - 3' TNC-ft Upper primer 5' – GTG TGA AGG CAT CCA CTG CCA T - 3' 86 Lower primer 5' – CCT CCA GCT GAC AGT AGC CGA AT - 3' TNC-v-A1 Upper primer 5' – GAG CTG GAA AAC CTC ACC GTG AC - 3' 60 Lower primer 5' – GGT CCA GTT GAG TCT GAG GCC AT - 3' Formatted: French (France) TNC-v-A2 Upper primer 5' – CCC AGG AGG ACT GAG GTC CA- 3' 97 Lower primer 5' – GGT TGT GCT GAA GTC CTG AGT GA - 3' TNC-v-A3 Upper primer 5' – AGG TTA GCT GGG ATG CTC TCA GAC T - 3' 87 Lower primer 5' – GGT CAG CCT CCT GGA CCT GAA TA - 3' TNC-v-A4 Upper primer 5' – CAA CTG GAC CGC AGC TGA CAA T - 3' 77 Lower primer 5' – GGG CTG CCT CCA CTT TGT TGA - 3' TNC-v-B Upper primer 5' – TGC TGA ACG AAC TGC CCA TAT CT - 3' 111 Lower primer 5' – GTG GCT GTG GCA CTG ATG GTT - 3' TNC-v-AD2 Upper primer 5' – TGA CAT AAC TCC CGA GAG CTT CAA - 3' 111 Lower primer 5' – TAT TCC ACA GTC TCC AGC AAC CTA TT - 3' TNC-v-AD1 Upper primer 5' – TCA CTG CAT GAG TCC CAG CAA TTC - 3' 74 Lower primer 5' – TTC TCC ACC AAG CCT GTG ATG TGA - 3' TNC-v-C Upper primer 5' – GGA CCC CCA GGA ATT CAC ACT TT - 3' 72 Lower primer 5' – CCA ATG CCA GTT ATG AGG CCT CTA A - 3' TNC-v-D Upper primer 5' – TGA GCC ACT GGA AAT AAC CCT ACT T - 3' 111 Lower primer 5' – CGC CTT CCT TTG CTT ATT CCA TA - 3' TBP Upper primer 5' – TGC ACA GGA GCC AAG AGT GAA – 3' 132 Lower primer 5' – CAC ATC ACA GCT CCC CAC CA– 3' RPLP0 Upper primer 5’ – GGC GAC CTG GAA GTC CAA CT – 3’ 149 Lower primer 5' – CCA TCA GCA CCA CAG CCT TC – 3' Supplementary table S3 : Genes differentially expressed between plexifom neurofibromas and MPNSTs (P<10-7) Sequence Name Sequence Code Sequence Description Ratio ANAPC11 Q9NYG5 Anaphase promoting complex subunit 11 homolog (yeast), an anaphase-promoting complex component that + contains a RING finger domain, displays ubiquitin ligase activity, interacts with the cullin domain of APC2, expression is upregulated in some cancers AP2B1 P21851 Adaptor-related protein complex 2 beta 1 subunit, a large subunit of the AP2 adaptor complex, involved + in clathrin coat assembly at the plasma membrane; may bind to the transmembrane envelope protein of HIV-1 and HTLV retroviruses BIRC5 O15392 Survivin, a member of the inhibitor of apoptosis protein family that is involved in G2-M transition and + exit of the mitotic cell cycle; may play a role in oncogenesis BOP1 AAH13980.1 Block of proliferation 1, has four WD40 repeats and PEST sequences, which likely mediate protein- + protein interactions, has strong similarity to mouse Bop1, which is a protein involved in 28S and 5.8S rRNA processing and large ribosomal subunit biogenesis CBX7 O95931 Protein containing a Chromo domain, which bind chromatin, has moderate similarity to a region of - chromobox homolog 4 Drosophila Pc class (human CBX4), which is a component of the HPC-HPH Polycomb group complex and functions as a transcriptional repressor CCNB2 O95067 Cyclin B2, a CDC2 kinase-associated cyclin that is involved in Golgi apparatus disassembly, may function + in p53 (TP53) -mediated cell cycle arrest at the G2/M transition, may mediate cell cycle arrest by linking CDC2 with TGFbeta type II receptor (TGFBR2) CCND2 P30279 Cyclin D2, a member of the cyclin family of CDK regulatory subunits, forms active kinase complexes with + cyclin dependent kinases that phosphorylate RB1 to promote G1 to S-phase progression, plays a role in viral infection and oncogenesis CDK4 AAH15669.1 Cyclin dependent kinase 4, complex with cyclin D1(CCND1)is required for cell cycle progression, + phosphorylates Rb1 and inactivates its repressor function; mutation in corresponding gene is associated with familial melanoma tumors CKS2 P33552 Protein that binds to CDC2/CDC28 protein kinase, regulates CDK-cyclin complexes; similar to S. pombe + p13suc1 CSNK2B P13862 Casein kinase II beta subunit, regulatory subunit of casein kinase II (CK2), confers stability and + specificity to CK2 catalytic subunits, may mediate formation of the tetrameric CK2 complex, and may be involved in heat stress response DC6 AAF89829.1 Protein of unknown function + DF AAA35527.1 Adipsin (complement factor D), a serine protease that functions in the alternative complement pathway - to cleave complement factor B when complexed to component C3, deficiency in humans results in increased susceptibility to Neisseria meningitidis DIA1 P00387 NADH-dependent cytochrome b5 reductase (diaphorase), soluble erythrocyte-specific form functions in - methemoglobin reduction, ubiquitous membrane-bound form functions in lipid metabolism; mutations in the gene cause methemoglobinemia types I and II DNMT3A Q9Y6K1 DNA methyltransferase 3A, a putative DNA (cytosine-5-)-methyltransferase; corresponding gene is + overexpressed in leukemias DPT Q07507 Dermatopontin, a putative component of the extracellular matrix that is involved in cell adhesion, - regulated by various cytokines and matrix collagen, may be associated with systemic sclerosis and hypertrophic scar fibrosis DTYMK P23919 Deoxythymidylate kinase (dTMP kinase), phosphorylates dTMP to dTDP in dTTP biosynthesis, activity + and transcript abundance peak in S phase, rate limiting for activating zidovudine (AZT) EDG1 P21453 Endothelial differentiation gene-1, a G protein-coupled receptor activated by sphingosine-1-phosphate, - signals through Gi proteins and Rac, Ras and Rho signaling pathways, promotes cell adhesion, migration, and angiogenesis, inhibits apoptosis EPAS1 Q99814 Endothelial PAS domain protein 1, a transcription factor that forms a heterodimer with aryl - hydrocarbon receptor nuclear translocator (ARNT) to activate hypoxia inducible promoters, may play a role in angiogenesis during embryogenesis and tumorigenesis FLJ10044 BAA91419.1 Protein containing LIM domains, which may mediate protein-protein interactions - FLJ14050 BAB14829.1 Protein of unknown function - FLJ20401 AAH21860.1 Protein containing a DIL domain, which are found in dilute myosin heavy chain proteins - FLJ20535 BAA91242.1 Protein containing three TPR (tetratrico peptide repeat) domains, which may mediate protein-protein - interactions FLJ20539 BAA91245.1 Protein of unknown function, has low similarity to uncharacterized human KIAA1906 + FLJ22626 BAB15428.1 Protein of unknown function, has low similarity to uncharacterized C. elegans E01A2.4 + FOXO1A Q12778 Forkhead box O1A, a transcriptional activator as well as a transcriptional co-activator and corepressor; - a translocation resulting in fusion to PAX3 or PAX7 is associated with alveolar rhabdomyosarcoma FY Q16570 Duffy blood group, a C-C and C-X-C chemokine receptor for interleukin 8 (IL8) and malarial Plasmodium - parasites, may play a role in the interactions between granulocytes and postcapillary epithelial cells GPR56 AAH08770.1 G protein-coupled receptor 56, a putative G protein-coupled receptor that may function in cell adhesion, - cell-cell signaling, and is differentially expressed during metastatic progression of melanomas H2BFD P06899 H2B histone family member D, a component of nucleosomes, along with core histones H2A, H3, H4 and + DNA HMG4 O15347 High-mobility group (nonhistone chromosomal) protein 4, member of the HMG 1/2 family, which have a + common DNA-binding motif and bind DNA with low specificity and facilitate assembly of nucleoprotein complexes on bent DNA, may play a role in development HMGIC P52926 High mobility group I protein C, a chromatin component with AT-hook DNA-binding motifs, may play a + role in cell proliferation and adipogenesis; variants are associated with benign mesenchymal tumors and sarcomas HSPB2 Q16082 Heat shock protein 2 (27kD), a member of the alpha-crystallin/small heat shock protein family, - interacts with myotonic dystrophy protein kinase (DMPK) and protects it from heat shock; may play a role in myotonic dystrophy and chemoresistance I_1000035 AAH26078.1 Protein with high similarity to human C2orf6, which forms stable complexes with striatin (STRN)- - protein phosphatase 2A and GS2NA-protein phosphatase 2A and may participate in cytoskeletal regulation and cytokinesis, member of the Mob1 and phocein family I_1000690 AAB34266.1 Protein with high similarity to mouse Tcf15, which is a transcription factor required for regulation of + somite morphogenesis and subsequent patterning of the axial skeleton and skeletal muscles, contains a helix-loop-helix DNA-binding domain I_957430 CAC39772.1 Member of the SCP-like extracellular protein
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