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613 Up-Regulated Genes in SOS Compared to Control Livers (FDR Adjusted P-Value ≤ 0.05) Fold- Chang Adjusted P-Value E (SOS P-Value Gene Symbol Name (SOS Vs

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11/29/2010 Rubbia-Brandt et al. 1 Table S1: 613 up-regulated genes in SOS compared to control livers (FDR adjusted p-value ≤ 0.05) Fold- Chang adjusted p-value e (SOS p-value Gene Symbol Name (SOS vs. vs. (SOS vs. Control) Contro Control) l) CCL20 chemokine (C-C motif) ligand 20 10.97 0.0001 0.0142 COL15A1 collagen, type XV, alpha 1 5.42 0.0000 0.0057 DLK1 delta-like 1 homolog (Drosophila) 4.30 0.0002 0.0171 CHI3L1 chitinase 3-like 1 (cartilage glycoprotein-39) 4.14 0.0001 0.0130 CRP C-reactive protein 4.01 0.0127 0.0339 GABBR1 gamma-aminobutyric acid (GABA) B receptor, 1 3.77 0.0001 0.0167 SLC38A1 solute carrier family 38, member 1 3.70 0.0001 0.0155 pleckstrin homology-like domain, family A, PHLDA2 3.66 0.0007 0.0284 member 2 RASD1 RAS, dexamethasone-induced 1 3.65 0.0001 0.0168 FABP4 fatty acid binding protein 4, adipocyte 3.64 0.0000 0.0094 SOD2 superoxide dismutase 2, mitochondrial 3.50 0.0003 0.0205 COL1A2 collagen, type I, alpha 2 3.48 0.0001 0.0157 HBB hemoglobin, beta 3.46 0.0002 0.0173 heat shock protein 90kDa alpha (cytosolic), class HSP90AB1 3.43 0.0032 0.0498 B member 1 VWF von Willebrand factor 3.07 0.0000 0.0110 serpin peptidase inhibitor, clade E (nexin, SERPINE1 3.04 0.0018 0.0390 plasminogen activator inhibitor type fatty acid binding protein 5 (psoriasis- FABP5 3.04 0.0020 0.0412 associated) COL1A1 collagen, type I, alpha 1 3.03 0.0002 0.0171 GDF15 growth differentiation factor 15 3.02 0.0030 0.0487 EGF-containing fibulin-like extracellular matrix EFEMP1 2.99 0.0000 0.0057 protein 1 methylenetetrahydrofolate dehydrogenase MTHFD2 2.99 0.0000 0.0071 (NADP+ dependent) 2, methenyltetrahydrof BIRC3 baculoviral IAP repeat-containing 3 2.99 0.0011 0.0323 CASP4 caspase 4, apoptosis-related cysteine peptidase 2.97 0.0003 0.0206 BCAT1 branched chain aminotransferase 1, cytosolic 2.93 0.0000 0.0087 COL4A1 collagen, type IV, alpha 1 2.92 0.0000 0.0057 Fc fragment of IgG, high affinity Ib, receptor FCGR1B 2.89 0.0001 0.0130 (CD64) IFI16 interferon, gamma-inducible protein 16 2.86 0.0008 0.0300 F2RL1 coagulation factor II (thrombin) receptor-like 1 2.84 0.0015 0.0365 GPNMB glycoprotein (transmembrane) nmb 2.84 0.0009 0.0306 RGS4 regulator of G-protein signaling 4 2.82 0.0000 0.0057 SLC7A1 solute carrier family 7 (cationic amino acid 2.81 0.0001 0.0159 11/29/2010 Rubbia-Brandt et al. 2 transporter, y+ system), member 1 CCL2 chemokine (C-C motif) ligand 2 2.80 0.0009 0.0304 RRM2 ribonucleotide reductase M2 2.78 0.0000 0.0057 LON peptidase N-terminal domain and ring LONRF2 2.77 0.0002 0.0197 finger 2 IL32 interleukin 32 2.72 0.0006 0.0276 NAMPT nicotinamide phosphoribosyltransferase 2.72 0.0016 0.0372 G0S2 G0/G1switch 2 2.69 0.0010 0.0319 THBS2 thrombospondin 2 2.68 0.0000 0.0057 TNC tenascin C 2.64 0.0017 0.0379 CXCR4 chemokine (C-X-C motif) receptor 4 2.63 0.0009 0.0304 tankyrase, TRF1-interacting ankyrin-related TNKS2 2.61 0.0006 0.0272 ADP-ribose polymerase 2 CTHRC1 collagen triple helix repeat containing 1 2.60 0.0001 0.0130 THBS1 thrombospondin 1 2.58 0.0017 0.0379 SGMS2 sphingomyelin synthase 2 2.57 0.0020 0.0412 FRMD6 FERM domain containing 6 2.55 0.0009 0.0304 TNFAIP8 tumor necrosis factor, alpha-induced protein 8 2.53 0.0000 0.0079 EXT1 exostoses (multiple) 1 2.53 0.0025 0.0451 HSPA6 heat shock 70kDa protein 6 (HSP70B') 2.52 0.0007 0.0288 LBP lipopolysaccharide binding protein 2.52 0.0010 0.0320 BAG3 BCL2-associated athanogene 3 2.49 0.0007 0.0277 TOP2A topoisomerase (DNA) II alpha 170kDa 2.47 0.0001 0.0130 GK glycerol kinase 2.45 0.0005 0.0240 HBA1 /// HBA2 hemoglobin, alpha 1 /// hemoglobin, alpha 2 2.41 0.0001 0.0143 STC1 stanniocalcin 1 2.41 0.0000 0.0121 CCT2 chaperonin containing TCP1, subunit 2 (beta) 2.39 0.0022 0.0430 ODC1 ornithine decarboxylase 1 2.38 0.0011 0.0330 ER degradation enhancer, mannosidase alpha- EDEM3 2.38 0.0020 0.0410 like 3 GLIS3 GLIS family zinc finger 3 2.38 0.0002 0.0187 ZNF295 zinc finger protein 295 2.37 0.0023 0.0439 aryl hydrocarbon receptor nuclear translocator- ARNTL2 2.37 0.0016 0.0376 like 2 LOXL4 lysyl oxidase-like 4 2.37 0.0022 0.0427 LOC387763 hypothetical protein LOC387763 2.36 0.0002 0.0171 FAT1 FAT tumor suppressor homolog 1 (Drosophila) 2.36 0.0028 0.0471 methylenetetrahydrofolate dehydrogenase MTHFD1L 2.36 0.0001 0.0130 (NADP+ dependent) 1-like FCGR1A /// Fc fragment of IgG, high affinity Ia, receptor 2.35 0.0001 0.0159 FCGR1C (CD64) /// Fc fragment of IgG, hi procollagen-lysine, 2-oxoglutarate 5- PLOD2 2.34 0.0007 0.0277 dioxygenase 2 serpin peptidase inhibitor, clade B (ovalbumin), SERPINB1 2.34 0.0015 0.0365 member 1 11/29/2010 Rubbia-Brandt et al. 3 NCOA7 nuclear receptor coactivator 7 2.32 0.0004 0.0224 FNDC3B fibronectin type III domain containing 3B 2.29 0.0010 0.0314 CHSY3 chondroitin sulfate synthase 3 2.29 0.0012 0.0340 C12orf5 chromosome 12 open reading frame 5 2.28 0.0000 0.0130 CD69 CD69 molecule 2.28 0.0004 0.0230 GTP binding protein overexpressed in skeletal GEM 2.28 0.0011 0.0328 muscle CH25H cholesterol 25-hydroxylase 2.28 0.0011 0.0331 SOCS1 suppressor of cytokine signaling 1 2.27 0.0089 0.0491 PALLD palladin, cytoskeletal associated protein 2.26 0.0028 0.0469 DTL denticleless homolog (Drosophila) 2.26 0.0004 0.0226 TIMP1 TIMP metallopeptidase inhibitor 1 2.26 0.0000 0.0109 LOXL2 lysyl oxidase-like 2 2.25 0.0000 0.0057 serpin peptidase inhibitor, clade B (ovalbumin), SERPINB8 2.25 0.0012 0.0342 member 8 GPATCH4 G patch domain containing 4 2.25 0.0008 0.0300 LUM lumican 2.25 0.0004 0.0224 TOP1 topoisomerase (DNA) I 2.24 0.0019 0.0407 CTSC cathepsin C 2.24 0.0029 0.0478 potassium channel tetramerisation domain KCTD14 2.23 0.0028 0.0473 containing 14 PTGFRN prostaglandin F2 receptor negative regulator 2.23 0.0000 0.0124 VCAN versican 2.22 0.0026 0.0454 FBN1 fibrillin 1 2.22 0.0003 0.0221 MAP1B microtubule-associated protein 1B 2.22 0.0000 0.0083 ARL5B ADP-ribosylation factor-like 5B 2.22 0.0025 0.0449 COL4A2 collagen, type IV, alpha 2 2.21 0.0001 0.0141 STK17A serine/threonine kinase 17a 2.21 0.0006 0.0276 integrin, beta 1 (fibronectin receptor, beta ITGB1 2.20 0.0031 0.0492 polypeptide, antigen CD29 includes CSDA cold shock domain protein A 2.20 0.0003 0.0205 UDP-GlcNAc:betaGal beta-1,3-N- B3GNT5 2.19 0.0001 0.0159 acetylglucosaminyltransferase 5 VIM vimentin 2.18 0.0005 0.0241 pro-platelet basic protein (chemokine (C-X-C PPBP 2.17 0.0004 0.0235 motif) ligand 7) ATR ataxia telangiectasia and Rad3 related 2.17 0.0015 0.0367 IFNGR1 interferon gamma receptor 1 2.16 0.0006 0.0276 MKI67 (FHA domain) interacting nucleolar MKI67IP 2.16 0.0004 0.0236 phosphoprotein DDX21 DEAD (Asp-Glu-Ala-Asp) box polypeptide 21 2.15 0.0016 0.0372 SLC35C1 solute carrier family 35, member C1 2.15 0.0015 0.0365 GOLM1 golgi membrane protein 1 2.15 0.0004 0.0226 XAF1 XIAP associated factor 1 2.14 0.0008 0.0297 HSPA2 heat shock 70kDa protein 2 2.13 0.0003 0.0205 11/29/2010 Rubbia-Brandt et al. 4 interleukin 6 signal transducer (gp130, IL6ST 2.13 0.0120 0.0313 oncostatin M receptor) ANXA2 annexin A2 2.13 0.0001 0.0161 THBD thrombomodulin 2.13 0.0000 0.0130 apolipoprotein B mRNA editing enzyme, APOBEC3B 2.13 0.0003 0.0204 catalytic polypeptide-like 3B protein phosphatase 2, regulatory subunit B', PPP2R5E 2.13 0.0004 0.0235 epsilon isoform PBK PDZ binding kinase 2.13 0.0001 0.0141 TNFAIP3 tumor necrosis factor, alpha-induced protein 3 2.12 0.0006 0.0272 PLSCR1 phospholipid scramblase 1 2.12 0.0007 0.0287 DTNA dystrobrevin, alpha 2.12 0.0029 0.0478 NRP1 neuropilin 1 2.12 0.0014 0.0360 COL3A1 collagen, type III, alpha 1 2.12 0.0004 0.0223 LOC286434 hypothetical protein LOC286434 2.11 0.0007 0.0286 pregnancy-associated plasma protein A, PAPPA 2.11 0.0000 0.0065 pappalysin 1 DKC1 dyskeratosis congenita 1, dyskerin 2.11 0.0003 0.0221 NARG1 NMDA receptor regulated 1 2.10 0.0028 0.0471 TMEM165 transmembrane protein 165 2.09 0.0001 0.0153 CLEC7A C-type lectin domain family 7, member A 2.09 0.0032 0.0498 LOC100288985 hypothetical protein LOC100288985 2.09 0.0008 0.0292 structural maintenance of chromosomes flexible SMCHD1 2.09 0.0017 0.0384 hinge domain containing 1 karyopherin alpha 2 (RAG cohort 1, importin KPNA2 2.08 0.0001 0.0167 alpha 1) MINA MYC induced nuclear antigen 2.08 0.0016 0.0369 ETV6 ets variant 6 2.08 0.0013 0.0345 IER5 immediate early response 5 2.08 0.0002 0.0194 eukaryotic translation elongation factor 1 EEF1E1 2.07 0.0006 0.0265 epsilon 1 IGSF6 immunoglobulin superfamily, member 6 2.07 0.0021 0.0425 FAM169B family with sequence similarity 169, member B 2.06 0.0019 0.0402 LGALS3 lectin, galactoside-binding, soluble, 3 2.06 0.0007 0.0276 tumor necrosis factor receptor superfamily, TNFRSF10A 2.05 0.0007 0.0276 member 10a v-myc myelocytomatosis viral oncogene MYC 2.05 0.0025 0.0450 homolog (avian) EHBP1L1 EH domain binding protein 1-like 1 2.05 0.0001 0.0137 solute carrier family 6 (neurotransmitter SLC6A6 2.05 0.0000 0.0057 transporter, taurine), member 6 RAB27A RAB27A, member RAS oncogene family 2.05 0.0004 0.0229 GAS2L3 Growth arrest-specific 2 like 3 2.04 0.0001 0.0130 GJC1 gap junction protein, gamma 1, 45kDa 2.04 0.0000 0.0094 11/29/2010 Rubbia-Brandt et al.
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    www.nature.com/scientificreports OPEN Genome-wide DNA methylation analysis of KRAS mutant cell lines Ben Yi Tew1,5, Joel K. Durand2,5, Kirsten L. Bryant2, Tikvah K. Hayes2, Sen Peng3, Nhan L. Tran4, Gerald C. Gooden1, David N. Buckley1, Channing J. Der2, Albert S. Baldwin2 ✉ & Bodour Salhia1 ✉ Oncogenic RAS mutations are associated with DNA methylation changes that alter gene expression to drive cancer. Recent studies suggest that DNA methylation changes may be stochastic in nature, while other groups propose distinct signaling pathways responsible for aberrant methylation. Better understanding of DNA methylation events associated with oncogenic KRAS expression could enhance therapeutic approaches. Here we analyzed the basal CpG methylation of 11 KRAS-mutant and dependent pancreatic cancer cell lines and observed strikingly similar methylation patterns. KRAS knockdown resulted in unique methylation changes with limited overlap between each cell line. In KRAS-mutant Pa16C pancreatic cancer cells, while KRAS knockdown resulted in over 8,000 diferentially methylated (DM) CpGs, treatment with the ERK1/2-selective inhibitor SCH772984 showed less than 40 DM CpGs, suggesting that ERK is not a broadly active driver of KRAS-associated DNA methylation. KRAS G12V overexpression in an isogenic lung model reveals >50,600 DM CpGs compared to non-transformed controls. In lung and pancreatic cells, gene ontology analyses of DM promoters show an enrichment for genes involved in diferentiation and development. Taken all together, KRAS-mediated DNA methylation are stochastic and independent of canonical downstream efector signaling. These epigenetically altered genes associated with KRAS expression could represent potential therapeutic targets in KRAS-driven cancer. Activating KRAS mutations can be found in nearly 25 percent of all cancers1.
  • CDH12 Cadherin 12, Type 2 N-Cadherin 2 RPL5 Ribosomal

    CDH12 Cadherin 12, Type 2 N-Cadherin 2 RPL5 Ribosomal

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