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Supplementary Data aabb d ccd a b c d ab a b c d Supplementary Figure S1: Gene ontology analysis of genes upregulated in pancreatic CAFs relative to control fibroblasts. A candidate list of 200 genes upregulated 2.8 -fold or more in pancreatic CAFs relative to control fibroblasts was sorted into representative biological function groups using the Partek Gene Ontology analysis. The high enrichment scores in the biological adhesion and developmental process groups indicate that the candidate gene list is enriched for genes involved in these processes. Supplementary Figure S2: Characterization of HPNE. Immunohistochemical staining reveals that HPNE cells express the mesenchymal marker, vimentin (a) and do not express the marker of activated fibroblasts, alpha-smooth muscle actin (b). HPNE cells lack expression of the cytokeratin 19 (c), an epithelial marker expressed in the pancreatic ductal epithelial cell line HPDE (d). Magnification: A: x20; B, C, D: x10. Supplementary Figure S3: Characterization of pancreatic CAFs. Cells within the CAF cultures have both a stellate and spindle-type morphology and lack expression of the epithelial cell marker cytokeratin 19 (a). They contain cytoplasmic lipid droplets (b) and express the mesenchymal cytoskeletal filament vimentin (c) as well as alpha-SMA (d), a marker of activated fibroblasts. Magnification: A, C, D: x10; B: x20. Figure is representative of all CAFs. Supplementary Figure S4: Immunohistochemical analysis of Smo expression in normal pancreatic tissue. Paraffin embedded sections were probed with an antibody against vimentin (a) or against Smo (b). Arrows indicate normal fibroblasts expressing vimentin but not Smo. Magnification: x20. 1 Supplementary Figure S5: Immunohistochemical analysis of Smo expression in whole tissue sections from pancreatic cancer tissue: Paraffin-embedded sections from primary pancreatic cancer tissue were probed with an antibody against alpha-SMA (a,c; low and high power images of the same section) to highlight the activated cancer associated fibroblasts. Consecutive sections were then probed with an antibody against Smo (b,d; low and high power images of the same section). Note that Smo expression is also detected in pancreatic cancer cells (b, d). Magnification: A, B: x10, C, D: x20. 2 Table 1. Genes Upregulated in Pancreatic CAFs Relative to Control Fibroblasts Gene symbolGene Assignment P value Fold Change BMPER NM_133468 // BMP binding endothelial regulator 0.0000 4.9 LOX NM_002317 // lysyl oxidase 0.0000 4.0 POSTN NM_006475 // periostin, osteoblast specific factor 0.0000 70.4 TNS1 NM_022648 // tensin 1 0.0000 4.8 KIAA1199 NM_018689 // KIAA1199 0.0000 35.1 OLFM1 NM_014279 // olfactomedin 1 0.0000 3.1 PKP2 NM_004572 // plakophilin 2 0.0000 11.6 MAPK13 NM_002754 // mitogen-activated protein kinase 13 0.0000 3.3 PTGFRN NM_020440 // prostaglandin F2 receptor negative regulator 0.0000 12.6 KRT19 NM_002276 // keratin 19 0.0000 3.5 KRT7 NM_005556 // keratin 7 0.0000 20.6 CCDC80 NM_199511 // coiled-coil domain containing 80 0.0000 3.3 ST6GALNAC5NM_030965 // ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1 0.0000 8.7 FZD7 NM_003507 // frizzled homolog 7 (Drosophila) 0.0000 3.3 NFIB NM_005596 // nuclear factor I/B 0.0000 9.9 ADAM12 NM_003474 // ADAM metallopeptidase domain 12 (meltrin alpha) 0.0000 24.3 KLHL13 NM_033495 // kelch-like 13 (Drosophila) 0.0000 15.2 TNIK NM_015028 // TRAF2 and NCK interacting kinase 0.0000 5.9 PTGIS NM_000961 // prostaglandin I2 (prostacyclin) synthase 0.0000 61.8 PTPRF NM_130440 // protein tyrosine phosphatase, receptor type, F 0.0000 2.8 KIAA0746 NM_015187 // KIAA0746 protein 0.0000 15.6 NKX2-3 NM_145285 // NK2 transcription factor related, locus 3 (Drosophila) 0.0000 3.5 VLDLR NM_003383 // very low density lipoprotein receptor 0.0000 7.3 CDKN1A NM_078467 // cyclin-dependent kinase inhibitor 1A 0.0000 2.9 LOC196264NM_198275 // hypothetical protein LOC196264 0.0000 3.4 C13orf33 NM_032849 // chromosome 13 open reading frame 33 0.0000 14.8 GATA6 NM_005257 // GATA binding protein 6 0.0000 4.8 NRXN3 NM_138970 // neurexin 3 0.0000 2.8 SYNC1 NM_030786 // syncoilin, intermediate filament 1 0.0000 5.5 HAPLN3 NM_178232 // hyaluronan and proteoglycan link protein 3 0.0000 3.8 DACT1 NM_016651 // dapper, antagonist of beta-catenin, homolog 1 0.0000 8.1 OSAP NM_032623 // ovary-specific acidic protein 0.0000 4.0 HAS2 NM_005328 // hyaluronan synthase 2 0.0000 5.1 FAM110B NM_147189 // family with sequence similarity 110, member B 0.0000 7.4 CREBL1 NM_004381 // cAMP responsive element binding protein-like 1 0.0000 3.1 LRRC2 NM_024750 // leucine rich repeat containing 2 0.0001 4.6 FST NM_013409 // follistatin 0.0001 8.8 DAPK1 NM_004938 // death-associated protein kinase 1 0.0001 5.4 TMEPAI NM_199170 // transmembrane, prostate androgen induced RNA 0.0001 5.9 SERPING1 NM_000062 // serpin peptidase inhibitor, clade G (C1 inhibitor) 0.0001 5.0 TSKU NM_015516 // tsukushin 0.0001 2.9 CDH2 NM_001792 // cadherin 2 0.0001 4.4 NDN NM_002487 // necdin homolog (mouse) 0.0001 5.4 C21orf56 BC084577 // chromosome 21 open reading frame 56 0.0001 2.8 GREM2 NM_022469 // gremlin 2, cysteine knot superfamily, homolog 0.0001 3.3 HSPB7 NM_014424 // heat shock 27kDa protein family, member 7 0.0001 5.2 ROR2 NM_004560 // receptor tyrosine kinase-like orphan receptor 2 0.0001 5.0 TNFAIP6 NM_007115 // tumor necrosis factor, alpha-induced protein 6 0.0001 9.6 LRIG1 NM_015541 // leucine-rich repeats and immunoglobulin-like domains 1 0.0002 3.1 BC036082 BC036082 // galectin-related protein 0.0002 3.5 DEPDC6 NM_022783 // DEP domain containing 6 0.0002 24.8 IL1A NM_000575 // interleukin 1, alpha 0.0002 5.6 SULF1 NM_015170 // sulfatase 1 0.0002 3.8 ADAM23 NM_003812 // ADAM metallopeptidase domain 23 0.0003 3.0 DPP4 NM_001935 // dipeptidyl-peptidase 4 0.0003 8.2 CDH13 NM_001257 // cadherin 13, H-cadherin (heart) 0.0003 4.2 SULF2 NM_198596 // sulfatase 2 0.0003 4.4 DOK5 NM_018431 // docking protein 5 0.0003 18.4 PTGS2 NM_000963 // prostaglandin-endoperoxide synthase 2 0.0003 7.2 LRRC32 NM_005512 // leucine rich repeat containing 32 0.0004 4.6 MYH10 NM_005964 // myosin, heavy chain 10, non-muscle 0.0004 6.1 ALDH1A3 NM_000693 // aldehyde dehydrogenase 1 family, member A3 0.0004 9.2 BST1 NM_004334 // bone marrow stromal cell antigen 1 0.0004 4.0 BC101260 BC101260 // ring finger protein 212 0.0004 4.0 MFAP5 NM_003480 // microfibrillar associated protein 5 0.0004 31.1 DIRAS1 NM_145173 // DIRAS family, GTP-binding RAS-like 1 0.0004 3.7 SLIT3 NM_003062 // slit homolog 3 (Drosophila) 0.0005 6.5 APOD NM_001647 // apolipoprotein D 0.0005 4.1 CDH11 NM_001797 // cadherin 11, type 2, OB-cadherin (osteoblast) 0.0006 12.5 SPOCK1 NM_004598 // sparc/osteonectin, cwcv and kazal-like domains 0.0006 16.4 ULBP1 NM_025218 // UL16 binding protein 1 0.0007 14.0 TSPYL5 NM_033512 // TSPY-like 5 0.0007 3.6 HOXC8 NM_022658 // homeobox C8 0.0007 4.1 FLJ11151 NM_018340 // hypothetical protein FLJ11151 0.0007 5.2 LRRC17 NM_001031692 // leucine rich repeat containing 17 0.0008 5.8 LAMC2 NM_005562 // laminin, gamma 2 0.0009 4.1 LOXL4 NM_032211 // lysyl oxidase-like 4 0.0010 3.7 SMO NM_005631 // smoothened homolog (Drosophila) 0.0010 2.9 MALL NM_005434 // mal, T-cell differentiation protein-like 0.0010 10.0 XYLT1 NM_022166 // xylosyltransferase I 0.0010 6.1 GDF15 NM_004864 // growth differentiation factor 15 0.0010 3.6 ISLR NM_201526 // immunoglobulin superfamily containing leucine-rich repeat 0.0011 26.6 KCTD15 NM_024076 // potassium channel tetramerisation domain containing 15 0.0011 3.0 GJA1 NM_000165 // gap junction protein, alpha 1 0.0012 4.5 IER3 NM_003897 // immediate early response 3 0.0013 4.2 C6orf85 NM_021945 // chromosome 6 open reading frame 85 0.0013 3.9 LOC387758NM_203371 // similar to RIKEN cDNA 0.0016 13.2 RHOJ NM_020663 // ras homolog gene family, member J 0.0017 13.3 HSD17B14 NM_016246 // hydroxysteroid (17-beta) dehydrogenase 14 0.0019 3.6 PTX3 NM_002852 // pentraxin-related gene, rapidly induced by IL-1 beta 0.0020 6.1 FGF2 NM_002006 // fibroblast growth factor 2 (basic) 0.0021 3.1 DPYSL3 NM_001387 // dihydropyrimidinase-like 3 0.0024 7.1 ID2 NM_002166 // inhibitor of DNA binding 2 0.0024 4.1 CNN1 NM_001299 // calponin 1, basic, smooth muscle 0.0024 3.8 CDCP1 NM_022842 // CUB domain containing protein 1 0.0028 4.4 THY1 NM_006288 // Thy-1 cell surface antigen1 0.0028 6.0 CGREF1 NM_006569 // cell growth regulator with EF-hand domain 1 0.0028 5.9 MATN2 NM_002380 // matrilin 2 0.0029 2.9 THBS2 NM_003247 // thrombospondin 2 0.0029 4.6 NGFB NM_002506 // nerve growth factor, beta polypeptide 0.0030 7.9 TINAGL1 NM_022164 // tubulointerstitial nephritis antigen-like 1 0.0031 4.4 USP53 NM_019050 // ubiquitin specific peptidase 53 0.0033 4.2 ANKRD37 NM_181726 // ankyrin repeat domain 37 0.0035 4.2 SH3PXD2B NM_001017995 // SH3 and PX domains 2B 0.0037 4.1 MGP NM_000900 // matrix Gla protein 0.0037 9.2 CD200 NM_001004196 // CD200 molecule 0.0039 5.3 NUAK1 NM_014840 // NUAK family, SNF1-like kinase, 1 0.0041 4.7 MBP NM_001025101 // myelin basic protein 0.0041 8.2 NEK7 NM_133494 // NIMA (never in mitosis gene a)-related kinase 0.0041 3.4 SNX25 NM_031953 // sorting nexin 25 0.0043 5.4 TNFRSF11BNM_002546 // tumor necrosis factor receptor superfamily, member 11b 0.0045 11.7 MEST NM_002402 // mesoderm specific transcript homolog (mouse) 0.0047 4.6 LOC554202AK124391 // hypothetical LOC554202 0.0049 2.8 CUGBP2 NM_006561 // CUG triplet repeat, RNA binding protein 2 0.0051 3.1 C10orf72 NM_001031746 // chromosome 10 open reading frame 72 0.0051 3.6 VCAN NM_004385 // versican 0.0052 3.6 FANK1 NM_145235 // fibronectin type III
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