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Probe Set Name Symbol 1598 G at Growth Arres

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Supplementary Table 2. List of stroma related genes (i.e. probe sets overexpressed in core relative to FNA biopsies of the same cancer) Probe set Name Symbol 1598_g_at growth arrest-specific 6 GAS6 200048_s_at jumping translocation breakpoint JTB 200054_at zinc finger protein 259 ZNF259 200055_at TAF10 RNA polymerase II, TATA box binding protein (TBP)-associatedTAF10 factor, 30kDa 200059_s_at ras homolog gene family, member A RHOA 200060_s_at RNA binding protein S1, serine-rich domain RNPS1 200070_at chromosome 2 open reading frame 24 C2orf24 200613_at adaptor-related protein complex 2, mu 1 subunit AP2M1 200663_at CD63 molecule CD63 200665_s_at secreted protein, acidic, cysteine-rich (osteonectin) SPARC 200671_s_at spectrin, beta, non-erythrocytic 1 SPTBN1 200696_s_at gelsolin (amyloidosis, Finnish type) GSN 200704_at lipopolysaccharide-induced TNF factor LITAF 200738_s_at phosphoglycerate kinase 1 PGK1 200760_s_at ADP-ribosylation-like factor 6 interacting protein 5 ARL6IP5 200762_at dihydropyrimidinase-like 2 DPYSL2 200770_s_at laminin, gamma 1 (formerly LAMB2) LAMC1 200771_at laminin, gamma 1 (formerly LAMB2) LAMC1 200772_x_at prothymosin, alpha PTMA 200778_s_at septin 2 2-Sep 200782_at annexin A5 ANXA5 200784_s_at low density lipoprotein-related protein 1 (alpha-2-macroglobulin receptor)LRP1 200785_s_at low density lipoprotein-related protein 1 (alpha-2-macroglobulin receptor)LRP1 200795_at SPARC-like 1 (hevin) SPARCL1 200799_at heat shock 70kDa protein 1A HSPA1A 200807_s_at heat shock 60kDa protein 1 (chaperonin) HSPD1 200811_at cold inducible RNA binding protein CIRBP 200813_s_at platelet-activating factor acetylhydrolase, isoform Ib, alpha subunit PAFAH1B145kDa 200816_s_at platelet-activating factor acetylhydrolase, isoform Ib, alpha subunit PAFAH1B145kDa 200822_x_at triosephosphate isomerase 1 TPI1 200866_s_at prosaposin PSAP 200874_s_at NOP56 ribonucleoprotein homolog (yeast) NOP56 200875_s_at NOP56 ribonucleoprotein homolog (yeast) NOP56 200878_at endothelial PAS domain protein 1 EPAS1 200882_s_at proteasome (prosome, macropain) 26S subunit, non-ATPase, 4 PSMD4 200883_at ubiquinol-cytochrome c reductase core protein II UQCRC2 200896_x_at hepatoma-derived growth factor (high-mobility group protein 1-like) HDGF 200897_s_at palladin, cytoskeletal associated protein PALLD 200903_s_at S-adenosylhomocysteine hydrolase AHCY 200906_s_at palladin, cytoskeletal associated protein PALLD 200907_s_at palladin, cytoskeletal associated protein PALLD 200911_s_at transforming, acidic coiled-coil containing protein 1 TACC1 200931_s_at vinculin VCL 200951_s_at cyclin D2 CCND2 200953_s_at cyclin D2 CCND2 200954_at ATPase, H+ transporting, lysosomal 16kDa, V0 subunit c ATP6V0C 200966_x_at aldolase A, fructose-bisphosphate ALDOA 200971_s_at stress-associated endoplasmic reticulum protein 1 SERP1 200973_s_at tetraspanin 3 TSPAN3 200974_at actin, alpha 2, smooth muscle, aorta ACTA2 200982_s_at annexin A6 ANXA6 200984_s_at CD59 molecule, complement regulatory protein CD59 200986_at serpin peptidase inhibitor, clade G (C1 inhibitor), member 1 SERPING1 200997_at RNA binding motif protein 4 RBM4 201012_at annexin A1 ANXA1 201028_s_at CD99 molecule CD99 201034_at adducin 3 (gamma) ADD3 201041_s_at dual specificity phosphatase 1 DUSP1 201044_x_at dual specificity phosphatase 1 DUSP1 201046_s_at RAD23 homolog A (S. cerevisiae) RAD23A 201058_s_at myosin, light chain 9, regulatory MYL9 201061_s_at stomatin STOM 201069_at matrix metallopeptidase 2 (gelatinase A, 72kDa gelatinase, 72kDa typeMMP2 IV collagenase) 201105_at lectin, galactoside-binding, soluble, 1 LGALS1 201107_s_at thrombospondin 1 THBS1 201108_s_at thrombospondin 1 THBS1 201109_s_at thrombospondin 1 THBS1 201110_s_at thrombospondin 1 THBS1 201111_at CSE1 chromosome segregation 1-like (yeast) CSE1L 201116_s_at carboxypeptidase E CPE 201117_s_at carboxypeptidase E CPE 201119_s_at cytochrome c oxidase subunit 8A (ubiquitous) COX8A 201125_s_at integrin, beta 5 ITGB5 201133_s_at praja ring finger 2 PJA2 201137_s_at major histocompatibility complex, class II, DP beta 1 HLA-DPB1 201141_at glycoprotein (transmembrane) nmb GPNMB 201147_s_at TIMP metallopeptidase inhibitor 3 TIMP3 201148_s_at TIMP metallopeptidase inhibitor 3 TIMP3 201149_s_at TIMP metallopeptidase inhibitor 3 TIMP3 201150_s_at TIMP metallopeptidase inhibitor 3 TIMP3 201151_s_at muscleblind-like (Drosophila) MBNL1 201162_at insulin-like growth factor binding protein 7 IGFBP7 201163_s_at insulin-like growth factor binding protein 7 IGFBP7 201175_at thioredoxin-related transmembrane protein 2 TMX2 201185_at HtrA serine peptidase 1 HTRA1 201205_at ribosome binding protein 1 homolog 180kDa (dog) RRBP1 201215_at plastin 3 (T isoform) PLS3 201220_x_at C-terminal binding protein 2 CTBP2 201224_s_at serine/arginine repetitive matrix 1 SRRM1 201255_x_at HLA-B associated transcript 3 BAT3 201261_x_at biglycan BGN 201262_s_at biglycan BGN 201278_at disabled homolog 2, mitogen-responsive phosphoprotein (Drosophila)DAB2 201279_s_at disabled homolog 2, mitogen-responsive phosphoprotein (Drosophila)DAB2 201280_s_at disabled homolog 2, mitogen-responsive phosphoprotein (Drosophila)DAB2 201289_at cysteine-rich, angiogenic inducer, 61 CYR61 201300_s_at prion protein PRNP 201305_x_at acidic (leucine-rich) nuclear phosphoprotein 32 family, member B ANP32B 201307_at septin 11 11-Sep 201310_s_at chromosome 5 open reading frame 13 C5orf13 201324_at epithelial membrane protein 1 EMP1 201325_s_at epithelial membrane protein 1 EMP1 201326_at chaperonin containing TCP1, subunit 6A (zeta 1) CCT6A 201328_at v-ets erythroblastosis virus E26 oncogene homolog 2 (avian) ETS2 201329_s_at v-ets erythroblastosis virus E26 oncogene homolog 2 (avian) ETS2 201336_at vesicle-associated membrane protein 3 (cellubrevin) VAMP3 201337_s_at vesicle-associated membrane protein 3 (cellubrevin) VAMP3 201338_x_at general transcription factor IIIA GTF3A 201348_at glutathione peroxidase 3 (plasma) GPX3 201350_at flotillin 2 FLOT2 201357_s_at splicing factor 3a, subunit 1, 120kDa SF3A1 201368_at zinc finger protein 36, C3H type-like 2 ZFP36L2 201390_s_at casein kinase 2, beta polypeptide CSNK2B 201391_at TNF receptor-associated protein 1 TRAP1 201399_s_at translocation associated membrane protein 1 TRAM1 201403_s_at microsomal glutathione S-transferase 3 MGST3 201426_s_at vimentin VIM 201430_s_at dihydropyrimidinase-like 3 DPYSL3 201431_s_at dihydropyrimidinase-like 3 DPYSL3 201438_at collagen, type VI, alpha 3 COL6A3 201441_at cytochrome c oxidase subunit Vib polypeptide 1 (ubiquitous) COX6B1 201445_at calponin 3, acidic CNN3 201463_s_at transaldolase 1 TALDO1 201464_x_at jun oncogene JUN 201472_at von Hippel-Lindau binding protein 1 VBP1 201494_at prolylcarboxypeptidase (angiotensinase C) PRCP 201496_x_at myosin, heavy chain 11, smooth muscle MYH11 201497_x_at myosin, heavy chain 11, smooth muscle MYH11 201505_at laminin, beta 1 LAMB1 201508_at insulin-like growth factor binding protein 4 IGFBP4 201511_at angio-associated, migratory cell protein AAMP 201531_at zinc finger protein 36, C3H type, homolog (mouse) ZFP36 201539_s_at four and a half LIM domains 1 FHL1 201540_at four and a half LIM domains 1 FHL1 201551_s_at lysosomal-associated membrane protein 1 LAMP1 201558_at RAE1 RNA export 1 homolog (S. pombe) RAE1 201559_s_at chloride intracellular channel 4 CLIC4 201560_at chloride intracellular channel 4 CLIC4 201563_at sorbitol dehydrogenase SORD 201590_x_at annexin A2 ANXA2 201615_x_at caldesmon 1 CALD1 201616_s_at caldesmon 1 CALD1 201617_x_at caldesmon 1 CALD1 201621_at neuroblastoma, suppression of tumorigenicity 1 NBL1 201630_s_at acid phosphatase 1, soluble ACP1 201645_at tenascin C TNC 201647_s_at scavenger receptor class B, member 2 SCARB2 201655_s_at heparan sulfate proteoglycan 2 HSPG2 201666_at TIMP metallopeptidase inhibitor 1 TIMP1 201667_at gap junction protein, alpha 1, 43kDa GJA1 201669_s_at myristoylated alanine-rich protein kinase C substrate MARCKS 201677_at chromosome 3 open reading frame 37 C3orf37 201680_x_at serrate RNA effector molecule homolog (Arabidopsis) SRRT 201690_s_at tumor protein D52 TPD52 201694_s_at early growth response 1 EGR1 201708_s_at nipsnap homolog 1 (C. elegans) NIPSNAP1 201709_s_at nipsnap homolog 1 (C. elegans) NIPSNAP1 201718_s_at erythrocyte membrane protein band 4.1-like 2 EPB41L2 201719_s_at erythrocyte membrane protein band 4.1-like 2 EPB41L2 201739_at serum/glucocorticoid regulated kinase 1 SGK1 201743_at CD14 molecule CD14 201744_s_at lumican LUM 201749_at endothelin converting enzyme 1 ECE1 201751_at Josephin domain containing 1 JOSD1 201753_s_at adducin 3 (gamma) ADD3 201759_at tubulin folding cofactor D TBCD 201785_at ribonuclease, RNase A family, 1 (pancreatic) RNASE1 201787_at fibulin 1 FBLN1 201792_at AE binding protein 1 AEBP1 201796_s_at valyl-tRNA synthetase VARS 201798_s_at myoferlin MYOF 201809_s_at endoglin ENG 201811_x_at SH3-domain binding protein 5 (BTK-associated) SH3BP5 201827_at SWI/SNF related, matrix associated, actin dependent regulator of chromatin,SMARCD2 subfamily d, member 2 201839_s_at epithelial cell adhesion molecule EPCAM 201842_s_at EGF-containing fibulin-like extracellular matrix protein 1 EFEMP1 201843_s_at EGF-containing fibulin-like extracellular matrix protein 1 EFEMP1 201852_x_at collagen, type III, alpha 1 COL3A1 201853_s_at cell division cycle 25 homolog B (S. pombe) CDC25B 201860_s_at plasminogen activator, tissue PLAT 201893_x_at decorin DCN 201896_s_at proline/serine-rich coiled-coil 1 PSRC1 201912_s_at G1 to S phase transition 1 GSPT1 201913_s_at Coenzyme A synthase COASY 201953_at
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  • (12) United States Patent (10) Patent No.: US 9.284.609 B2 Tomlins Et Al

    (12) United States Patent (10) Patent No.: US 9.284.609 B2 Tomlins Et Al

    USOO9284609B2 (12) United States Patent (10) Patent No.: US 9.284.609 B2 Tomlins et al. (45) Date of Patent: Mar. 15, 2016 (54) RECURRENT GENE FUSIONS IN PROSTATE 4,683, 195 A 7, 1987 Mullis et al. CANCER 4,683.202 A 7, 1987 Mullis et al. 4,800,159 A 1/1989 Mullis et al. 4,873,191 A 10/1989 Wagner et al. (75) Inventors: Scott Tomlins, Ann Arbor, MI (US); 4,965,188 A 10/1990 Mullis et al. Daniel Rhodes, Ann Arbor, MI (US); 4,968,103 A 1 1/1990 McNab et al. Arul Chinnaiyan, Ann Arbor, MI (US); 5,130,238 A 7, 1992 Malek et al. Rohit Mehra, Ann Arbor, MI (US); 5,225,326 A 7/1993 Bresser 5,270,184 A 12/1993 Walker et al. Mark Rubin New York, NY (US); 5,283,174. A 2/1994 Arnold, Jr. et al. Xiao-Wei Sun, New York, NY (US); 5,283,317. A 2/1994 Saifer et al. Sven Perner, Ellwaugen (DE); Charles 5,399,491 A 3, 1995 Kacian et al. Lee, Marlborough, MA (US); Francesca 5,455,166 A 10/1995 Walker Demichelis, New York, NY (US) 5,480,784. A 1/1996 Kacian et al. s s 5,545,524 A 8, 1996 Trent 5,614,396 A 3/1997 Bradley et al. (73) Assignees: THE BRIGHAMAND WOMENS 5,631, 169 A 5/1997 Lakowicz et al. HOSPITAL, INC., Boston, MA (US); 5,710,029 A 1/1998 Ryder et al. THE REGENTS OF THE 5,776,782 A 7/1998 Tsuji UNIVERSITY OF MICHIGAN, Ann 5,814,447 A 9/1998 Ishiguro et al.
  • Supplemental Material Annexin A2-S100A10 Represents the Regulatory Component of Maxi-Cl Channel Dependent on Protein Tyrosine De

    Supplemental Material Annexin A2-S100A10 Represents the Regulatory Component of Maxi-Cl Channel Dependent on Protein Tyrosine De

    Supplemental Material Annexin A2-S100A10 Represents the Regulatory Component of Maxi-Cl Channel Dependent on Protein Tyrosine Dephosphorylation and Intracellular Ca2+ Md. Rafiqul Islama Toshiaki Okadaa Petr G. Merzlyaka,b Abduqodir H. Toychieva,c Yuhko Ando-Akatsukad Ravshan Z. Sabirova,b Yasunobu Okadaa,e aDivision of Cell Signaling, National Institute for Physiological Sciences (NIPS), Okazaki, Japan, bInstitute of Biophysics and Biochemistry, National University of Uzbekistan, Tashkent, Uzbekistan, cDepartment of Biological Sciences, State University of New York College of Optometry, New York, NY, USA, dDepartment of Cell Physiology, Faculty of Pharmaceutical Sciences, Suzuka University of Medical Science, Suzuka, Japan, eDepartment of Physiology, Kyoto Prefectural University of Medicine, Kyoto, Japan Supplementary Material Supplementary Fig. 1. Maxi-Cl currents in C127 cells were unaffected by siRNA- mediated silencing of three annexin family member genes, Anxa1, Anxa3 and Anxa11. Effects of knockdown mediated by Anxa1-specific siRNA (A), Anxa3-specific siRNA (B) and Anxa11-specific siRNA (C). Top panels: The effects on expression of ANXA mRNAs in C127 cells treated with non-targeting siRNA (cnt) or Anxa1/3/11-specific siRNA (si) detected by RT-PCR using Gapdh as a control. M: molecular size markers (100-bp ladder). These data represent triplicate experiments. Upper-middle panels: Representative time courses of Maxi-Cl current activation recorded at +25 mV after patch excision from C127 cells transfected with Anxa1/3/11-specific siRNA. Lower-middle panels: Voltage- dependent inactivation pattern of Maxi-Cl currents elicited by applying single voltage step pulses from 0 to 25 and 50 mV. Bottom panels: Summary of the effects of non-targeting siRNA (Control) and Anxa1/3/11-specific siRNA on the mean Maxi-Cl currents recorded at +25 mV.
  • Effects of Glycosylation on the Enzymatic Activity and Mechanisms of Proteases

    Effects of Glycosylation on the Enzymatic Activity and Mechanisms of Proteases

    International Journal of Molecular Sciences Review Effects of Glycosylation on the Enzymatic Activity and Mechanisms of Proteases Peter Goettig Structural Biology Group, Faculty of Molecular Biology, University of Salzburg, Billrothstrasse 11, 5020 Salzburg, Austria; [email protected]; Tel.: +43-662-8044-7283; Fax: +43-662-8044-7209 Academic Editor: Cheorl-Ho Kim Received: 30 July 2016; Accepted: 10 November 2016; Published: 25 November 2016 Abstract: Posttranslational modifications are an important feature of most proteases in higher organisms, such as the conversion of inactive zymogens into active proteases. To date, little information is available on the role of glycosylation and functional implications for secreted proteases. Besides a stabilizing effect and protection against proteolysis, several proteases show a significant influence of glycosylation on the catalytic activity. Glycans can alter the substrate recognition, the specificity and binding affinity, as well as the turnover rates. However, there is currently no known general pattern, since glycosylation can have both stimulating and inhibiting effects on activity. Thus, a comparative analysis of individual cases with sufficient enzyme kinetic and structural data is a first approach to describe mechanistic principles that govern the effects of glycosylation on the function of proteases. The understanding of glycan functions becomes highly significant in proteomic and glycomic studies, which demonstrated that cancer-associated proteases, such as kallikrein-related peptidase 3, exhibit strongly altered glycosylation patterns in pathological cases. Such findings can contribute to a variety of future biomedical applications. Keywords: secreted protease; sequon; N-glycosylation; O-glycosylation; core glycan; enzyme kinetics; substrate recognition; flexible loops; Michaelis constant; turnover number 1.