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238 Parametric P- Value FDR Geom Mean of Intensities in Class 1 (Plate

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Geom mean Geom mean Ratio of geom Parametric p- of intensities of intensities FDR means Description value in class 1 in class 2 Pla/Bag 238 (Plate) (Bag) coagulation factor XIII, A1 206 0,0005558 0,1940962 1313,3 29,7 44,219 polypeptide interleukin 12B (natural killer cell stimulatory factor 2, cytotoxic lymphocyte maturation 0,0017883 0,2490398 1535,5 81,1 18,933 factor 2, p40) Immunoglobuli 0,0063804 0,3394787 3050,5 258,7 11,792 n epsilon chain interferon, alpha-inducible 11 4,62E-05 0,1541482 347,2 33,4 10,395 protein 27 0,0035346 0,3039332 226,8 22 10,309 astrotactin 2 deoxyribonucle 0,0040473 0,3148984 1155,1 125 9,241 ase I-like 3 0,0010495 0,2205294 213,2 24,1 8,846 follistatin galectin- 0,0315078 0,4885675 644,8 76,2 8,462 related protein androgen- 0,0013899 0,238971 287 35,4 8,107 induced 1 A kinase (PRKA) anchor protein (gravin) 236 1,06E-05 0,115911 2061,4 256,7 8,03 12 tumor necrosis factor receptor superfamily, member 11a, 0,002746 0,2846759 405 50,5 8,02 NFKB activator lipoma HMGIC 248 0,0008375 0,2147006 240,6 32,3 7,449 fusion partner glutathione S- transferase 0,0183462 0,4368809 557,1 80,1 6,955 theta 1 solute carrier family 18 (vesicular monoamine), 122 3,94E-05 0,1541482 121,5 17,6 6,903 member 2 signal transducing adaptor family 233 6,27E-05 0,1541482 354,3 51,6 6,866 member 1 Transcribed 0,0050276 0,3240923 140,3 20,6 6,811 locus aldehyde dehydrogenas e 5 family, member A1 (succinate- semialdehyde dehydrogenas 0,0294865 0,4819829 236,6 38,2 6,194 e) guanylate cyclase activator 1A 0,0074099 0,3504479 339,1 55 6,165 (retina) 0,0028748 0,288618 160,9 27,3 5,894 astrotactin 2 cadherin 1, type 1, E- cadherin 0,0474256 0,521195 164,4 27,9 5,892 (epithelial) Hypothetical gene supported by 32 0,0001602 0,1541482 131 22,7 5,771 BC008048 chemokine (C- C motif) ligand 0,0310777 0,487288 855,2 156,3 5,472 26 solute carrier family 18 (vesicular monoamine), 211 0,0004192 0,1940962 87,5 16,2 5,401 member 2 cornichon homolog 3 0,0239715 0,4638862 184,6 34,4 5,366 (Drosophila) solute carrier family 47, 0,0281004 0,4758739 416,2 78,3 5,315 member 1 phospholipase 0,0437213 0,5141825 389,1 74,3 5,237 A2, group V A kinase (PRKA) anchor protein (gravin) 80 0,0010055 0,2205294 349,2 66,8 5,228 12 cytochrome P450, family 7, subfamily B, 0,006242 0,3373399 96,9 18,6 5,21 polypeptide 1 NK3 0,0014765 0,2418041 179,5 34,7 5,173 homeobox 1 0,0396349 0,5083518 1364 264,1 5,165 CD1b molecule receptor (G protein- coupled) activity modifying 0,0032019 0,2999829 1881,5 367,3 5,123 protein 1 Primary neuroblastoma cDNA, clone:Nbla036 14, full insert 0,0079462 0,3545654 320,5 62,8 5,104 sequence CDNA clone IMAGE:525927 0,0495077 0,5248641 98 19,5 5,026 2 24- dehydrocholest 0,0205742 0,4485902 249,5 50 4,99 erol reductase 84 0,0008316 0,2144704 812,7 163 4,986 mucolipin 2 retinoic acid receptor responder (tazarotene 0,0421942 0,5127624 520,8 105,9 4,918 induced) 1 sphingosine-1- phosphate 71 6,66E-05 0,1541482 410,3 83,9 4,89 phosphotase 2 scavenger receptor class 0,0050935 0,3253354 643,3 131,8 4,881 B, member 1 signaling lymphocytic activation molecule family member 0,0149731 0,4142987 1953,1 401,4 4,866 1 tight junction protein 1 (zona 0,0073091 0,3490175 66,7 13,8 4,833 occludens 1) chemokine (C- C motif) ligand 0,018084 0,4355503 298,8 62,6 4,773 13 chemokine (C- C motif) ligand 153 0,000125 0,1541482 502,8 106,6 4,717 24 T-cell lymphoma invasion and 150 0,0001568 0,1541482 633,5 138 4,591 metastasis 2 protein kinase (cAMP- dependent, catalytic) 0,0141052 0,4075754 84 18,4 4,565 inhibitor beta scavenger receptor class 0,0062598 0,3373399 294 64,5 4,558 B, member 1 tetratricopeptid e repeat, ankyrin repeat and coiled-coil 0,0039924 0,3136271 63,2 13,9 4,547 containing 1 carboxypeptida se, vitellogenic- 0,0285783 0,4776731 1087,6 239,5 4,541 like fermitin family homolog 2 0,0022605 0,2690842 136,5 30,1 4,535 (Drosophila) 0,0416725 0,5120746 1037,8 229 4,532 CD1c molecule 0,011718 0,3891601 1346,3 297,5 4,525 cathepsin C 274 9,00E-06 0,115911 542,3 120 4,519 follistatin Transcribed locus, strongly similar to XP_001102524 .1 PREDICTED: similar to Olfactory receptor 2I1 [Macaca 119 8,85E-05 0,1541482 153,1 33,9 4,516 mulatta] sphingosine-1- phosphate 0,0062873 0,3375417 652,1 145,9 4,469 phosphotase 2 Lipoma HMGIC fusion 0,0013062 0,2351565 219,2 49,1 4,464 partner collagen, type 2 0,0010016 0,2205294 320,4 72,3 4,432 VI, alpha 1 lymphocyte 0,0067543 0,3434229 471,8 106,6 4,426 antigen 9 N- acylsphingosin e amidohydrolas e (acid ceramidase)- 263 0,000473 0,1940962 429,4 97,3 4,413 like signal transducing adaptor family 117 0,000103 0,1541482 170,2 38,9 4,375 member 1 N- acylsphingosin e amidohydrolas e (acid ceramidase)- 116 0,0001433 0,1541482 615,1 141,6 4,344 like glycine amidinotransfe rase (L- arginine:glycin e amidinotransfe 0,0280974 0,4758739 275,4 63,4 4,344 rase) phospholipase A2, group VII (platelet- activating factor acetylhydrolas 0,0180192 0,4353512 1789,3 412,5 4,338 e, plasma) angiotensin I converting enzyme (peptidyl- dipeptidase A) 0,0175825 0,4322644 434,3 100,4 4,326 1 C-type lectin- 31 0,0001711 0,1541482 280 65 4,308 like 1 MRNA; cDNA DKFZp547N07 4 (from clone DKFZp547N07 0,003848 0,3114214 492,3 116,7 4,219 4) STAM binding 0,019092 0,4414157 657,4 158,7 4,142 protein-like 1 tubulin, beta 0,0057809 0,3304939 1902 460,5 4,13 2A oligonucleotide /oligosaccharid e-binding fold 0,0020139 0,2572019 2160,3 524,4 4,12 containing 2A Transcribed 0,0048751 0,3211399 1002,5 247,8 4,046 locus 232 7,72E-05 0,1541482 151,3 38 3,982 paraoxonase 2 pleckstrin homology domain containing, family A 115 0,0001465 0,1541482 78,8 20 3,94 member 5 coiled-coil- helix-coiled-coil- helix domain 214 0,0003296 0,1766753 1278,7 327,1 3,909 containing 7 glycoprotein, alpha- galactosyltrans ferase 1 /// similar to glycoprotein galactosyltrans ferase alpha 1, 0,0124535 0,3960995 1533,8 392,9 3,904 3 0,0225747 0,4591785 224,6 57,7 3,893 stabilin 1 CDNA: FLJ21706 fis, clone 0,0131398 0,402701 642,4 165,2 3,889 COL09945 BCL2-like 14 (apoptosis 0,00221 0,2672586 646,8 166,7 3,88 facilitator) endonuclease domain 264 0,0004664 0,1940962 363,1 93,6 3,879 containing 1 homer homolog 2 37 4,67E-05 0,1541482 411,5 106,2 3,875 (Drosophila) MRNA; cDNA DKFZp434N02 20 (from clone DKFZp434N02 0,0011304 0,2251019 890 231 3,853 20) guanylate cyclase activator 1A 0,0118389 0,3891601 196,9 51,1 3,853 (retina) regulator of G- protein 0,0101599 0,3757604 134,1 34,9 3,842 signaling 20 complement factor H /// complement factor H- 0,0206706 0,4485902 74,8 19,5 3,836 related 1 quinolinate phosphoribosyl transferase (nicotinate- nucleotide pyrophosphory lase (carboxylating) 0,0047126 0,3197234 278,3 73,1 3,807 ) 271 0,000108 0,1541482 304,1 80,5 3,778 paraoxonase 2 Ets homologous 0,0068533 0,344282 1004,5 267,5 3,755 factor phospholipid 0,0022486 0,2690201 57,8 15,5 3,729 scramblase 4 0,022179 0,4567432 135,3 36,4 3,717 myosin X 0,0020777 0,2599502 70,2 18,9 3,714 follistatin prostaglandin F2 receptor negative 0,0131804 0,4030416 225,5 60,9 3,703 regulator UDP-N-acetyl- alpha-D- galactosamine: polypeptide N- acetylgalactos aminyltransfer ase 12 0,0387338 0,5072367 3319,8 905,4 3,667 (GalNAc-T12) DKFZP564O0 267 0,000264 0,1708912 66,9 18,3 3,656 823 protein fatty acid binding protein 3, muscle and heart (mammary- derived growth 0,014124 0,4075754 405,7 111,6 3,635 inhibitor) ets homologous 0,0291209 0,4811681 216,4 60 3,607 factor oligonucleotide /oligosaccharid e-binding fold 0,0018083 0,2490398 4687,2 1302,6 3,598 containing 2A interleukin 12A (natural killer cell stimulatory factor 1, cytotoxic lymphocyte maturation 0,0071785 0,3462686 108,9 30,4 3,582 factor 1, p35) beta-site APP- cleaving 0,04198 0,5123056 255,1 72 3,543 enzyme 1 0,0027505 0,2846759 1926,1 546 3,528 mucolipin 2 stomatin 235 1,75E-05 0,1541482 250,2 71,8 3,485 (EPB72)-like 1 Immunoglobuli 0,0166367 0,425997 499,8 144 3,471 n epsilon chain A kinase (PRKA) anchor protein (gravin) 228 9,86E-05 0,1541482 34,3 9,9 3,465 12 Transcribed 0,0055367 0,3279506 270,3 79 3,422 locus tweety homolog 2 0,034351 0,4961771 1033,7 304,4 3,396 (Drosophila) phospholipase 0,040654 0,5112983 271,7 80,5 3,375 A2, group V peptidylglycine alpha- amidating monooxygenas 0,0491023 0,5242469 409,9 121,5 3,374 e chromosome 21 open reading frame 135 0,0006555 0,2000194 73,5 21,9 3,356 42 RAS guanyl releasing protein 1 (calcium and DAG- 185 0,0002483 0,1674922 328,7 98,4 3,34 regulated) Full length insert cDNA clone 0,0016114 0,2418041 585,7 175,8 3,332 YB31B05 tumor necrosis factor receptor superfamily, member 11a, 0,0030824 0,2932482 109,3 33 3,312 NFKB activator guanylate cyclase 1, soluble, alpha 0,0076154 0,3505421 131,8 39,8 3,312 3 0,0193729 0,4417307 5384,2 1630,8 3,302 cathepsin C Transcribed 0,0150151 0,4143327 203,9 61,8 3,299 locus lanosterol synthase (2,3- oxidosqualene- lanosterol 0,0013798 0,238971 930,1 282,6 3,291 cyclase) solute carrier family 37 (glycerol-3- phosphate transporter), 183 0,0004615 0,1940962 484 147,2 3,288 member 3 discoidin, CUB and LCCL domain 0,0077193 0,3505421 170,3 52,3 3,256 containing 1 prostaglandin- endoperoxide synthase 1 (prostaglandin G/H synthase and cyclooxygenas 0,0186765 0,4390102 1348,3 414,4 3,254 e) 0,0050558 0,3244435 585,6 180,1 3,252 formin-like 2 StAR-related lipid transfer (START) domain 0,028078 0,4758739 450 138,7 3,244 containing 5 STAM binding 0,03559 0,4984838 207,4 64 3,241 protein-like 1 ankyrin repeat and BTB (POZ) domain 252 0,0006348 0,1980347 704,5 219,1 3,215 containing 2 ADP- ribosylation 0,0154154 0,4170396 200 62,2 3,215 factor-like 5B Wolfram syndrome 1 0,0327223
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    MARIE EVE BERGERON EFFET DE LA CRYPTORCHIDIE SUR LE TRANSCRIPTOME TESTICULAIRE HUMAIN Mémoire présenté à la Faculté des études supérieures et postdoctorales de l’Université Laval dans le cadre du programme de maîtrise en Physiologie-Endocrinologie pour l’obtention du grade de Maître ès sciences (M.Sc.) DÉPARTEMENT D’OBSTÉTRIQUE ET DE GYNÉCOLOGIE FACULTÉ DE MÉDECINE UNIVERSITÉ LAVAL QUÉBEC 2012 © Marie Eve Bergeron, 2012 Résumé Les niveaux d’expression de nombreux gènes peuvent être affectés par l’environnement et mener au développement de la cryptorchidie. Cette malformation congénitale est la plus commune dont une des conséquences majeures est l’infertilité masculine due au testicule non-descendu, auquel un risque plus élevé de cancer testiculaire est associé. L’expression des ARN totaux isolés à partir de biopsies testiculaires ont été analysés par micropuces, puis par une analyse bio-informatique et une validation par RT-qPCR de plusieurs gènes sélectionnés. Ces analyses m’ont permis d’identifier plus de deux milles candidats montrant une expression différente entre des sujets cryptorchides et normaux. Certains de ces gènes sélectionnés peuvent être associés à la descente testiculaire, d’autres au cancer testiculaire ou encore aux divers types cellulaires retrouvés dans cet organe. Les différences dans le transcriptome dues à la cryptorchidie vont nous aider à comprendre la cause génétique de cette maladie. ii Abstract Expression level of numerous genes may be affected by environmental condition and lead to development of cryptorchidism. The most common congenital malformation in male is cryptorchidism. One major consequence of this anomaly is infertility due to undescended testis, to which an increased risk of testicular cancer is associated.
  • A Dissertation Entitled the Androgen Receptor

    A Dissertation Entitled the Androgen Receptor

    A Dissertation entitled The Androgen Receptor as a Transcriptional Co-activator: Implications in the Growth and Progression of Prostate Cancer By Mesfin Gonit Submitted to the Graduate Faculty as partial fulfillment of the requirements for the PhD Degree in Biomedical science Dr. Manohar Ratnam, Committee Chair Dr. Lirim Shemshedini, Committee Member Dr. Robert Trumbly, Committee Member Dr. Edwin Sanchez, Committee Member Dr. Beata Lecka -Czernik, Committee Member Dr. Patricia R. Komuniecki, Dean College of Graduate Studies The University of Toledo August 2011 Copyright 2011, Mesfin Gonit This document is copyrighted material. Under copyright law, no parts of this document may be reproduced without the expressed permission of the author. An Abstract of The Androgen Receptor as a Transcriptional Co-activator: Implications in the Growth and Progression of Prostate Cancer By Mesfin Gonit As partial fulfillment of the requirements for the PhD Degree in Biomedical science The University of Toledo August 2011 Prostate cancer depends on the androgen receptor (AR) for growth and survival even in the absence of androgen. In the classical models of gene activation by AR, ligand activated AR signals through binding to the androgen response elements (AREs) in the target gene promoter/enhancer. In the present study the role of AREs in the androgen- independent transcriptional signaling was investigated using LP50 cells, derived from parental LNCaP cells through extended passage in vitro. LP50 cells reflected the signature gene overexpression profile of advanced clinical prostate tumors. The growth of LP50 cells was profoundly dependent on nuclear localized AR but was independent of androgen. Nevertheless, in these cells AR was unable to bind to AREs in the absence of androgen.
  • Supplemental Figure S1 Differentially Methylated Regions (Dmrs

    Supplemental Figure S1 Differentially Methylated Regions (Dmrs

    Supplemental Figure S1 '$$#0#,2'**7+#2&7*2#"0#%'-,11 #25##,"'1#1#122#1 '!2-0'*"#.'!2'-,-$122&#20,1'2'-,$0-+2- !"Q !"2-$%," $ 31',% 25-$-*" !&,%# ," ' 0RTRW 1 !32V-$$ !0'2#0'T - #.0#1#,22'-, -$ "'$$#0#,2'**7+#2&7*2#"%#,#11',.0#,2&#1#1,"2&#'0 #&4'-022&#20,1'2'-, #25##,"'$$#0#,2"'1#1#122#1T-*!)00-51',"'!2#&7.#0+#2&7*2#"%#,#1Q%0700-51 &7.-+#2&7*2#"%#,#1Q31',%25-$-*"!&,%#,"'0RTRW1!32V-$$!0'2#0'T-%#,#1 +#22&# -4#!0'2#0'22&#20,1'2'-,$0-+$%2-$Q5#2&#0#$-0#*1-',!*3"#" %#,#15'2&V4*3#0RTRWT$$#!2#"%#,10#&'%&*'%&2#" 712#0'1)1#T Supplemental Figure S2 Validation of results from the HELP assay using Epityper MassarrayT #13*21 $0-+ 2&# 1$ 117 5#0# !-00#*2#" 5'2& /3,2'22'4# +#2&7*2'-, ,*78#" 7 '13*$'2#11007$-04V-,"6U-%#,#.0-+-2#00#%'-,1T11007 51.#0$-0+#"31',%**4'* *#1+.*#1T S Supplemental Fig. S1 A unique hypermethylated genes (methylation sites) 454 (481) 5693 (6747) 120 (122) NLMGUS NEWMM REL 2963 (3207) 1338 (1560) 5 (5) unique hypomethylated genes (methylation sites) B NEWMM 0 (0) MGUS 454 (481) 0 (0) NEWMM REL NL 3* (2) 2472 (3066) NEWMM 2963 REL (3207) 2* (2) MGUS 0 (0) REL 2 (2) NEWMM 0 (0) REL Supplemental Fig. S2 A B ARID4B DNMT3A Methylation by MassArray Methylation by MassArray 0 0.2 0.4 0.6 0.8 1 1.2 0.5 0.6 0.7 0.8 0.9 1 2 0 NL PC MGUS 1.5 -0.5 NEW MM 1 REL MM -1 0.5 -1.5 0 -2 -0.5 -1 -2.5 -1.5 -3 Methylation by HELP Assay Methylation by HELP Methylation by HELP Assay Methylation by HELP -2 -3.5 -2.5 -4 Supplemental tables "3..*#+#,2*6 *#"SS 9*','!*!&0!2#0'12'!1-$.2'#,21+.*#1 DZ_STAGE Age Gender Ethnicity MM isotype PCLI Cytogenetics
  • Chemical Agent and Antibodies B-Raf Inhibitor RAF265

    Chemical Agent and Antibodies B-Raf Inhibitor RAF265

    Supplemental Materials and Methods: Chemical agent and antibodies B-Raf inhibitor RAF265 [5-(2-(5-(trifluromethyl)-1H-imidazol-2-yl)pyridin-4-yloxy)-N-(4-trifluoromethyl)phenyl-1-methyl-1H-benzp{D, }imidazol-2- amine] was kindly provided by Novartis Pharma AG and dissolved in solvent ethanol:propylene glycol:2.5% tween-80 (percentage 6:23:71) for oral delivery to mice by gavage. Antibodies to phospho-ERK1/2 Thr202/Tyr204(4370), phosphoMEK1/2(2338 and 9121)), phospho-cyclin D1(3300), cyclin D1 (2978), PLK1 (4513) BIM (2933), BAX (2772), BCL2 (2876) were from Cell Signaling Technology. Additional antibodies for phospho-ERK1,2 detection for western blot were from Promega (V803A), and Santa Cruz (E-Y, SC7383). Total ERK antibody for western blot analysis was K-23 from Santa Cruz (SC-94). Ki67 antibody (ab833) was from ABCAM, Mcl1 antibody (559027) was from BD Biosciences, Factor VIII antibody was from Dako (A082), CD31 antibody was from Dianova, (DIA310), and Cot antibody was from Santa Cruz Biotechnology (sc-373677). For the cyclin D1 second antibody staining was with an Alexa Fluor 568 donkey anti-rabbit IgG (Invitrogen, A10042) (1:200 dilution). The pMEK1 fluorescence was developed using the Alexa Fluor 488 chicken anti-rabbit IgG second antibody (1:200 dilution).TUNEL staining kits were from Promega (G2350). Mouse Implant Studies: Biopsy tissues were delivered to research laboratory in ice-cold Dulbecco's Modified Eagle Medium (DMEM) buffer solution. As the tissue mass available from each biopsy was limited, we first passaged the biopsy tissue in Balb/c nu/Foxn1 athymic nude mice (6-8 weeks of age and weighing 22-25g, purchased from Harlan Sprague Dawley, USA) to increase the volume of tumor for further implantation.