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Supplemental Table S5 A Probe Symbol Description Fold Change raw p-value BH-value 1424032_at 0610039P13Rik RIKEN cDNA 0610039P13 gene 0.55161976 0.001110473 0.035847968 1438176_x_at 1110031B06Rik RIKEN cDNA 1110031B06 gene 1.546320853 0.000575527 0.026980808 1455040_s_at 1110062M06Rik RIKEN cDNA 1110062M06 gene 0.53766793 0.000526255 0.025845734 1438511_a_at 1190002H23Rik RIKEN cDNA 1190002H23 gene 0.625269719 0.000480693 0.024788481 1456603_at 1500005K14Rik RIKEN cDNA 1500005K14 gene 0.672783447 0.000191911 0.0193647 1429907_at 1700094D03Rik RIKEN cDNA 1700094D03 gene 1.21499778 0.000577376 0.027011654 1418319_at 1810047C23Rik RIKEN cDNA 1810047C23 gene 0.814393041 0.000460153 0.024569357 1425333_at 1810048P08Rik RIKEN cDNA 1810048P08 gene 1.258622557 0.000635157 0.028093004 1439465_x_at 2310016E02Rik RIKEN cDNA 2310016E02 gene 1.465167974 0.00158772 0.040937929 1452365_at 4732435N03Rik RIKEN cDNA 4732435N03 gene 1.188684952 7.75E-05 0.01343138 1420721_at 4921536K21Rik RIKEN cDNA 4921536K21 gene 0.792184179 0.000702317 0.029455789 1454606_at 4933426M11Rik RIKEN cDNA 4933426M11 gene 1.440890915 0.000243944 0.020147563 1422906_at Abcg2 ATP-binding cassette, sub-family G (WHITE), member 1.519610931 0.000582547 0.027086027 1416863_at Abhd8 abhydrolase domain containing 8 1.335858135 0.001597529 0.041026484 1448213_at Anxa1 annexin A1 0.618671358 0.00046908 0.024637532 1460330_at Anxa3 annexin A3 0.754566129 1.87E-05 0.007312522 1421223_a_at Anxa4 annexin A4 1.691634746 0.000942316 0.033257546 1424457_at Apbb3 amyloid beta (A4) precursor protein-binding, family B, m 1.285350473 0.000274466 0.020621301 1423714_at Asf1b ASF1 anti-silencing function 1 homolog B (S. cerevisiae 0.755897287 0.000188676 0.0193647 1435112_a_at Atp5h ATP synthase, H+ transporting, mitochondrial F0 comp 0.893930371 0.002370621 0.049943713 1439456_x_at Atp6ap2 ATPase, H+ transporting, lysosomal accessory protein 0.788529376 0.000671988 0.028874457 1415866_at AW538196 expressed sequence AW538196 1.41407995 0.001433524 0.039558885 1419216_at Azi1 5-azacytidine induced gene 1 1.436787766 2.45E-05 0.008650593 1424516_at B230354K17Rik RIKEN cDNA B230354K17 gene 1.644133266 2.78E-05 0.009007606 1427511_at B2m beta-2 microglobulin 1.821673191 5.52E-05 0.011854561 1451836_at BC022651 cDNA sequence BC022651 0.7189456 0.002095949 0.047029738 1435087_at BC039093 cDNA sequence BC039093 1.162684776 0.001865749 0.044272805 1417493_at Bmi1 B lymphoma Mo-MLV insertion region 1 1.464126734 0.000185258 0.0193647 1416924_at Bri3 brain protein I3 1.544927994 1.57E-05 0.006947722 1415692_s_at Canx calnexin 0.570928425 0.001566949 0.040836276 1424093_x_at Cd151 CD151 antigen 1.969029848 0.000427831 0.024208219 1416072_at Cd34 CD34 antigen 2.748385281 0.000185502 0.0193647 1435220_s_at Cdc42se2 CDC42 small effector 2 1.490715314 0.001418475 0.039399923 1460682_s_at Ceacam2 CEA-related cell adhesion molecule 2 0.717390438 0.001825051 0.043866955 1454641_at Cggbp1 CGG triplet repeat binding protein 1 1.23704051 4.37E-05 0.010452948 1460338_a_at Crlf3 cytokine receptor-like factor 3 1.893360719 0.001641848 0.041577611 1449129_a_at Csen calsenilin, presenilin binding protein, EF hand transcript 0.694555516 2.83E-05 0.009007606 1448471_a_at Ctla2a cytotoxic T lymphocyte-associated protein 2 alpha 14.59057271 0.000823149 0.031435038 1416811_s_at Ctla2a cytotoxic T lymphocyte-associated protein 2 alpha 12.52573452 0.001097247 0.035668373 1451019_at Ctsf cathepsin F 1.420020257 0.000272363 0.020544695 1433908_a_at Cttn cortactin 3.545420566 0.000346366 0.022010729 1417039_a_at Cul7 cullin 7 2.428570811 0.000783045 0.030689178 1451426_at D11Lgp2e DNA segment, Chr 11, Lothar Hennighausen 2, express 1.540855922 0.001449052 0.039714556 1416708_a_at D7Bwg0611e DNA segment, Chr 7, Brigham & Women's Genetics 06 1.649383802 6.09E-05 0.01214869 1421936_at Dapp1 dual adaptor for phosphotyrosine and 3-phosphoinositid 1.688791945 0.000307889 0.021628489 1438093_x_at Dbi diazepam binding inhibitor 0.812441491 0.000571863 0.026946643 1453251_at Dhx30 DEAH (Asp-Glu-Ala-His) box polypeptide 30 1.396776146 3.95E-05 0.010273107 1432066_at Dnaja3 DnaJ (Hsp40) homolog, subfamily A, member 3 0.775673094 0.000346752 0.022010729 1448892_at Dock7 dedicator of cytokinesis 7 1.953168002 0.000167317 0.018590066 1417540_at Elf1 E74-like factor 1 1.641853799 0.000964438 0.033511647 1418059_at Eltd1 EGF, latrophilin seven transmembrane domain containi 3.089304358 9.88E-07 0.003195994 1418058_at Eltd1 EGF, latrophilin seven transmembrane domain containi 1.976743655 0.001341902 0.038444124 1421699_at Enam enamelin 0.777099544 0.000214446 0.019463139 1432176_a_at Eng endoglin 3.043337922 0.001250496 0.037089871 1426010_a_at Epb4.1l3 erythrocyte protein band 4.1-like 3 1.433511604 0.001675235 0.041860363 1454169_a_at Epsti1 epithelial stromal interaction 1 (breast) 1.726629133 0.00107982 0.035612091 1450935_at Ercc5 excision repair cross-complementing rodent repair defic 1.200987769 0.00156758 0.040836276 1433514_at Etnk1 ethanolamine kinase 1 1.241741274 0.000129338 0.016038504 1449023_a_at Ezh1 enhancer of zeste homolog 1 (Drosophila) 1.490365658 0.000396436 0.023168317 1437308_s_at F2r coagulation factor II (thrombin) receptor 4.359222809 0.000933971 0.033257546 1451263_a_at Fabp4 fatty acid binding protein 4, adipocyte 3.577193161 0.000297772 0.021234667 1417023_a_at Fabp4 fatty acid binding protein 4, adipocyte 4.026932533 0.000693637 0.029289558 1456615_a_at Falz fetal Alzheimer antigen 1.273713777 0.000204266 0.019394441 1452828_at Fbxo21 F-box only protein 21 1.443035251 0.000928404 0.033212087 1426750_at Flnb filamin, beta 0.62700177 0.002320182 0.049459781 1417544_a_at Flot2 flotillin 2 0.798688809 0.000593962 0.027336709 1426982_at Flywch1 FLYWCH-type zinc finger 1 1.240072961 0.002205207 0.048173129 1434831_a_at Foxo3a forkhead box O3a 1.323710341 0.000640584 0.028147188 1416418_at Gabarapl1 gamma-aminobutyric acid (GABA(A)) receptor-associat 1.937325453 0.000385043 0.022692514 1423391_at Git2 G protein-coupled receptor kinase-interactor 2 1.603162562 0.000598999 0.027381311 1426236_a_at Glul glutamate-ammonia ligase (glutamine synthase) 1.49257497 0.000219717 0.019623685 1427509_at Gm937 gene model 937, (NCBI) 0.653842735 0.001235094 0.03697134 1431777_a_at Hmgn3 high mobility group nucleosomal binding domain 3 2.09912002 0.000750263 0.029906908 1434875_a_at Hmgn3 high mobility group nucleosomal binding domain 3 2.08770845 0.002245373 0.048773132 1437234_x_at Hrmt1l1 heterogeneous nuclear ribonucleoprotein methyltransfe 2.998888853 0.001913835 0.044814164 1451567_a_at Ifi203 interferon activated gene 203 2.69880229 0.000209475 0.019403341 1448775_at Ifi203 interferon activated gene 203 2.840385069 0.000263963 0.020544695 1452231_x_at Ifi205 interferon activated gene 205 2.229101287 4.52E-05 0.010682119 1426906_at Ifi205 interferon activated gene 205 1.963936527 0.000383253 0.022692514 1426278_at Ifi27 interferon, alpha-inducible protein 27 1.961905894 0.000336059 0.022010729 1426276_at Ifih1 interferon induced with helicase C domain 1 1.446599099 6.52E-05 0.012336168 1436420_a_at Ipo4 importin 4 1.962136373 0.000783122 0.030689178 1418265_s_at Irf2 interferon regulatory factor 2 1.396881173 0.00013516 0.016647297 1421322_a_at Isgf3g interferon dependent positive acting transcription factor 1.564587343 4.05E-05 0.010273107 1449841_at Kif3a kinesin family member 3A 1.822950986 6.66E-06 0.005058848 1455434_a_at Ktn1 kinectin 1 1.488731636 0.002165271 0.047971001 1430447_a_at Lair1 leukocyte-associated Ig-like receptor 1 0.571315127 6.30E-05 0.012233107 1416148_at Laptm4b lysosomal-associated protein transmembrane 4B 1.234185345 0.000515862 0.025556575 1438932_at LOC381240 0.669312138 0.002375533 0.0499506 1421571_a_at Ly6c lymphocyte antigen 6 complex, locus C 0.706563041 1.50E-05 0.006856421 1434674_at Lyst lysosomal trafficking regulator 0.710491778 0.001144698 0.035954864 1423284_at Mansc1 MANSC domain containing 1 2.013237954 0.00147673 0.040102612 1426759_at Map4k3 mitogen-activated protein kinase kinase kinase kinase 3 1.829204605 0.000270745 0.020544695 1427040_at Mdfic MyoD family inhibitor domain containing 1.321351611 0.00212479 0.047482467 1424852_at Mef2c myocyte enhancer factor 2C 2.148000054 2.16E-05 0.008053739 1451506_at Mef2c myocyte enhancer factor 2C 2.04930192 0.000607506 0.027404188 1450992_a_at Meis1 myeloid ecotropic viral integration site 1 2.861538387 0.00058067 0.027054197 1415897_a_at Mgst1 microsomal glutathione S-transferase 1 0.70632491 3.13E-05 0.009595536 1449188_at Midn midnolin 1.456788898 0.001276816 0.037510427 1423595_at Mina myc induced nuclear antigen 1.23113095 0.000120047 0.015654383 1439364_a_at Mmp2 matrix metallopeptidase 2 1.425531335 0.002097447 0.047029738 1455099_at Mogat2 monoacylglycerol O-acyltransferase 2 0.700957917 0.002088546 0.047022518 1415762_x_at Mrpl52 mitochondrial ribosomal protein L52 1.532231346 8.82E-05 0.014274707 1415761_at Mrpl52 mitochondrial ribosomal protein L52 1.582529657 0.000124731 0.015899693 1427938_at Mycbp c-myc binding protein 0.868832879 0.000487675 0.024936677 1426864_a_at Ncam1 neural cell adhesion molecule 1 0.614068028 0.000198 0.0193647 1425609_at Ncf1 neutrophil cytosolic factor 1 0.693384284 0.00074276 0.029891318 1452196_a_at Nckap1 NCK-associated protein 1 2.232540223 0.000947607 0.033283609 1451109_a_at Nedd4 neural precursor cell expressed, developmentally down 1.662670568 0.001659437 0.041765717 1419078_at Nin ninein 0.626381147 0.00143006 0.039522621 1455143_at Nlgn2 neuroligin 2 1.845548456 0.001607032 0.041151825
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  • Supplemental Table1a.Xlsx

    Supplemental Table1a.Xlsx

    Electronic Supplementary Material (ESI) for Analyst This journal is © The Royal Society of Chemistry 2013 Supplemental Table 1A This table includes the taxonomically significant peptides from HeLa cultured VACV samples purified by filter purification. The peptide, uniprot ID and protein name from one of the homologous proteins is provided. The species specificity is provided along with the frequency of observation (n = 10). Peptides observed in more than replicate data set are included. Peptide Uniprot ID Protein Description Specificity Freq. LLNENSYVPR P02786 protein 1 Primates, racoon 0.9 LATQLTGPVMPVR A8K4C8 60S ribosomal protein L13 Homo sapiens 0.8 HVGK B0JYN6 Alpha-2-HS-glycoprotein Bos taurus0.8 LAVDEEENADNNTK F8WBE5 protein 1 Great Apes 0.8 VTLTSEEEAR B4DJI1 L-lactate dehydrogenase Primates, Hamster 0.7 LGEYGFQNELIVR B0JYQ0 ALB protein Bos taurus 0.6 GTVTDFPGFDER D6RCN3 Annexin A5 Elephant 0.6 YTPSGQAGAAASESLF Fructose-bisphosphate Great apes, cucumber VSNHAY H3BR68 aldolase A (Fragment) and some rodents 0.6 VGGHAAEYGAEALER P01966 Hemoglobin subunit alpha Bos taurus 0.6 ALTGHLEEVVLALLK P04083 Annexin A1 some rodents 0.5 AQGPAASAEEPKPVEA Brain acid soluble protein PAANSDQTVTVKE P80723 1 Homo sapiens 0.5 FYALSASFEPFSNK P27797 Calreticulin Primates not gorilla 0.5 PK P02081 beta Bos taurus0.5 NLK F5H6B1 protein 1Gorilla 0.5 K P02786 protein 1Primates 0.5 YNSQLLSFVR P02786 protein 1 Great Apes 0.5 TPIVGQPSIPGGPVR B0JYN6 Alpha-2-HS-glycoprotein Bos taurus 0.4 AGTDLLNFLSSFIDPK P81644 Apolipoprotein A-II Bos taurus 0.4 SELPLDPLPVPTEEGNP
  • Differential Proteomic Analysis of Hepatocellular Carcinomas From

    Differential Proteomic Analysis of Hepatocellular Carcinomas From

    CANCER GENOMICS & PROTEOMICS 17 : 669-685 (2020) doi:10.21873/cgp.20222 Differential Proteomic Analysis of Hepatocellular Carcinomas from Ppp2r5d Knockout Mice and Normal (Knockout) Livers CAROLINE LAMBRECHT 1, GABRIELA BOMFIM FERREIRA 2, JUDIT DOMÈNECH OMELLA 1, LOUIS LIBBRECHT 3, RITA DE VOS 4, RITA DERUA 1, CHANTAL MATHIEU 2, LUT OVERBERGH 2, ETIENNE WAELKENS 1 and VEERLE JANSSENS 1,5 1Laboratory of Protein Phosphorylation and Proteomics, Department Cellular and Molecular Medicine, University of Leuven (KU Leuven), Leuven, Belgium; 2Clinical and Experimental Endocrinology, Department Clinical and Experimental Medicine, University of Leuven (KU Leuven), Leuven, Belgium; 3Department of Pathology, Université Catholique de Louvain (UCL), Brussels, Belgium; 4Translational Cell and Tissue Research, Department Imaging and Pathology, University of Leuven (KU Leuven), Leuven, Belgium; 5LKI, KU Leuven Cancer Institute, Leuven, Belgium Abstract. Background: Hepatocellular carcinoma (HCC) ‘gastrointestinal disease’ as top hits. Conclusion: We is the major type of primary liver cancer. Mice lacking the identified several proteins for further exploration as novel tumor-suppressive protein phosphatase 2A subunit B56 δ potential HCC biomarkers, and independently underscored (Ppp2r5d ) spontaneously develop HCC, correlating with the relevance of Ppp2r5d knockout mice as a valuable increased c-MYC oncogenicity. Materials and Methods: We hepatocarcinogenesis model. used two-dimensional difference gel electrophoresis-coupled matrix-assisted laser desorption/ionization time-of-flight Hepatocellular carcinoma (HCC) is the most common primary mass spectrometry to identify differential proteomes of livers liver cancer, and the second leading cause of cancer-related death from wild-type, non-cancerous and HCC-affected B56 δ worldwide (1). Most patients with HCC are diagnosed at an knockout mice.
  • Annexin A1 Released in Extracellular Vesicles by Pancreatic Cancer Cells Activates Components of the Tumor Microenvironment

    Annexin A1 Released in Extracellular Vesicles by Pancreatic Cancer Cells Activates Components of the Tumor Microenvironment

    cells Article Annexin A1 Released in Extracellular Vesicles by Pancreatic Cancer Cells Activates Components of the Tumor Microenvironment, through Interaction with the Formyl-Peptide Receptors Nunzia Novizio 1, Raffaella Belvedere 1 , Emanuela Pessolano 1,2 , Alessandra Tosco 1 , Amalia Porta 1 , Mauro Perretti 2, Pietro Campiglia 1 , Amelia Filippelli 3 and Antonello Petrella 1,* 1 Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Italy; [email protected] (N.N.); [email protected] (R.B.); [email protected] (E.P.); [email protected] (A.T.); [email protected] (A.P.); [email protected] (P.C.) 2 The William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK; [email protected] 3 Department of Medicine, Surgery and Dentistry, University of Salerno, Via S. Allende 43, 84081 Baronissi, Italy; afi[email protected] * Correspondence: [email protected]; Tel.: +39-089-969-762; Fax: +39-089-969-602 Received: 17 November 2020; Accepted: 17 December 2020; Published: 18 December 2020 Abstract: Pancreatic cancer (PC) is one of the most aggressive cancers in the world. Several extracellular factors are involved in its development and metastasis to distant organs. In PC, the protein Annexin A1 (ANXA1) appears to be overexpressed and may be identified as an oncogenic factor, also because it is a component in tumor-deriving extracellular vesicles (EVs). Indeed, these microvesicles are known to nourish the tumor microenvironment. Once we evaluated the autocrine role of ANXA1-containing EVs on PC MIA PaCa-2 cells and their pro-angiogenic action, we investigated the ANXA1 paracrine effect on stromal cells like fibroblasts and endothelial ones.
  • Anoctamin 1 (Tmem16a) Ca -Activated Chloride Channel Stoichiometrically Interacts with an Ezrin–Radixin–Moesin Network

    Anoctamin 1 (Tmem16a) Ca -Activated Chloride Channel Stoichiometrically Interacts with an Ezrin–Radixin–Moesin Network

    Anoctamin 1 (Tmem16A) Ca2+-activated chloride channel stoichiometrically interacts with an ezrin–radixin–moesin network Patricia Perez-Cornejoa,1, Avanti Gokhaleb,1, Charity Duranb,1, Yuanyuan Cuib, Qinghuan Xiaob, H. Criss Hartzellb,2, and Victor Faundezb,2 aPhysiology Department, School of Medicine, Universidad Autónoma de San Luis Potosí, San Luis Potosí, SLP 78210, Mexico; and bDepartment of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322 Edited by David E. Clapham, Howard Hughes Medical Institute, Children’s Hospital Boston, Boston, MA, and approved May 9, 2012 (received for review January 4, 2012) The newly discovered Ca2+-activated Cl− channel (CaCC), Anocta- approach to identify Ano1-interacting proteins. We find that min 1 (Ano1 or TMEM16A), has been implicated in vital physiolog- Ano1 forms a complex with two high stochiometry interactomes. ical functions including epithelial fluid secretion, gut motility, and One protein network is centered on the signaling/scaffolding smooth muscle tone. Overexpression of Ano1 in HEK cells or Xen- actin-binding regulatory proteins ezrin, radixin, moesin, and opus oocytes is sufficient to generate Ca2+-activated Cl− currents, RhoA. The ezrin–radixin–moesin (ERM) proteins organize the but the details of channel composition and the regulatory factors cortical cytoskeleton by linking actin to the plasma membrane that control channel biology are incompletely understood. We and coordinate cell signaling events by scaffolding signaling used a highly sensitive quantitative SILAC proteomics approach molecules (19). The other major interactome is centered on the to obtain insights into stoichiometric protein networks associated SNARE and SM proteins VAMP3, syntaxins 2 and -4, and the with the Ano1 channel.