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Propranolol-Mediated Attenuation of MMP-9 Excretion in Infants with Hemangiomas

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Supplementary Online Content Thaivalappil S, Bauman N, Saieg A, Movius E, Brown KJ, Preciado D. Propranolol-mediated attenuation of MMP-9 excretion in infants with hemangiomas. JAMA Otolaryngol Head Neck Surg. doi:10.1001/jamaoto.2013.4773 eTable. List of All of the Proteins Identified by Proteomics This supplementary material has been provided by the authors to give readers additional information about their work. © 2013 American Medical Association. All rights reserved. Downloaded From: https://jamanetwork.com/ on 10/01/2021 eTable. List of All of the Proteins Identified by Proteomics Protein Name Prop 12 mo/4 Pred 12 mo/4 Δ Prop to Pred mo mo Myeloperoxidase OS=Homo sapiens GN=MPO 26.00 143.00 ‐117.00 Lactotransferrin OS=Homo sapiens GN=LTF 114.00 205.50 ‐91.50 Matrix metalloproteinase‐9 OS=Homo sapiens GN=MMP9 5.00 36.00 ‐31.00 Neutrophil elastase OS=Homo sapiens GN=ELANE 24.00 48.00 ‐24.00 Bleomycin hydrolase OS=Homo sapiens GN=BLMH 3.00 25.00 ‐22.00 CAP7_HUMAN Azurocidin OS=Homo sapiens GN=AZU1 PE=1 SV=3 4.00 26.00 ‐22.00 S10A8_HUMAN Protein S100‐A8 OS=Homo sapiens GN=S100A8 PE=1 14.67 30.50 ‐15.83 SV=1 IL1F9_HUMAN Interleukin‐1 family member 9 OS=Homo sapiens 1.00 15.00 ‐14.00 GN=IL1F9 PE=1 SV=1 MUC5B_HUMAN Mucin‐5B OS=Homo sapiens GN=MUC5B PE=1 SV=3 2.00 14.00 ‐12.00 MUC4_HUMAN Mucin‐4 OS=Homo sapiens GN=MUC4 PE=1 SV=3 1.00 12.00 ‐11.00 HRG_HUMAN Histidine‐rich glycoprotein OS=Homo sapiens GN=HRG 1.00 12.00 ‐11.00 PE=1 SV=1 TKT_HUMAN Transketolase OS=Homo sapiens GN=TKT PE=1 SV=3 17.00 28.00 ‐11.00 CATG_HUMAN Cathepsin G OS=Homo sapiens GN=CTSG PE=1 SV=2 4.00 14.00 ‐10.00 MUCB_HUMAN Ig mu heavy chain disease protein OS=Homo sapiens 2.00 11.00 ‐9.00 PE=1 SV=1 ANXA1_HUMAN Annexin A1 OS=Homo sapiens GN=ANXA1 PE=1 SV=2 22.00 31.00 ‐9.00 S10AC_HUMAN Protein S100‐A12 OS=Homo sapiens GN=S100A12 1.00 8.00 ‐7.00 PE=1 SV=2 TCO1_HUMAN Transcobalamin‐1 OS=Homo sapiens GN=TCN1 PE=1 1.00 8.00 ‐7.00 SV=2 PLSL_HUMAN Plastin‐2 OS=Homo sapiens GN=LCP1 PE=1 SV=6 11.00 18.00 ‐7.00 ITAM_HUMAN Integrin alpha‐M OS=Homo sapiens GN=ITGAM PE=1 2.00 8.00 ‐6.00 SV=2 MYH9_HUMAN Myosin‐9 OS=Homo sapiens GN=MYH9 PE=1 SV=4 5.00 11.00 ‐6.00 S100P_HUMAN Protein S100‐P OS=Homo sapiens GN=S100P PE=1 6.00 12.00 ‐6.00 © 2013 American Medical Association. All rights reserved. Downloaded From: https://jamanetwork.com/ on 10/01/2021 SV=2 ANXA3_HUMAN Annexin A3 OS=Homo sapiens GN=ANXA3 PE=1 SV=3 8.00 14.00 ‐6.00 TALDO_HUMAN Transaldolase OS=Homo sapiens GN=TALDO1 PE=1 2.00 7.50 ‐5.50 SV=2 CEAM5_HUMAN Carcinoembryonic antigen‐related cell adhesion 8.00 13.00 ‐5.00 molecule 5 OS=Homo sapiens GN=CEACAM5 PE=1 SV=2 STOM_HUMAN Erythrocyte band 7 integral membrane protein 1.00 5.00 ‐4.00 OS=Homo sapiens GN=STOM PE=1 SV=3 CAMP_HUMAN Cathelicidin antimicrobial peptide OS=Homo sapiens 2.00 6.00 ‐4.00 GN=CAMP PE=1 SV=1 BASP1_HUMAN Brain acid soluble protein 1 OS=Homo sapiens 2.00 6.00 ‐4.00 GN=BASP1 PE=1 SV=2 IGHM_HUMAN Ig mu chain C region OS=Homo sapiens GN=IGHM PE=1 5.00 8.50 ‐3.50 SV=3 SPA12_HUMAN Serpin A12 OS=Homo sapiens GN=SERPINA12 PE=2 1.00 4.17 ‐3.17 SV=1 CPNS2_HUMAN Calpain small subunit 2 OS=Homo sapiens GN=CAPNS2 1.00 4.00 ‐3.00 PE=2 SV=2 PSA5_HUMAN Proteasome subunit alpha type‐5 OS=Homo sapiens 1.00 4.00 ‐3.00 GN=PSMA5 PE=1 SV=3 PGRP1_HUMAN Peptidoglycan recognition protein 1 OS=Homo sapiens 1.00 4.00 ‐3.00 GN=PGLYRP1 PE=1 SV=1 APOA1_HUMAN Apolipoprotein A‐I OS=Homo sapiens GN=APOA1 5.25 8.20 ‐2.95 PE=1 SV=1 SPB6_HUMAN Serpin B6 OS=Homo sapiens GN=SERPINB6 PE=1 SV=3 0.33 3.00 ‐2.67 DSC2_HUMAN Desmocollin‐2 OS=Homo sapiens GN=DSC2 PE=1 SV=1 0.33 2.50 ‐2.17 IQGA1_HUMAN Ras GTPase‐activating‐like protein IQGAP1 OS=Homo 1.00 3.00 ‐2.00 sapiens GN=IQGAP1 PE=1 SV=1 DMBT1_HUMAN Deleted in malignant brain tumors 1 protein 1.00 3.00 ‐2.00 OS=Homo sapiens GN=DMBT1 PE=1 SV=2 PSB4_HUMAN Proteasome subunit beta type‐4 OS=Homo sapiens 1.00 3.00 ‐2.00 GN=PSMB4 PE=1 SV=4 PSA2_HUMAN Proteasome subunit alpha type‐2 OS=Homo sapiens 1.00 3.00 ‐2.00 © 2013 American Medical Association. All rights reserved. Downloaded From: https://jamanetwork.com/ on 10/01/2021 GN=PSMA2 PE=1 SV=2 SBSN_HUMAN Suprabasin OS=Homo sapiens GN=SBSN PE=2 SV=1 1.00 3.00 ‐2.00 SPB8_HUMAN Serpin B8 OS=Homo sapiens GN=SERPINB8 PE=1 SV=2 1.00 3.00 ‐2.00 SODM_HUMAN Superoxide dismutase [Mn], mitochondrial OS=Homo 1.00 3.00 ‐2.00 sapiens GN=SOD2 PE=1 SV=2 VASP_HUMAN Vasodilator‐stimulated phosphoprotein OS=Homo 1.00 3.00 ‐2.00 sapiens GN=VASP PE=1 SV=3 PAI2_HUMAN Plasminogen activator inhibitor 2 OS=Homo sapiens 1.00 3.00 ‐2.00 GN=SERPINB2 PE=1 SV=2 ITB2_HUMAN Integrin beta‐2 OS=Homo sapiens GN=ITGB2 PE=1 SV=2 1.00 3.00 ‐2.00 MDHM_HUMAN Malate dehydrogenase, mitochondrial OS=Homo 2.00 4.00 ‐2.00 sapiens GN=MDH2 PE=1 SV=3 CEAM1_HUMAN Carcinoembryonic antigen‐related cell adhesion 4.00 6.00 ‐2.00 molecule 1 OS=Homo sapiens GN=CEACAM1 PE=1 SV=2 VTNC_HUMAN Vitronectin OS=Homo sapiens GN=VTN PE=1 SV=1 0.75 2.67 ‐1.92 ANGT_HUMAN Angiotensinogen OS=Homo sapiens GN=AGT PE=1 SV=1 0.33 2.20 ‐1.87 PROM1_HUMAN Prominin‐1 OS=Homo sapiens GN=PROM1 PE=1 SV=1 0.14 2.00 ‐1.86 CLM9_HUMAN CMRF35‐like molecule 9 OS=Homo sapiens 0.17 2.00 ‐1.83 GN=CD300LG PE=1 SV=2 S10A7_HUMAN Protein S100‐A7 OS=Homo sapiens GN=S100A7 PE=1 1.18 3.00 ‐1.82 SV=4 CATH_HUMAN Cathepsin H OS=Homo sapiens GN=CTSH PE=1 SV=4 1.00 2.75 ‐1.75 CASPE_HUMAN Caspase‐14 OS=Homo sapiens GN=CASP14 PE=1 SV=2 1.22 2.85 ‐1.62 COMP_HUMAN Cartilage oligomeric matrix protein OS=Homo sapiens 0.43 2.00 ‐1.57 GN=COMP PE=1 SV=2 MOES_HUMAN Moesin OS=Homo sapiens GN=MSN PE=1 SV=3 1.50 3.00 ‐1.50 LCN1_HUMAN Lipocalin‐1 OS=Homo sapiens GN=LCN1 PE=1 SV=1 1.00 2.25 ‐1.25 GGCT_HUMAN Gamma‐glutamylcyclotransferase OS=Homo sapiens 1.00 2.21 ‐1.21 GN=GGCT PE=1 SV=1 CATA_HUMAN Catalase OS=Homo sapiens GN=CAT PE=1 SV=3 1.00 2.20 ‐1.20 IGHA1_HUMAN Ig alpha‐1 chain C region OS=Homo sapiens GN=IGHA1 1.48 2.57 ‐1.09 PE=1 SV=2 © 2013 American Medical Association. All rights reserved. Downloaded From: https://jamanetwork.com/ on 10/01/2021 CEAM8_HUMAN Carcinoembryonic antigen‐related cell adhesion 1.14 2.20 ‐1.06 molecule 8 OS=Homo sapiens GN=CEACAM8 PE=1 SV=2 SH3L3_HUMAN SH3 domain‐binding glutamic acid‐rich‐like protein 3 1.17 2.20 ‐1.03 OS=Homo sapiens GN=SH3BGRL3 PE=1 SV=1 AFAM_HUMAN Afamin OS=Homo sapiens GN=AFM PE=1 SV=1 1.00 2.00 ‐1.00 GRP78_HUMAN 78 kDa glucose‐regulated protein OS=Homo sapiens 1.00 2.00 ‐1.00 GN=HSPA5 PE=1 SV=2 A2ML1_HUMAN Alpha‐2‐macroglobulin‐like protein 1 OS=Homo 1.00 2.00 ‐1.00 sapiens GN=A2ML1 PE=1 SV=3 SPB7_HUMAN Serpin B7 OS=Homo sapiens GN=SERPINB7 PE=2 SV=1 1.00 2.00 ‐1.00 RNAS7_HUMAN Ribonuclease 7 OS=Homo sapiens GN=RNASE7 PE=1 1.00 2.00 ‐1.00 SV=2 CAP1_HUMAN Adenylyl cyclase‐associated protein 1 OS=Homo sapiens 1.00 2.00 ‐1.00 GN=CAP1 PE=1 SV=5 PSA1_HUMAN Proteasome subunit alpha type‐1 OS=Homo sapiens 1.00 2.00 ‐1.00 GN=PSMA1 PE=1 SV=1 LV301_HUMAN Ig lambda chain V‐III region SH OS=Homo sapiens PE=1 1.00 2.00 ‐1.00 SV=1 GSTO1_HUMAN Glutathione S‐transferase omega‐1 OS=Homo sapiens 1.00 2.00 ‐1.00 GN=GSTO1 PE=1 SV=2 RAB7A_HUMAN Ras‐related protein Rab‐7a OS=Homo sapiens 1.00 2.00 ‐1.00 GN=RAB7A PE=1 SV=1 TAGL2_HUMAN Transgelin‐2 OS=Homo sapiens GN=TAGLN2 PE=1 SV=3 1.00 2.00 ‐1.00 BST1_HUMAN ADP‐ribosyl cyclase 2 OS=Homo sapiens GN=BST1 PE=1 1.00 2.00 ‐1.00 SV=2 PSA6_HUMAN Proteasome subunit alpha type‐6 OS=Homo sapiens 1.00 2.00 ‐1.00 GN=PSMA6 PE=1 SV=1 INO80_HUMAN Putative DNA helicase INO80 complex homolog 1 1.00 2.00 ‐1.00 OS=Homo sapiens GN=INO80 PE=1 SV=2 LYSC_HUMAN Lysozyme C OS=Homo sapiens GN=LYZ PE=1 SV=1 1.00 2.00 ‐1.00 PSB1_HUMAN Proteasome subunit beta type‐1 OS=Homo sapiens 1.00 2.00 ‐1.00 GN=PSMB1 PE=1 SV=2 PAPP1_HUMAN Pappalysin‐1 OS=Homo sapiens GN=PAPPA PE=1 SV=3 1.00 2.00 ‐1.00 © 2013 American Medical Association.
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    Supplementary Table 1: Adhesion genes data set PROBE Entrez Gene ID Celera Gene ID Gene_Symbol Gene_Name 160832 1 hCG201364.3 A1BG alpha-1-B glycoprotein 223658 1 hCG201364.3 A1BG alpha-1-B glycoprotein 212988 102 hCG40040.3 ADAM10 ADAM metallopeptidase domain 10 133411 4185 hCG28232.2 ADAM11 ADAM metallopeptidase domain 11 110695 8038 hCG40937.4 ADAM12 ADAM metallopeptidase domain 12 (meltrin alpha) 195222 8038 hCG40937.4 ADAM12 ADAM metallopeptidase domain 12 (meltrin alpha) 165344 8751 hCG20021.3 ADAM15 ADAM metallopeptidase domain 15 (metargidin) 189065 6868 null ADAM17 ADAM metallopeptidase domain 17 (tumor necrosis factor, alpha, converting enzyme) 108119 8728 hCG15398.4 ADAM19 ADAM metallopeptidase domain 19 (meltrin beta) 117763 8748 hCG20675.3 ADAM20 ADAM metallopeptidase domain 20 126448 8747 hCG1785634.2 ADAM21 ADAM metallopeptidase domain 21 208981 8747 hCG1785634.2|hCG2042897 ADAM21 ADAM metallopeptidase domain 21 180903 53616 hCG17212.4 ADAM22 ADAM metallopeptidase domain 22 177272 8745 hCG1811623.1 ADAM23 ADAM metallopeptidase domain 23 102384 10863 hCG1818505.1 ADAM28 ADAM metallopeptidase domain 28 119968 11086 hCG1786734.2 ADAM29 ADAM metallopeptidase domain 29 205542 11085 hCG1997196.1 ADAM30 ADAM metallopeptidase domain 30 148417 80332 hCG39255.4 ADAM33 ADAM metallopeptidase domain 33 140492 8756 hCG1789002.2 ADAM7 ADAM metallopeptidase domain 7 122603 101 hCG1816947.1 ADAM8 ADAM metallopeptidase domain 8 183965 8754 hCG1996391 ADAM9 ADAM metallopeptidase domain 9 (meltrin gamma) 129974 27299 hCG15447.3 ADAMDEC1 ADAM-like,
  • 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
  • Learning from Cadherin Structures and Sequences: Affinity Determinants and Protein Architecture

    Learning from Cadherin Structures and Sequences: Affinity Determinants and Protein Architecture

    Learning from cadherin structures and sequences: affinity determinants and protein architecture Klára Fels ıvályi Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Graduate School of Arts and Sciences COLUMBIA UNIVERSITY 2014 © 2014 Klara Felsovalyi All rights reserved ABSTRACT Learning from cadherin structures and sequences: affinity determinants and protein architecture Klara Felsovalyi Cadherins are a family of cell-surface proteins mediating adhesion that are important in development and maintenance of tissues. The family is defined by the repeating cadherin domain (EC) in their extracellular region, but they are diverse in terms of protein size, architecture and cellular function. The best-understood subfamily is the type I classical cadherins, which are found in vertebrates and have five EC domains. Among the five different type I classical cadherins, the binding interactions are highly specific in their homo- and heterophilic binding affinities, though their sequences are very similar. As previously shown, E- and N-cadherins, two prototypic members of the subfamily, differ in their homophilic K D by about an order of magnitude, while their heterophilic affinity is intermediate. To examine the source of the binding affinity differences among type I cadherins, we used crystal structures, analytical ultracentrifugation (AUC), surface plasmon resonance (SPR), and electron paramagnetic resonance (EPR) studies. Phylogenetic analysis and binding affinity behavior show that the type I cadherins can be further divided into two subgroups, with E- and N-cadherin representing each. In addition to the affinity differences in their wild-type binding through the strand-swapped interface, a second interface also shows an affinity difference between E- and N-cadherin.
  • 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.