Deficiency of Annexins A5 and A6 Induces Complex Changes in the Transcriptome of Growth Plate Cartilage but Does Not Inhibit the Induction of Mineralization
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Propranolol-Mediated Attenuation of MMP-9 Excretion in Infants with Hemangiomas
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 -
Apoptosis and Differentiation Commitment: Novel Insights Revealed by Gene Profiling Studies in Mouse Embryonic Stem Cells
Cell Death and Differentiation (2006) 13, 564–575 & 2006 Nature Publishing Group All rights reserved 1350-9047/06 $30.00 www.nature.com/cdd Apoptosis and differentiation commitment: novel insights revealed by gene profiling studies in mouse embryonic stem cells D Duval1,2,4, M Trouillas3,4, C Thibault2, D Dembele´ 2, Introduction F Diemunsch2, B Reinhardt2, AL Mertz2, A Dierich2 Mouse embryonic stem (ES) cells, which are maintained and H Bœuf*,3 pluripotent in vitro with leukemia inhibitory factor (LIF) cytokine, are instrumental to study LIF-dependent cell 1 UMR5096-CNRS/UP/IRD, Perpignan, France 2 IGBMC/CNRS/INSERM, Strasbourg, France pluripotency as well as the first steps of differentiation 3 UMR-5164-CNRS-CIRID/Universite´ Bordeaux2, Bordeaux, France commitment triggered upon LIF starvation. As we recently 4 These authors contributed equally to this work reported, these cells could also be used to unravel the early * Corresponding author: H Bœuf, UMR-5164-CNRS-CIRID, Universite´ steps of apoptosis, a physiological cell death process Bordeaux2, Bat.1B, BP14, 146 rue Le´o Saignat, 33076 Bordeaux, France. occurring during the first embryogenesis stages. Indeed, the Tel: þ 05 57 57 46 33; Fax: þ 05 57 57 14 72; formation of the cavities, which starts at the blastocyst stage, E-mail:helene.bœ[email protected] is dependent on a specific cell death program, which includes caspase 3 cleavage and induction of the apoptosis-inducing Received 10.3.05; revised 01.9.05; accepted 01.9.05; published online 25.11.05 1 Edited by R De Maria factor (AIF)-complex proteins. -
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
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. -
2812 Matrix Vesicles: Structure, Composition, Formation and Function in Ca
[Frontiers in Bioscience 16, 2812-2902, June 1, 2011] Matrix vesicles: structure, composition, formation and function in calcification Roy E. Wuthier Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208 TABLE OF CONTENTS 1. Abstract 2. Introduction 3. Morphology of matrix vesicles (MVs) 3.1. Conventional transmission electron microscopy 3.2. Cryofixation, freeze-substitution electron microscopy 3.3. Freeze-fracture studies 4. Isolation of MVs 4.1. Crude collagenase digestion methods 4.2. Non-collagenase dependent methods 4.3. Cell culture methods 4.4. Modified collagenase digestion methods 4.5. Other isolation methods 5. MV proteins 5.1. Early SDS-PAGE studies 5.2. Isolation and identification of major MV proteins 5.3. Sequential extraction, separation and characterization of major MV proteins 5.4. Proteomic characterization of MV proteins 6. MV-associated extracellular matrix proteins 6.1. Type VI collagen 6.2. Type X collagen 6.3. Proteoglycan link protein and aggrecan core protein 6.4. Fibrillin-1 and fibrillin-2 7. MV annexins – acidic phospholipid-dependent ca2+-binding proteins 7.1. Annexin A5 7.2. Annexin A6 7.3. Annexin A2 7.4. Annexin A1 7.5. Annexin A11 and Annexin A4 8. MV enzymes 8.1. Tissue-nonspecific alkaline phosphatase(TNAP) 8.1.1. Molecular structure 8.1.2. Amino acid sequence 8.1.3. 3-D structure 8.1.4. Disposition in the MV membrane 8.1.5. Catalytic properties 8.1.6. Collagen-binding properties 8.2. Nucleotide pyrophosphate phosphodiesterase (NPP1, PC1) 8.3. PHOSPHO-1 (Phosphoethanolamine/Phosphocholine phosphatase 8.4. Acid phosphatase 8.5. -
Cell Surface-Expressed Phosphatidylserine As Therapeutic Target to Enhance Phagocytosis of Apoptotic Cells
Cell Death and Differentiation (2013) 20, 49–56 & 2013 Macmillan Publishers Limited All rights reserved 1350-9047/13 www.nature.com/cdd Cell surface-expressed phosphatidylserine as therapeutic target to enhance phagocytosis of apoptotic cells K Schutters1, DHM Kusters1, MLL Chatrou1, T Montero-Melendez2, M Donners3, NM Deckers1, DV Krysko4,5, P Vandenabeele4,5, M Perretti2, LJ Schurgers1 and CPM Reutelingsperger*,1 Impaired efferocytosis has been shown to be associated with, and even to contribute to progression of, chronic inflammatory diseases such as atherosclerosis. Enhancing efferocytosis has been proposed as strategy to treat diseases involving inflammation. Here we present the strategy to increase ‘eat me’ signals on the surface of apoptotic cells by targeting cell surface- expressed phosphatidylserine (PS) with a variant of annexin A5 (Arg-Gly-Asp–annexin A5, RGD–anxA5) that has gained the function to interact with avb3 receptors of the phagocyte. We describe design and characterization of RGD–anxA5 and show that introduction of RGD transforms anxA5 from an inhibitor into a stimulator of efferocytosis. RGD–anxA5 enhances engulfment of apoptotic cells by phorbol-12-myristate-13-acetate-stimulated THP-1 (human acute monocytic leukemia cell line) cells in vitro and resident peritoneal mouse macrophages in vivo. In addition, RGD–anxA5 augments secretion of interleukin-10 during efferocytosis in vivo, thereby possibly adding to an anti-inflammatory environment. We conclude that targeting cell surface- expressed PS is an attractive strategy -
Proteomic Analysis of Exosome-Like Vesicles Derived from Breast Cancer Cells
ANTICANCER RESEARCH 32: 847-860 (2012) Proteomic Analysis of Exosome-like Vesicles Derived from Breast Cancer Cells GEMMA PALAZZOLO1, NADIA NINFA ALBANESE2,3, GIANLUCA DI CARA3, DANIEL GYGAX4, MARIA LETIZIA VITTORELLI3 and IDA PUCCI-MINAFRA3 1Institute for Biomedical Engineering, Laboratory of Biosensors and Bioelectronics, ETH Zurich, Switzerland; 2Department of Physics, University of Palermo, Palermo, Italy; 3Centro di Oncobiologia Sperimentale (C.OB.S.), Oncology Department La Maddalena, Palermo, Italy; 4Institute of Chemistry and Bioanalytics, University of Applied Sciences Northwestern Switzerland FHNW, Muttenz, Switzerland Abstract. Background/Aim: The phenomenon of membrane that vesicle production allows neoplastic cells to exert different vesicle-release by neoplastic cells is a growing field of interest effects, according to the possible acceptor targets. For instance, in cancer research, due to their potential role in carrying a vesicles could potentiate the malignant properties of adjacent large array of tumor antigens when secreted into the neoplastic cells or activate non-tumoral cells. Moreover, vesicles extracellular medium. In particular, experimental evidence show could convey signals to immune cells and surrounding stroma that at least some of the tumor markers detected in the blood cells. The present study may significantly contribute to the circulation of mammary carcinoma patients are carried by knowledge of the vesiculation phenomenon, which is a critical membrane-bound vesicles. Thus, biomarker research in breast device for trans cellular communication in cancer. cancer can gain great benefits from vesicle characterization. Materials and Methods: Conditioned medium was collected The phenomenon of membrane release in the extracellular from serum starved MDA-MB-231 sub-confluent cell cultures medium has long been known and was firstly described by and exosome-like vesicles (ELVs) were isolated by Paul H. -
ANXA3 Is Upregulated by Hypoxia-Inducible Factor 1-Alpha and Promotes Colon Cancer Growth
7449 Original Article ANXA3 is upregulated by hypoxia-inducible factor 1-alpha and promotes colon cancer growth Kunli Du1, Jiahui Ren2, Zhongxue Fu3, Xingye Wu3, Jianyong Zheng1, Xing Li4 1Department of Gastrointestinal Surgery, The First Affiliated Hospital of Air Force Medical University, Xi’an, China; 2Department of Anus and Intestine Surgery, Xi’an Mayinglong Anorectal Hospital, Xi’an, China; 3Department of Gastrointestinal Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China; 4Nanjing Yuheming Medical Nutrition Research Institute, Nanjing, China Contributions: (I) Conception and design: J Zheng; (II) Administrative support: X Li; (III) Provision of study materials or patients: K Du, J Ren, Z Fu; (IV) Collection and assembly of data: K Du, J Ren, Z Fu; (V) Data analysis and interpretation: X Wu; (VI) Manuscript writing: All authors; (VII) Final approval of manuscript: All authors. Correspondence to: Xingye Wu. Department of Gastrointestinal Surgery, The First Affiliated Hospital of Chongqing Medical University, Youyi Road 1st, Yuzhong District, Chongqing 400016, China. Email: [email protected]; Jianyong Zheng. Department of Gastrointestinal Surgery, The First Affiliated Hospital of Air Force Medical University, 127 Changle West Road, Xincheng District, Xi’an 710000, China. Email: [email protected]. Background: Annexin A3 (ANXA3) is overexpressed in various cancers and is a potential target for cancer treatment. However, clinical implication and biological function of ANXA3 in colon cancer remain unknown. This study aimed to investigate the relationship between hypoxia-inducible factor 1-alpha (HIF-1α) and ANXA3, and explore the function of ANXA3 in colon carcinoma. Methods: Expression levels of HIF-1α and ANXA3 in human colon carcinoma specimens and colon cancer cell lines were detected by immunohistochemistry, real-time PCR and Western blot analysis. -
Supplementary Data
Progressive Disease Signature Upregulated probes with progressive disease U133Plus2 ID Gene Symbol Gene Name 239673_at NR3C2 nuclear receptor subfamily 3, group C, member 2 228994_at CCDC24 coiled-coil domain containing 24 1562245_a_at ZNF578 zinc finger protein 578 234224_at PTPRG protein tyrosine phosphatase, receptor type, G 219173_at NA NA 218613_at PSD3 pleckstrin and Sec7 domain containing 3 236167_at TNS3 tensin 3 1562244_at ZNF578 zinc finger protein 578 221909_at RNFT2 ring finger protein, transmembrane 2 1552732_at ABRA actin-binding Rho activating protein 59375_at MYO15B myosin XVB pseudogene 203633_at CPT1A carnitine palmitoyltransferase 1A (liver) 1563120_at NA NA 1560098_at AKR1C2 aldo-keto reductase family 1, member C2 (dihydrodiol dehydrogenase 2; bile acid binding pro 238576_at NA NA 202283_at SERPINF1 serpin peptidase inhibitor, clade F (alpha-2 antiplasmin, pigment epithelium derived factor), m 214248_s_at TRIM2 tripartite motif-containing 2 204766_s_at NUDT1 nudix (nucleoside diphosphate linked moiety X)-type motif 1 242308_at MCOLN3 mucolipin 3 1569154_a_at NA NA 228171_s_at PLEKHG4 pleckstrin homology domain containing, family G (with RhoGef domain) member 4 1552587_at CNBD1 cyclic nucleotide binding domain containing 1 220705_s_at ADAMTS7 ADAM metallopeptidase with thrombospondin type 1 motif, 7 232332_at RP13-347D8.3 KIAA1210 protein 1553618_at TRIM43 tripartite motif-containing 43 209369_at ANXA3 annexin A3 243143_at FAM24A family with sequence similarity 24, member A 234742_at SIRPG signal-regulatory protein gamma -
Calmodulin Dependent Wound Repair in Dictyostelium Cell Membrane
cells Article Ca2+–Calmodulin Dependent Wound Repair in Dictyostelium Cell Membrane Md. Shahabe Uddin Talukder 1,2, Mst. Shaela Pervin 1,3, Md. Istiaq Obaidi Tanvir 1, Koushiro Fujimoto 1, Masahito Tanaka 1, Go Itoh 4 and Shigehiko Yumura 1,* 1 Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Yamaguchi 753-8511, Japan; [email protected] (M.S.U.T.); [email protected] (M.S.P.); [email protected] (M.I.O.T.); [email protected] (K.F.); [email protected] (M.T.) 2 Institute of Food and Radiation Biology, AERE, Bangladesh Atomic Energy Commission, Savar, Dhaka 3787, Bangladesh 3 Rajshahi Diabetic Association General Hospital, Luxmipur, Jhautala, Rajshahi 6000, Bangladesh 4 Department of Molecular Medicine and Biochemistry, Akita University Graduate School of Medicine, Akita 010-8543, Japan; [email protected] * Correspondence: [email protected]; Tel./Fax: +81-83-933-5717 Received: 2 April 2020; Accepted: 21 April 2020; Published: 23 April 2020 Abstract: Wound repair of cell membrane is a vital physiological phenomenon. We examined wound repair in Dictyostelium cells by using a laserporation, which we recently invented. We examined the influx of fluorescent dyes from the external medium and monitored the cytosolic Ca2+ after wounding. The influx of Ca2+ through the wound pore was essential for wound repair. Annexin and ESCRT components accumulated at the wound site upon wounding as previously described in animal cells, but these were not essential for wound repair in Dictyostelium cells. We discovered that calmodulin accumulated at the wound site upon wounding, which was essential for wound repair. -
Supplementary Table 5
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 -
Research and Application of Hydrostatic High Pressure in Tumor Vaccines (Review)
ONCOLOGY REPORTS 45: 75, 2021 Research and application of hydrostatic high pressure in tumor vaccines (Review) SHUAI YAN1, KAI LIU2, LIN MU3, JIANFENG LIU2, WAN TANG1 and BIN LIU2 Departments of 1Operating Room, 2Hand and Foot Surgery, and 3Radiology, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China Received February 19, 2020; Accepted March 5, 2021 DOI: 10.3892/or.2021.8026 Abstract. It is well known that hydrostatic pressure (HP) is a 5. High hydrostatic pressure and immunogenic cell death of physical parameter that is now regarded as an important vari‑ tumors able for life. High hydrostatic pressure (HHP) technology has 6. High hydrostatic pressure and dendritic cell‑based tumor influenced biological systems for more than 100 years. Food vaccines and bioscience researchers have shown great interest in HHP 7. Tumor vaccines and Annexin A5 technology over the past few decades. The development of 8. Conclusions and outlooks knowledge related to this area can better facilitate the applica‑ tion of HHP in the life sciences. Furthermore, new applications for HHP may come from these current studies, particularly in 1. Introduction tumor vaccines. Currently, cancer recurrence and metastasis continue to pose a serious threat to human health. The limited High hydrostatic pressure (HHP) is a traditional technology efficacy of conventional treatments has led to the need for used to produce steel, alloys, ceramics, and synthetic mate‑ breakthroughs in immunotherapy and other related areas. rials (1). Over the past few decades, HHP has also been used for Research into tumor vaccines is providing new insights for non‑heat pasteurization of processed foods, designed to extend cancer treatment.