Derivation of Induced Pluripotent Stem Cells from Pig Somatic Cells
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Screening and Identification of Key Biomarkers in Clear Cell Renal Cell Carcinoma Based on Bioinformatics Analysis
bioRxiv preprint doi: https://doi.org/10.1101/2020.12.21.423889; this version posted December 23, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Screening and identification of key biomarkers in clear cell renal cell carcinoma based on bioinformatics analysis Basavaraj Vastrad1, Chanabasayya Vastrad*2 , Iranna Kotturshetti 1. Department of Biochemistry, Basaveshwar College of Pharmacy, Gadag, Karnataka 582103, India. 2. Biostatistics and Bioinformatics, Chanabasava Nilaya, Bharthinagar, Dharwad 580001, Karanataka, India. 3. Department of Ayurveda, Rajiv Gandhi Education Society`s Ayurvedic Medical College, Ron, Karnataka 562209, India. * Chanabasayya Vastrad [email protected] Ph: +919480073398 Chanabasava Nilaya, Bharthinagar, Dharwad 580001 , Karanataka, India bioRxiv preprint doi: https://doi.org/10.1101/2020.12.21.423889; this version posted December 23, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Abstract Clear cell renal cell carcinoma (ccRCC) is one of the most common types of malignancy of the urinary system. The pathogenesis and effective diagnosis of ccRCC have become popular topics for research in the previous decade. In the current study, an integrated bioinformatics analysis was performed to identify core genes associated in ccRCC. An expression dataset (GSE105261) was downloaded from the Gene Expression Omnibus database, and included 26 ccRCC and 9 normal kideny samples. Assessment of the microarray dataset led to the recognition of differentially expressed genes (DEGs), which was subsequently used for pathway and gene ontology (GO) enrichment analysis. -
A Shared Pathway of Exosome Biogenesis Operates at Plasma And
bioRxiv preprint doi: https://doi.org/10.1101/545228; this version posted February 11, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. A shared pathway of exosome biogenesis operates at plasma and endosome membranes Francis K. Fordjour1, George G. Daaboul2, and Stephen J. Gould1* 1Department of Biological Chemistry Johns Hopkins University Baltimore, MD USA 2Nanoview Biosciences Boston, MA USA Corresponding author: Stephen J. Gould, Ph.D. Department of Biological Chemistry Johns Hopkins University Baltimore, MD USA Email: [email protected] Tel (01) 443 847 9918 1 bioRxiv preprint doi: https://doi.org/10.1101/545228; this version posted February 11, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Summary: This study of exosome cargo protein budding reveals that cells use a common pathway for budding exosomes from plasma and endosome membranes, providing a new mechanistic explanation for exosome heterogeneity and a rational roadmap for exosome engineering. Keywords: Protein budding, tetraspanin, endosome, plasma membrane, extracellular vesicle, CD9, CD63, CD81, SPIR, interferometry Abbreviations: EV, extracellular vesicles; IB, immunoblot; IFM, immunofluorescence microscopy; IPMC, intracellular plasma membrane-connected compartment; MVB, multivesicular body; SPIR, single-particle interferometric reflectance; SPIRI, single-particle interferometric reflectance imaging 2 bioRxiv preprint doi: https://doi.org/10.1101/545228; this version posted February 11, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. -
Expression of the Tetraspanins CD9, CD37, CD63, and CD151 in Merkel Cell Carcinoma: Strong Evidence for a Posttranscriptional Fine-Tuning of CD9 Gene Expression
Modern Pathology (2010) 23, 751–762 & 2010 USCAP, Inc. All rights reserved 0893-3952/10 $32.00 751 Expression of the tetraspanins CD9, CD37, CD63, and CD151 in Merkel cell carcinoma: strong evidence for a posttranscriptional fine-tuning of CD9 gene expression Markus Woegerbauer1, Dietmar Thurnher1, Roland Houben2, Johannes Pammer3, Philipp Kloimstein1, Gregor Heiduschka1, Peter Petzelbauer4 and Boban M Erovic1 1Department of Otorhinolaryngology, Head and Neck Surgery, Medical University of Vienna, Vienna, Austria; 2Department of Dermatology, Medical University of Wuerzburg, Germany; 3Department of Clinical Pathology, Medical University of Vienna, Vienna, Austria and 4Department of Dermatology, Medical University of Vienna, Vienna, Austria Tetraspanins including CD9, CD37, CD63, and CD151 are linked to cellular adhesion, cell differentiation, migration, carcinogenesis, and tumor progression. The aim of the study was to detect, quantify, and evaluate the prognostic value of these tetraspanins in Merkel cell carcinoma and to study the regulation of CD9 mRNA expression in Merkel cell carcinoma cell lines in detail. Immunohistochemical staining of 28 Merkel cell carcinoma specimens from 25 patients showed a significant correlation of CD9 (P ¼ 0.03) and CD151 (P ¼ 0.043) expression to overall survival. CD9 and CD63 expression correlated significantly to patients’ disease-free interval (P ¼ 0.017 and P ¼ 0.058). Of primary Merkel cell carcinoma tumors, 42% were CD9 positive in contrast to only 21% of the subcutaneous in-transit metastases. Characterization of the 50 untranslated region (UTR) of the CD9 mRNA from two cultured Merkel cell carcinoma cell lines revealed the presence of two major RNA species differing only in the length of their 50 termini (183 versus 102 nucleotides). -
Extracellular Vesicle Human CD9/CD63/CD81 Antibody Panel
Extracellular Vesicle Human CD9/CD63/CD81 Antibody Panel Antibody panel for the detection of extracellular vesicles using CD9, CD63, and CD81 markers Catalog #100-0211 1 Kit Product Description The Extracellular Vesicle Human CD9/CD63/CD81 Antibody Panel is suitable for the detection of extracellular vesicles (EVs) derived from human cells. It comprises three primary antibodies that are immunoreactive toward human CD9, CD63, and CD81; these are proteins that are typically expressed on EVs and widely used as markers to analyze and isolate these cell-derived particles. CD9, CD63, and CD81 belong to the tetraspanin family of membrane proteins, which possess four transmembrane domains and interact with diverse proteins on the cell surface to form multimolecular networks termed tetraspanin-enriched microdomains. CD9, CD63, and CD81 proteins are expressed on the surface of many cells, including B cells, T cells, NK cells, monocytes, dendritic cells, thymocytes, endothelial cells, and fibroblasts, and are involved in modulating a variety of cellular processes including cell activation, adhesion, differentiation, and tumor invasion. The antibodies provided in this panel have been reported for use in analyzing primary cells, cell lines, and EVs by ELISA, flow cytometry, immunocytochemistry, immunoprecipitation, and Western blotting. They have been reported to cross-react with their cognate antigens in non-human primates, including baboons and rhesus and cynomolgus macaques. Product Information The following products comprise the Extracellular -
Aberrant Expression of Tetraspanin Molecules in B-Cell Chronic Lymphoproliferative Disorders and Its Correlation with Normal B-Cell Maturation
Leukemia (2005) 19, 1376–1383 & 2005 Nature Publishing Group All rights reserved 0887-6924/05 $30.00 www.nature.com/leu Aberrant expression of tetraspanin molecules in B-cell chronic lymphoproliferative disorders and its correlation with normal B-cell maturation S Barrena1,2, J Almeida1,2, M Yunta1,ALo´pez1,2, N Ferna´ndez-Mosteirı´n3, M Giralt3, M Romero4, L Perdiguer5, M Delgado1, A Orfao1,2 and PA Lazo1 1Instituto de Biologı´a Molecular y Celular del Ca´ncer, Centro de Investigacio´n del Ca´ncer, Consejo Superior de Investigaciones Cientı´ficas-Universidad de Salamanca, Salamanca, Spain; 2Servicio de Citometrı´a, Universidad de Salamanca and Hospital Universitario de Salamanca, Salamanca, Spain; 3Servicio de Hematologı´a, Hospital Universitario Miguel Servet, Zaragoza, Spain; 4Hematologı´a-hemoterapia, Hospital Universitario Rı´o Hortega, Valladolid, Spain; and 5Servicio de Hematologı´a, Hospital de Alcan˜iz, Teruel, Spain Tetraspanin proteins form signaling complexes between them On the cell surface, tetraspanin antigens are present either as and with other membrane proteins and modulate cell adhesion free molecules or through interaction with other proteins.25,26 and migration properties. The surface expression of several tetraspanin antigens (CD9, CD37, CD53, CD63, and CD81), and These interacting proteins include other tetraspanins, integri- F 22,27–30F their interacting proteins (CD19, CD21, and HLA-DR) were ns particularly those with the b1 subunit HLA class II 31–33 34,35 analyzed during normal B-cell maturation and compared to a moleculesFeg HLA DR -, CD19, the T-cell recep- group of 67 B-cell neoplasias. Three patterns of tetraspanin tor36,37 and several other members of the immunoglobulin expression were identified in normal B cells. -
Tetraspanin CD9: a Key Regulator of Cell Adhesion in the Immune System
MINI REVIEW published: 30 April 2018 doi: 10.3389/fimmu.2018.00863 Tetraspanin CD9: A Key Regulator of Cell Adhesion in the Immune System Raquel Reyes1, Beatriz Cardeñes1, Yesenia Machado-Pineda1 and Carlos Cabañas 1,2* 1 Departamento de Biología Celular e Inmunología, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Madrid, Spain, 2 Departamento de Inmunología, Oftalmología y OTR (IO2), Facultad de Medicina, Universidad Complutense, Madrid, Spain The tetraspanin CD9 is expressed by all the major subsets of leukocytes (B cells, CD4+ T cells, CD8+ T cells, natural killer cells, granulocytes, monocytes and macrophages, and immature and mature dendritic cells) and also at a high level by endothelial cells. As a typical member of the tetraspanin superfamily, a prominent feature of CD9 is its propensity to engage in a multitude of interactions with other tetraspanins as well as with different transmembrane and intracellular proteins within the context of defined membranal domains termed tetraspanin-enriched microdomains (TEMs). Through these associations, CD9 influences many cellular activities in the different subtypes of leuko- cytes and in endothelial cells, including intracellular signaling, proliferation, activation, survival, migration, invasion, adhesion, and diapedesis. Several excellent reviews have Edited by: already covered the topic of how tetraspanins, including CD9, regulate these cellular Manfred B. Lutz, processes in the different cells of the immune system. In this mini-review, however, we Universität Würzburg, Germany will focus particularly on describing and discussing the regulatory effects exerted by CD9 Reviewed by: on different adhesion molecules that play pivotal roles in the physiology of leukocytes José Mordoh, and endothelial cells, with a particular emphasis in the regulation of adhesion molecules Leloir Institute Foundation (FIL), Argentina of the integrin and immunoglobulin superfamilies. -
Expression of Tetraspanins in Human Lung Cancer Cells: Frequent Downregulation of CD9 and Its Contribution to Cell Motility in Small Cell Lung Cancer
Oncogene (2003) 22, 674–687 & 2003 Nature Publishing Group All rights reserved 0950-9232/03 $25.00 www.nature.com/onc Expression of tetraspanins in human lung cancer cells: frequent downregulation of CD9 and its contribution to cell motility in small cell lung cancer Toshiki Funakoshi1, Isao Tachibana*,1, Yoshihiko Hoshida2, Hiromi Kimura1, Yoshito Takeda1, Takashi Kijima3, Kazumi Nishino1, Hiroyuki Goto1, Tsutomu Yoneda1, Toru Kumagai1, Tadashi Osaki1, Seiji Hayashi1, Katsuyuki Aozasa2 and Ichiro Kawase1 1Department of Molecular Medicine, Osaka University Graduate School of Medicine, 2-2 Yamada-oka, Sutia, Osaka 565-0871, Japan; 2Department of Pathology, Osaka University Graduate School of Medicine, 2-2 Yamada-oka, Sutia, Osaka 565-0871, Japan; 3Division of Thoracic and Adult Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 44 Binney Street, Boston, MA 02115, USA Small cell lung cancer (SCLC) invades locally and lungcancer (SCLC) and nonsmall cell lungcancer metastasizes distantly extremely early when compared (NSCLC). SCLC is characterized by several neuroendo- with nonsmall cell lung cancer (NSCLC). The underlying crine features, as evidenced by the presence of dense core molecular mechanisms, however, have not been elucidated. granules, high enzymatic activities of L-dopa decarbox- Accumulating evidence suggests that downregulation of ylase, production of hormones and neuropeptides, and several members of tetraspanins is associated with expression of neural cell adhesion molecule (N-CAM) progression of solid tumors, thus indicating poor prog- (Carney et al., 1985). Clinically, SCLC is distinct from nosis. Here we screened 30 lung cancer cell lines for NSCLC in that most patients are inoperable at expression of tetraspanins, CD9, CD63, CD81, CD82, diagnosis, because the tumor locally invades and CD151, and NAG-2. -
Product Sheet: Exosome Antibodies and Elisas
System Biosciences Accelerating discoveries through innovations Exosome Research Exosome Antibodies, Arrays and ELISAs Track, Verify and Quantitate Exosomes with Validated Antibody Systems Exosomes are small membrane vesicles secreted by most cell types in vivo and in Highlights vitro. Exosomes are found in cell culture media, blood, urine, amniotic fluid, malignant ascite fluids and contain distinct subsets of microRNAs and proteins • Exosome antibodies for Westerns depending upon the tissue from which they are secreted. SBI's ExoELISA kits are designed for fast and quantitative analysis of well-characterized exosomal protein • Validated CD63, CD9, CD81 and Hsp70 markers: CD63, CD9, CD81 or Hsp70. The exosome antibody kits allow for the • Exosome ELISAs for quantitation confirmation of exosome recoveries and the ExoELISA kit enables the specific quantitation of CD63, CD9 or CD81 positive exosome microvesicles. The exosome • Measure exact number of exosome antibody and ExoELISA kits are fully compatible with exosomes isolated by SBI's particles isolated from your samples ExoQuick or ExoQuick-TC as well as ultracentrifugation methods. Exosome antibodies for Western blots Exosome antibody arrays to check recoveries For Western blotting analysis, we recommend The Exo-Check antibody array has 12 pre-printed spots and resuspending the exosome pellet in 1XRIPA features 8 antibodies for known exosome markers (CD63, CD81, buffer with the appropriate protease inhibitor ALIX, FLOT1, ICAM1, EpCam, ANXA5 and TSG101) and a GM130 cocktail. SBI offers individual antibodies for CD63, cis-Golgi marker to monitor any cellular contamination in your CD9, CD81 and Hsp70 as well as a Western blot exosome isolations. Your exosome preparations are lysed and sampler kit (Catalog# EXOAB-KIT-1) which then incubated with the array for the pre-printed antibodies to includes four exosomal marker antibodies: CD63, capture their respective exosome proteins. -
Identification and SNP Detection for Preimplantation Active Genes and Their Association with Embryo Development and Male Fertility in Cattle
Institut für Tierwissenschaften, Abt. Tierzucht und Tierhaltung der Rheinischen Friedrich – Wilhelms – Universität Bonn ______________________________________________________________________ Identification and SNP detection for preimplantation active genes and their association with embryo development and male fertility in cattle I n a u g u r a l – D i s s e r t a t i o n zur Erlangung des Grades Doktor der Agrarwissenschaft (Dr. agr.) der Hohen Landwirtschaftlichen Fakultät der Rheinischen Friedrich – Wilhelms – Universität zu Bonn vorgelegt im November 2007 von Hossein Daghigh Kia aus Tabriz, Iran Referent : Prof. Dr. K. Schellander Korreferent: Prof. Dr. B. Petersen Tag der mündlichen Prüfung: 18 December 2007 Diese Dissertation ist auf dem Hochschulschriftenserver der ULB Bonn http://hss.ulb.uni-bonn.de/diss_online elektronisch publiziert. Dedicated to my parents and My family Identifikation und SNP-Detektion von preimplativ aktiven Genen und ihre Assoziation mit der Embryonalentwicklung und Bullenfruchtbarkeit Vorangegangene Studien legten ihre Schwerpunkte auf die Identifikation und Charakterisierung von Genen die die frühe Entwicklung beeinflussen. Die Erkenntnisse über die Sequenzunterschiede und deren Beziehung zu den Fruchtbarkeitsmerkmalen sind begrenzt. Das Ziel diese Studie war es, SNPs (Einzelbasenaustasch) in den Genen CDH1, DSC2, TJP1, PKP1, COX-2, CD9, GJA1, PLCζ, AKR1B1, N-PAC und EEF1α zu identifizieren und ihre Assoziation mit den männlichen Fruchtbarkeitsmerkmalen Non Return Rate (NRR), Spermaqualität (Volumen je Ejakulation, Konzentration, Motilität und Überlebensfähigkeit) und Spermium-Qualitätsmerkmale (Plasma Membran Integrität, Akrosomen Integrität und DNA Integrität), sowie der frühen Embryoentwicklung zu klären. Zur Detektion der Polymorphismen, wurden die Genotypen von 11 verschiedenen Rinderassen analysiert. Aus dem Sperma von 310 Bullen der Rasse Deutsche Holstein wurde genomische DNA isoliert und für die Auswahl der Kandidatengene genotypisiert. -
Multiplexed Profiling of Single-Cell Extracellular Vesicles Secretion
Multiplexed profiling of single-cell extracellular vesicles secretion Yahui Jia,b, Dongyuan Qic, Linmei Lia, Haoran Sua,b, Xiaojie Lib, Yong Luod, Bo Sune, Fuyin Zhange, Bingcheng Lina, Tingjiao Liub,1, and Yao Lua,1 aDepartment of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 116023 Dalian, China; bCollege of Stomatology, Dalian Medical University, 116044 Dalian, China; cFirst Affiliated Hospital of Dalian Medical University, 116011 Dalian, China; dState Key Laboratory of Fine Chemicals, Department of Chemical Engineering, Dalian University of Technology, 116024 Dalian, China; and eSecond Affiliated Hospital of Dalian Medical University, 116027 Dalian, China Edited by David A. Weitz, Harvard University, Cambridge, MA, and approved February 11, 2019 (received for review August 21, 2018) Extracellular vesicles (EVs) are important intercellular mediators markers on EVs from large numbers of single cells is still lacking regulating health and diseases. Conventional methods for EV sur- and will help to address a host of important biological questions face marker profiling, which was based on population measure- ranging from intertumor and intratumor diversity to the cell−cell ments, masked the cell-to-cell heterogeneity in the quantity and communication network, and will be of great value to clinical ap- phenotypes of EV secretion. Herein, by using spatially patterned plications like personalized diagnostics and medicine. antibody barcodes, we realized multiplexed profiling of single-cell Herein, we demonstrate a microchip platform for multiplexed EV secretion from more than 1,000 single cells simultaneously. Ap- profiling of single-cell EV secretion to address the critical need for plying this platform to profile human oral squamous cell carci- technologies to dissect the communication spectrum of tumor cells noma (OSCC) cell lines led to a deep understanding of previously mediated by EVs. -
Proteomic Comparison Defines Novel Markers to Characterize Heterogeneous Populations of Extracellular Vesicle Subtypes
Proteomic comparison defines novel markers to characterize heterogeneous populations of extracellular vesicle subtypes Joanna Kowala, Guillaume Arrasb, Marina Colomboa, Mabel Jouvea, Jakob Paul Moratha, Bjarke Primdal-Bengtsona, Florent Dinglib, Damarys Loewb, Mercedes Tkacha, and Clotilde Thérya,1 aInstitut Curie, PSL Research University, INSERM U932, Department “Immunité et Cancer”, 75248 Paris, France; and bInstitut Curie, PSL Research University, Centre de Recherche, Laboratoire de Spectrométrie de masse Protéomique, 75248 Paris, France Edited by Randy Schekman, University of California, Berkeley, CA, and approved January 5, 2016 (received for review October 28, 2015) Extracellular vesicles (EVs) have become the focus of rising interest or recovered by high-speed ultracentrifugation (8), in the ab- because of their numerous functions in physiology and pathology. sence of demonstration of their intracellular origin. Such iso- Cells release heterogeneous vesicles of different sizes and intra- lation procedures coisolate mixed EV populations, which we will cellular origins, including small EVs formed inside endosomal call “small EVs” (sEVs), for lack of better term, in the rest of this compartments (i.e., exosomes) and EVs of various sizes budding article. Because EVs of different intracellular origins probably from the plasma membrane. Specific markers for the analysis and have different functional properties (9, 10), the mixed nature of isolation of different EV populations are missing, imposing EV preparations has made the growing literature increasingly important limitations to understanding EV functions. Here, EVs confusing, with contradictory proposed functions and clinical uses from human dendritic cells were first separated by their sedimen- of vesicles being regularly published. The lack of specific purifi- tation speed, and then either by their behavior upon upward cation and characterization tools prevents a clear understanding of floatation into iodixanol gradients or by immuno-isolation. -
HIV-1 Specifically Traps CD9 and CD81 Tetraspanins Within Viral Buds And
bioRxiv preprint doi: https://doi.org/10.1101/293860; this version posted May 17, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. HIV-1 specifically traps CD9 and CD81 tetraspanins within viral buds and induces their membrane depletion Short title: tetraspanin trapping within HIV-1 buds Selma Dahmane1*, Christine Doucet1*, Antoine Le Gall1, Célia Chamontin2, Patrice Dosset1, Florent Murcy1, Laurent Fernandez1, Desirée Salas Pastene1, Eric Rubinstein3,4, Marylène Mougel2, Marcelo Nollmann1, Pierre-Emmanuel Milhiet1# 1 Centre de Biochimie Structurale (CBS), INSERM, CNRS, Université de Montpellier 2 IRIM, CNRS, University of Montpellier, Montpellier, France 3 Inserm, U935, Villejuif, France 4 Université Paris Sud, Institut André Lwoff, Villejuif, France # to whom correspondence should be addressed * These two authors equally contributed to the work. bioRxiv preprint doi: https://doi.org/10.1101/293860; this version posted May 17, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. SUMMARY HIV-1 assembly specifically alters both partitioning and dynamics of the tetraspanins CD9 and CD81 forming enriched areas where the virus buds. Importantly the presence of these proteins at exit sites and in viral particles inhibits virus-induced membrane fusion. To get molecular insights into tetraspanins partitioning in this viral context, we correlated nanoscale CD9 mapping obtained by super resolution microscopy to membrane topography probed by Atomic Force Microscopy (AFM). We demonstrated that CD9 is specifically trapped within the nascent viral particles, especially at buds tips, and that Gag mediate CD9 and CD81 depletion from cellular surfaces, even in the absence of Vpu and Nef, resulting from tetraspanins escaping from the plasma membrane during HIV-1 release.