Tetraspanin CD9: a Key Regulator of Cell Adhesion in the Immune System
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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 The copyright holder for this preprint (which was not certified by peer review) is the author/funder.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 The copyright holder for this preprint (which was not certified by peer review) is the author/funder.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. -
Derivation of Induced Pluripotent Stem Cells from Pig Somatic Cells
Derivation of induced pluripotent stem cells from pig somatic cells Toshihiko Ezashia, Bhanu Prakash V. L. Telugua, Andrei P. Alexenkoa, Shrikesh Sachdevb, Sunilima Sinhaa, and R. Michael Robertsa,b,1 Divisions of aAnimal Sciences and bBiochemistry, University of Missouri, Columbia, MO 65211 Contributed by R. Michael Roberts, May 13, 2009 (sent for review April 15, 2009) For reasons that are unclear the production of embryonic stem cells For reasons that are unclear, the establishment of porcine ESC from ungulates has proved elusive. Here, we describe induced from ICM of blastocysts and the epiblast of slightly older pluripotent stem cells (iPSC) derived from porcine fetal fibroblasts embryos has proven to be elusive. There has been a similar lack by lentiviral transduction of 4 human (h) genes, hOCT4,hSOX2, of success with other ungulate species. The earliest reports hKLF4, and hc-MYC, the combination commonly used to create iPSC announcing the derivation of ESC-like cells from ICM of pigs in mouse and human. Cells were cultured on irradiated mouse appeared in the early 1990s (19–21), but these ESC-like cells and embryonic fibroblasts (MEF) and in medium supplemented with many others since then, including ones for cattle, goat, and knockout serum replacement and FGF2. Compact colonies of alka- sheep, as well as for pig, have failed to meet the full criteria to line phosphatase-positive cells emerged after Ϸ22 days, providing define them as ESC (11–13). There are a number of reasons that an overall reprogramming efficiency of Ϸ0.1%. The cells expressed might explain the problems encountered, including choice of the porcine OCT4, NANOG, and SOX2 and had high telomerase activity, wrong stage of embryo development to establish the cultures, inappropriate culture and cell passage conditions, and contam- but also continued to express the 4 human transgenes. -
ALCAM Regulates Mediolateral Retinotopic Mapping in the Superior Colliculus
15630 • The Journal of Neuroscience, December 16, 2009 • 29(50):15630–15641 Development/Plasticity/Repair ALCAM Regulates Mediolateral Retinotopic Mapping in the Superior Colliculus Mona Buhusi,1 Galina P. Demyanenko,1 Karry M. Jannie,2 Jasbir Dalal,1 Eli P. B. Darnell,1 Joshua A. Weiner,2 and Patricia F. Maness1 1Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599, and 2Department of Biology, University of Iowa, Iowa City, Iowa 52242 ALCAM [activated leukocyte cell adhesion molecule (BEN/SC-1/DM-GRASP)] is a transmembrane recognition molecule of the Ig superfamily (IgSF) containing five Ig domains (two V-type, three C2-type). Although broadly expressed in the nervous and immune systems, few of its developmental functions have been elucidated. Because ALCAM has been suggested to interact with the IgSF adhesion molecule L1, a determi- nant of retinocollicular mapping, we hypothesized that ALCAM might direct topographic targeting to the superior colliculus (SC) by serving as a substrate within the SC for L1 on incoming retinal ganglion cell (RGC) axons. ALCAM was expressed in the SC during RGC axon targeting and on RGC axons as they formed the optic nerve; however, it was downregulated distally on RGC axons as they entered the SC. Axon tracing with DiI revealedpronouncedmistargetingofRGCaxonsfromthetemporalretinahalfofALCAMnullmicetoabnormallylateralsitesinthecontralateral SC, in which these axons formed multiple ectopic termination zones. ALCAM null mutant axons were -
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. -
L1 Cell Adhesion Molecule in Cancer, a Systematic Review on Domain-Specific Functions
International Journal of Molecular Sciences Review L1 Cell Adhesion Molecule in Cancer, a Systematic Review on Domain-Specific Functions Miriam van der Maten 1,2, Casper Reijnen 1,3, Johanna M.A. Pijnenborg 1,* and Mirjam M. Zegers 2,* 1 Department of Obstetrics and Gynaecology, Radboud university medical center, 6525 GA Nijmegen, The Netherlands 2 Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud university medical center, 6525 GA Nijmegen, The Netherlands 3 Department of Obstetrics and Gynaecology, Canisius-Wilhelmina Hospital, 6532 SZ Nijmegen, The Netherlands * Correspondence: [email protected] (J.M.A.P); [email protected] (M.M.Z.) Received: 24 June 2019; Accepted: 23 August 2019; Published: 26 August 2019 Abstract: L1 cell adhesion molecule (L1CAM) is a glycoprotein involved in cancer development and is associated with metastases and poor prognosis. Cellular processing of L1CAM results in expression of either full-length or cleaved forms of the protein. The different forms of L1CAM may localize at the plasma membrane as a transmembrane protein, or in the intra- or extracellular environment as cleaved or exosomal forms. Here, we systematically analyze available literature that directly relates to L1CAM domains and associated signaling pathways in cancer. Specifically, we chart its domain-specific functions in relation to cancer progression, and outline pre-clinical assays used to assess L1CAM. It is found that full-length L1CAM has both intracellular and extracellular targets, including interactions with integrins, and linkage with ezrin. Cellular processing leading to proteolytic cleavage and/or exosome formation results in extracellular soluble forms of L1CAM that may act through similar mechanisms as compared to full-length L1CAM, such as integrin-dependent signals, but also through distinct mechanisms. -
Supplementary Material DNA Methylation in Inflammatory Pathways Modifies the Association Between BMI and Adult-Onset Non- Atopic
Supplementary Material DNA Methylation in Inflammatory Pathways Modifies the Association between BMI and Adult-Onset Non- Atopic Asthma Ayoung Jeong 1,2, Medea Imboden 1,2, Akram Ghantous 3, Alexei Novoloaca 3, Anne-Elie Carsin 4,5,6, Manolis Kogevinas 4,5,6, Christian Schindler 1,2, Gianfranco Lovison 7, Zdenko Herceg 3, Cyrille Cuenin 3, Roel Vermeulen 8, Deborah Jarvis 9, André F. S. Amaral 9, Florian Kronenberg 10, Paolo Vineis 11,12 and Nicole Probst-Hensch 1,2,* 1 Swiss Tropical and Public Health Institute, 4051 Basel, Switzerland; [email protected] (A.J.); [email protected] (M.I.); [email protected] (C.S.) 2 Department of Public Health, University of Basel, 4001 Basel, Switzerland 3 International Agency for Research on Cancer, 69372 Lyon, France; [email protected] (A.G.); [email protected] (A.N.); [email protected] (Z.H.); [email protected] (C.C.) 4 ISGlobal, Barcelona Institute for Global Health, 08003 Barcelona, Spain; [email protected] (A.-E.C.); [email protected] (M.K.) 5 Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain 6 CIBER Epidemiología y Salud Pública (CIBERESP), 08005 Barcelona, Spain 7 Department of Economics, Business and Statistics, University of Palermo, 90128 Palermo, Italy; [email protected] 8 Environmental Epidemiology Division, Utrecht University, Institute for Risk Assessment Sciences, 3584CM Utrecht, Netherlands; [email protected] 9 Population Health and Occupational Disease, National Heart and Lung Institute, Imperial College, SW3 6LR London, UK; [email protected] (D.J.); [email protected] (A.F.S.A.) 10 Division of Genetic Epidemiology, Medical University of Innsbruck, 6020 Innsbruck, Austria; [email protected] 11 MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, W2 1PG London, UK; [email protected] 12 Italian Institute for Genomic Medicine (IIGM), 10126 Turin, Italy * Correspondence: [email protected]; Tel.: +41-61-284-8378 Int. -
And MUC1 in Mammary Epithelial Cells
Linköping University Post Print Loss of ICAM-1 signaling induces psoriasin (S100A7) and MUC1 in mammary epithelial cells Stina Petersson, E. Shubbar, M. Yhr, A. Kovacs and Charlotta Enerbäck N.B.: When citing this work, cite the original article. The original publication is available at www.springerlink.com: Stina Petersson, E. Shubbar, M. Yhr, A. Kovacs and Charlotta Enerbäck, Loss of ICAM-1 signaling induces psoriasin (S100A7) and MUC1 in mammary epithelial cells, 2011, Breast Cancer Research and Treatment, (125), 1, 13-25. http://dx.doi.org/10.1007/s10549-010-0820-4 Copyright: Springer Science Business Media http://www.springerlink.com/ Postprint available at: Linköping University Electronic Press http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-63954 1 Loss of ICAM-1 signaling induces psoriasin (S100A7) and MUC1 in mammary epithelial cells Petersson S1, Shubbar E1, Yhr M1, Kovacs A2 and Enerbäck C3 Departments of 1Clinical Genetics and 2Pathology, Sahlgrenska University Hospital, SE-413 45 Gothenburg, Sweden; 3Department of Clinical and Experimental Medicine, Division of Cell Biology and Dermatology, Linköping University, SE-581 85 Linköping, Sweden E-mail: [email protected] E-mail: maria.yhr@ clingen.gu.se E-mail: [email protected] E-mail: [email protected] Correspondence: Stina Petersson, Department of Clinical Genetics, Sahlgrenska University Hospital, SE-413 45 Gothenburg, Sweden E-mail: [email protected] 2 Abstract Psoriasin (S100A7), a member of the S100 gene family, is highly expressed in high-grade comedo ductal carcinoma in situ (DCIS), with a higher risk of local recurrence. Psoriasin is therefore a potential biomarker for DCIS with a poor prognosis. -
Dual Role of ALCAM in Neuroinflammation and Blood–Brain
Dual role of ALCAM in neuroinflammation and PNAS PLUS blood–brain barrier homeostasis Marc-André Lécuyera, Olivia Saint-Laurenta, Lyne Bourbonnièrea, Sandra Larouchea, Catherine Larochellea, Laure Michela, Marc Charabatia, Michael Abadierb, Stephanie Zandeea, Neda Haghayegh Jahromib, Elizabeth Gowinga, Camille Pitteta, Ruth Lyckb, Britta Engelhardtb, and Alexandre Prata,c,1 aNeuroimmunology Research Laboratory, Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM), Montreal, QC, Canada H2X 0A9; bTheodor Kocher Institute, University of Bern, 3012 Bern, Switzerland; and cDepartment of Neurosciences, Faculty of Medicine, Université de Montréal, Montreal, QC, Canada H3T 1J4 Edited by Lawrence Steinman, Stanford University School of Medicine, Stanford, CA, and approved December 9, 2016 (received for review August 29, 2016) Activated leukocyte cell adhesion molecule (ALCAM) is a cell adhesion Although the roles of ICAM-1 and VCAM-1 during leukocyte moleculefoundonblood–brain barrier endothelial cells (BBB-ECs) that transmigration in most vascular beds have been extensively was previously shown to be involved in leukocyte transmigration studied (8–10), additional adhesion molecules have also been across the endothelium. In the present study, we found that ALCAM shown to partake in the transmigration process of encephalito- knockout (KO) mice developed a more severe myelin oligodendrocyte genic immune cells, including activated leukocyte cell adhesion glycoprotein (MOG)35–55–induced experimental autoimmune enceph- molecule (ALCAM/CD166) (11, 12), melanoma cell adhe- alomyelitis (EAE). The exacerbated disease was associated with a sig- sion molecule (MCAM) (13–15), mucosal vascular addressin cell nificant increase in the number of CNS-infiltrating proinflammatory adhesion molecule 1 (MAdCAM-1) (16, 17), vascular adhesion leukocytes compared with WT controls. -
Development and Validation of a Protein-Based Risk Score for Cardiovascular Outcomes Among Patients with Stable Coronary Heart Disease
Supplementary Online Content Ganz P, Heidecker B, Hveem K, et al. Development and validation of a protein-based risk score for cardiovascular outcomes among patients with stable coronary heart disease. JAMA. doi: 10.1001/jama.2016.5951 eTable 1. List of 1130 Proteins Measured by Somalogic’s Modified Aptamer-Based Proteomic Assay eTable 2. Coefficients for Weibull Recalibration Model Applied to 9-Protein Model eFigure 1. Median Protein Levels in Derivation and Validation Cohort eTable 3. Coefficients for the Recalibration Model Applied to Refit Framingham eFigure 2. Calibration Plots for the Refit Framingham Model eTable 4. List of 200 Proteins Associated With the Risk of MI, Stroke, Heart Failure, and Death eFigure 3. Hazard Ratios of Lasso Selected Proteins for Primary End Point of MI, Stroke, Heart Failure, and Death eFigure 4. 9-Protein Prognostic Model Hazard Ratios Adjusted for Framingham Variables eFigure 5. 9-Protein Risk Scores by Event Type This supplementary material has been provided by the authors to give readers additional information about their work. Downloaded From: https://jamanetwork.com/ on 10/02/2021 Supplemental Material Table of Contents 1 Study Design and Data Processing ......................................................................................................... 3 2 Table of 1130 Proteins Measured .......................................................................................................... 4 3 Variable Selection and Statistical Modeling ........................................................................................