The Emerging Role of Tetraspanins in the Proteolytic Processing of the Amyloid Precursor Protein
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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 The copyright holder for this preprint (which was not certified by peer review) is the author/funder.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 The copyright holder for this preprint (which was not certified by peer review) is the author/funder.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. -
RI-Mediated Mast Cell Activation Ε of Fc Tetraspanin CD151 Is A
Tetraspanin CD151 Is a Negative Regulator of Fc εRI-Mediated Mast Cell Activation Hiam Abdala-Valencia, Paul J. Bryce, Robert P. Schleimer, Joshua B. Wechsler, Lucas F. Loffredo, Joan M. Cook-Mills, This information is current as Chia-Lin Hsu and Sergejs Berdnikovs of September 26, 2021. J Immunol 2015; 195:1377-1387; Prepublished online 1 July 2015; doi: 10.4049/jimmunol.1302874 http://www.jimmunol.org/content/195/4/1377 Downloaded from Supplementary http://www.jimmunol.org/content/suppl/2015/07/01/jimmunol.130287 Material 4.DCSupplemental http://www.jimmunol.org/ References This article cites 63 articles, 28 of which you can access for free at: http://www.jimmunol.org/content/195/4/1377.full#ref-list-1 Why The JI? Submit online. • Rapid Reviews! 30 days* from submission to initial decision by guest on September 26, 2021 • No Triage! Every submission reviewed by practicing scientists • Fast Publication! 4 weeks from acceptance to publication *average Subscription Information about subscribing to The Journal of Immunology is online at: http://jimmunol.org/subscription Permissions Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html Email Alerts Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts The Journal of Immunology is published twice each month by The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2015 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. The Journal of Immunology Tetraspanin CD151 Is a Negative Regulator of Fc«RI-Mediated Mast Cell Activation Hiam Abdala-Valencia,* Paul J. -
Human and Mouse CD Marker Handbook Human and Mouse CD Marker Key Markers - Human Key Markers - Mouse
Welcome to More Choice CD Marker Handbook For more information, please visit: Human bdbiosciences.com/eu/go/humancdmarkers Mouse bdbiosciences.com/eu/go/mousecdmarkers Human and Mouse CD Marker Handbook Human and Mouse CD Marker Key Markers - Human Key Markers - Mouse CD3 CD3 CD (cluster of differentiation) molecules are cell surface markers T Cell CD4 CD4 useful for the identification and characterization of leukocytes. The CD CD8 CD8 nomenclature was developed and is maintained through the HLDA (Human Leukocyte Differentiation Antigens) workshop started in 1982. CD45R/B220 CD19 CD19 The goal is to provide standardization of monoclonal antibodies to B Cell CD20 CD22 (B cell activation marker) human antigens across laboratories. To characterize or “workshop” the antibodies, multiple laboratories carry out blind analyses of antibodies. These results independently validate antibody specificity. CD11c CD11c Dendritic Cell CD123 CD123 While the CD nomenclature has been developed for use with human antigens, it is applied to corresponding mouse antigens as well as antigens from other species. However, the mouse and other species NK Cell CD56 CD335 (NKp46) antibodies are not tested by HLDA. Human CD markers were reviewed by the HLDA. New CD markers Stem Cell/ CD34 CD34 were established at the HLDA9 meeting held in Barcelona in 2010. For Precursor hematopoetic stem cell only hematopoetic stem cell only additional information and CD markers please visit www.hcdm.org. Macrophage/ CD14 CD11b/ Mac-1 Monocyte CD33 Ly-71 (F4/80) CD66b Granulocyte CD66b Gr-1/Ly6G Ly6C CD41 CD41 CD61 (Integrin b3) CD61 Platelet CD9 CD62 CD62P (activated platelets) CD235a CD235a Erythrocyte Ter-119 CD146 MECA-32 CD106 CD146 Endothelial Cell CD31 CD62E (activated endothelial cells) Epithelial Cell CD236 CD326 (EPCAM1) For Research Use Only. -
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. -
Machine-Learning and Chemicogenomics Approach Defi Nes and Predicts Cross-Talk of Hippo and MAPK Pathways
Published OnlineFirst November 18, 2020; DOI: 10.1158/2159-8290.CD-20-0706 RESEARCH ARTICLE Machine -Learning and Chemicogenomics Approach Defi nes and Predicts Cross-Talk of Hippo and MAPK Pathways Trang H. Pham 1 , Thijs J. Hagenbeek 1 , Ho-June Lee 1 , Jason Li 2 , Christopher M. Rose 3 , Eva Lin 1 , Mamie Yu 1 , Scott E. Martin1 , Robert Piskol 2 , Jennifer A. Lacap 4 , Deepak Sampath 4 , Victoria C. Pham 3 , Zora Modrusan 5 , Jennie R. Lill3 , Christiaan Klijn 2 , Shiva Malek 1 , Matthew T. Chang 2 , and Anwesha Dey 1 ABSTRACT Hippo pathway dysregulation occurs in multiple cancers through genetic and non- genetic alterations, resulting in translocation of YAP to the nucleus and activation of the TEAD family of transcription factors. Unlike other oncogenic pathways such as RAS, defi ning tumors that are Hippo pathway–dependent is far more complex due to the lack of hotspot genetic alterations. Here, we developed a machine-learning framework to identify a robust, cancer type–agnostic gene expression signature to quantitate Hippo pathway activity and cross-talk as well as predict YAP/TEAD dependency across cancers. Further, through chemical genetic interaction screens and multiomics analyses, we discover a direct interaction between MAPK signaling and TEAD stability such that knockdown of YAP combined with MEK inhibition results in robust inhibition of tumor cell growth in Hippo dysregulated tumors. This multifaceted approach underscores how computational models combined with experimental studies can inform precision medicine approaches including predictive diagnostics and combination strategies. SIGNIFICANCE: An integrated chemicogenomics strategy was developed to identify a lineage- independent signature for the Hippo pathway in cancers. -
Tetraspanin CD53: an Overlooked Regulator of Immune Cell Function
Medical Microbiology and Immunology (2020) 209:545–552 https://doi.org/10.1007/s00430-020-00677-z REVIEW Tetraspanin CD53: an overlooked regulator of immune cell function V. E. Dunlock1 Received: 31 March 2020 / Accepted: 2 May 2020 / Published online: 21 May 2020 © The Author(s) 2020 Abstract Tetraspanins are membrane organizing proteins that play a role in organizing the cell surface through the formation of subcellular domains consisting of tetraspanins and their partner proteins. These complexes are referred to as tetraspanin enriched microdomains (TEMs) or the tetraspanin web. The formation of TEMs allows for the regulation of a variety of cellular processes such as adhesion, migration, signaling, and cell fusion. Tetraspanin CD53 is a member of the tetraspanin superfamily expressed exclusively within the immune compartment. Amongst others, B cells, CD4+ T cells, CD8+ T cells, dendritic cells, macrophages, and natural killer cells have all been found to express high levels of this protein on their sur- face. Almost three decades ago it was reported that patients who lacked CD53 sufered from an increased susceptibility to pathogens resulting in the clinical manifestation of recurrent viral, bacterial, and fungal infections. This clearly suggests a vital and non-redundant role for CD53 in immune function. Yet, despite this striking fnding, the specifc functional roles of CD53 within the immune system have remained elusive. This review aims to provide a concise overview of the published literature concerning CD53 and refect on the underappreciated role of this protein in immune cell regulation and function. Keywords Tetraspanins · Tetraspanin enriched microdomains · CD53 · Membrane organization · Immune cell signaling · Immune cell adhesion Introduction: tetraspanins in the immune surface or on intracellular membranes. -
Regulation of Leukocytes by Tspanc8 Tetraspanins And
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by University of Birmingham Research Portal University of Birmingham Regulation of Leukocytes by TspanC8 Tetraspanins and the “Molecular Scissor” ADAM10 Matthews, Alexandra; Koo, Chek Ziu; Szyroka, Justyna; Harrison, Neale; Kanhere, Aditi; Tomlinson, Michael DOI: 10.3389/fimmu.2018.01451 License: Creative Commons: Attribution (CC BY) Document Version Publisher's PDF, also known as Version of record Citation for published version (Harvard): Matthews, A, Koo, CZ, Szyroka, J, Harrison, N, Kanhere, A & Tomlinson, M 2018, 'Regulation of Leukocytes by TspanC8 Tetraspanins and the “Molecular Scissor” ADAM10', Frontiers in immunology, vol. 9, 1451. https://doi.org/10.3389/fimmu.2018.01451 Link to publication on Research at Birmingham portal Publisher Rights Statement: Matthews AL, Koo CZ, Szyroka J, Harrison N, Kanhere A and Tomlinson MG (2018) Regulation of Leukocytes by TspanC8 Tetraspanins and the “Molecular Scissor” ADAM10. Front. Immunol. 9:1451. doi: 10.3389/fimmu.2018.01451. First published by Frontiers Media. Checked 30/7/18. General rights Unless a licence is specified above, all rights (including copyright and moral rights) in this document are retained by the authors and/or the copyright holders. The express permission of the copyright holder must be obtained for any use of this material other than for purposes permitted by law. •Users may freely distribute the URL that is used to identify this publication. •Users may download and/or print one copy of the publication from the University of Birmingham research portal for the purpose of private study or non-commercial research. -
Dynamics Within Tetraspanin Pairs Affect MHC Class II Expression
328 Research Article Dynamics within tetraspanin pairs affect MHC class II expression Tineke van den Hoorn, Petra Paul, Lennert Janssen, Hans Janssen and Jacques Neefjes* Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands *Author for correspondence ([email protected]) Accepted 11 August 2011 Journal of Cell Science 125, 328–339 ß 2012. Published by The Company of Biologists Ltd doi: 10.1242/jcs.088047 Summary Late endosomal multivesicular bodies (MVBs) are complicated organelles with various subdomains located at the limiting membrane and the internal vesicles (ILVs). ILVs accumulate tetraspanins such as CD63 and CD82 that might form protein assemblies, including major histocompatibility complex class II (MHC-II) and its chaperone human leukocyte antigen (HLA)-DM. Here, we studied the effect of four late endosomal tetraspanin proteins on MHC-II expression. Silencing CD9, CD63 and CD81 enhanced MHC-II expression whereas silencing CD82 did not. No effect on peptide loading was observed. Using confocal FRET technology, we measured the dynamics of CD63 and CD82 interaction with MHC-II and its chaperone HLA-DM. CD63–CD82 interactions remained unaltered in the two MVB subdomains whereas the interactions between CD63 or CD82 homologous pairs changed. CD63 stably associated with MHC- II, and CD82 with HLA-DM, on both MVB subdomains whereas the CD82–MHC-II and CD63–HLA-DM interactions changed. These data visualize for the first time the protein dynamics of tetraspanin assemblies in MVB -
Systemic Induction of the Angiogenesis Switch by the Tetraspanin D6.1A/CO-029
Research Article Systemic Induction of the Angiogenesis Switch by the Tetraspanin D6.1A/CO-029 Sabine Gesierich,1 Igor Berezovskiy,1 Eduard Ryschich,2 and Margot Zo¨ller1,3 1Department of Tumor Progression and Immune Defence, German Cancer Research Centre; 2Department of Surgery, University of Heidelberg, Heidelberg; and 3Department of Applied Genetics, Faculty of Chemistry and Bioscience, University of Karlsruhe, Karlsruhe, Germany Abstract transcription of angiogenic factors (6, 7). Recent studies in Expression of the tetraspanin CO-029 is associated with poor knockout and transgenic mouse models have provided further prognosis in patients with gastrointestinal cancer. In a evidence that tumor angiogenesis is not only guided by the pancreatic tumor line, overexpression of the rat homologue, tumor cell itself, but is also closely tied to the tumor microenvi- ronment (8). D6.1A, induces lethally disseminated intravascular coagula- tion, suggesting D6.1A engagement in angiogenesis. D6.1A- Tetraspanins are a large family of proteins grouped according to overexpressing tumor cells induce the greatest amount of structural relatedness. The key feature of tetraspanins is their angiogenesis in vivo, and tumor cells as well as exosomes potential to associate with each other and with a multitude of derived thereof strikingly increase endothelial cell branching molecules from other protein families (9–11), the most prominent in vitro. Tumor cell–derived D6.1A stimulates angiogenic partners being integrins (12). The tetraspanin, D6.1A (rat)/CO-029 a h a h factor transcription, which includes increased matrix metal- (human), associates with 3 1 and 6 1 and, after disassembly of a h loproteinase and urokinase-type plasminogen activator se- hemidesmosomes, with 6 4. -
An Extracellular Site on Tetraspanin CD151 Determines Α3 and Α6
JCBArticle An extracellular site on tetraspanin CD151 determines ␣3 and ␣6 integrin–dependent cellular morphology Alexander R. Kazarov, Xiuwei Yang, Christopher S. Stipp, Bantoo Sehgal, and Martin E. Hemler Dana-Farber Cancer Institute and Department of Pathology, Harvard Medical School, Boston, MA 02115 he ␣31 integrin shows strong, stoichiometric, direct Brij 96–resistant) were independent of the QRD/TS151r lateral association with the tetraspanin CD151. As site, occurred late in biosynthesis, and involved mature T shown here, an extracellular CD151 site (QRD194–196) integrin subunits. Presence of the CD151–QRD194–196→INF is required for strong (i.e., Triton X-100–resistant) ␣31 mutant disrupted ␣3 and ␣6 integrin–dependent formation association and for maintenance of a key CD151 epitope of a network of cellular cables by Cos7 or NIH3T3 cells on (defined by monoclonal antibody TS151r) that is blocked basement membrane Matrigel and markedly altered cell upon ␣3 integrin association. Strong CD151 association spreading. These results provide definitive evidence that with integrin ␣61 also required the QRD194–196 site and strong lateral CD151–integrin association is functionally masked the TS151r epitope. For both ␣3 and ␣6 integrins, important, identify CD151 as a key player during ␣3 and strong QRD/TS151r-dependent CD151 association occurred ␣6 integrin–dependent matrix remodeling and cell spreading, early in biosynthesis and involved ␣ subunit precursor and support a model of CD151 as a transmembrane linker forms. In contrast, weaker associations of CD151 with itself, between extracellular integrin domains and intracellular integrins, or other tetraspanins (Triton X-100–sensitive but cytoskeleton/signaling molecules. -
A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus
Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated. -
To Study Mutant P53 Gain of Function, Various Tumor-Derived P53 Mutants
Differential effects of mutant TAp63γ on transactivation of p53 and/or p63 responsive genes and their effects on global gene expression. A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science By Shama K Khokhar M.Sc., Bilaspur University, 2004 B.Sc., Bhopal University, 2002 2007 1 COPYRIGHT SHAMA K KHOKHAR 2007 2 WRIGHT STATE UNIVERSITY SCHOOL OF GRADUATE STUDIES Date of Defense: 12-03-07 I HEREBY RECOMMEND THAT THE THESIS PREPARED UNDER MY SUPERVISION BY SHAMA KHAN KHOKHAR ENTITLED Differential effects of mutant TAp63γ on transactivation of p53 and/or p63 responsive genes and their effects on global gene expression BE ACCEPTED IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF Master of Science Madhavi P. Kadakia, Ph.D. Thesis Director Daniel Organisciak , Ph.D. Department Chair Committee on Final Examination Madhavi P. Kadakia, Ph.D. Steven J. Berberich, Ph.D. Michael Leffak, Ph.D. Joseph F. Thomas, Jr., Ph.D. Dean, School of Graduate Studies 3 Abstract Khokhar, Shama K. M.S., Department of Biochemistry and Molecular Biology, Wright State University, 2007 Differential effect of TAp63γ mutants on transactivation of p53 and/or p63 responsive genes and their effects on global gene expression. p63, a member of the p53 gene family, known to play a role in development, has more recently also been implicated in cancer progression. Mice lacking p63 exhibit severe developmental defects such as limb truncations, abnormal skin, and absence of hair follicles, teeth, and mammary glands. Germline missense mutations of p63 have been shown to be responsible for several human developmental syndromes including SHFM, EEC and ADULT syndromes and are associated with anomalies in the development of organs of epithelial origin.