Cargo-Loading of Misfolded Proteins Into Extracellular Vesicles
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Computational Genome-Wide Identification of Heat Shock Protein Genes in the Bovine Genome [Version 1; Peer Review: 2 Approved, 1 Approved with Reservations]
F1000Research 2018, 7:1504 Last updated: 08 AUG 2021 RESEARCH ARTICLE Computational genome-wide identification of heat shock protein genes in the bovine genome [version 1; peer review: 2 approved, 1 approved with reservations] Oyeyemi O. Ajayi1,2, Sunday O. Peters3, Marcos De Donato2,4, Sunday O. Sowande5, Fidalis D.N. Mujibi6, Olanrewaju B. Morenikeji2,7, Bolaji N. Thomas 8, Matthew A. Adeleke 9, Ikhide G. Imumorin2,10,11 1Department of Animal Breeding and Genetics, Federal University of Agriculture, Abeokuta, Nigeria 2International Programs, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, 14853, USA 3Department of Animal Science, Berry College, Mount Berry, GA, 30149, USA 4Departamento Regional de Bioingenierias, Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Queretaro, Mexico 5Department of Animal Production and Health, Federal University of Agriculture, Abeokuta, Nigeria 6Usomi Limited, Nairobi, Kenya 7Department of Animal Production and Health, Federal University of Technology, Akure, Nigeria 8Department of Biomedical Sciences, Rochester Institute of Technology, Rochester, NY, 14623, USA 9School of Life Sciences, University of KwaZulu-Natal, Durban, 4000, South Africa 10School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30032, USA 11African Institute of Bioscience Research and Training, Ibadan, Nigeria v1 First published: 20 Sep 2018, 7:1504 Open Peer Review https://doi.org/10.12688/f1000research.16058.1 Latest published: 20 Sep 2018, 7:1504 https://doi.org/10.12688/f1000research.16058.1 Reviewer Status Invited Reviewers Abstract Background: Heat shock proteins (HSPs) are molecular chaperones 1 2 3 known to bind and sequester client proteins under stress. Methods: To identify and better understand some of these proteins, version 1 we carried out a computational genome-wide survey of the bovine 20 Sep 2018 report report report genome. -
Organ Level Protein Networks As a Reference for the Host Effects of the Microbiome
Downloaded from genome.cshlp.org on October 6, 2021 - Published by Cold Spring Harbor Laboratory Press 1 Organ level protein networks as a reference for the host effects of the microbiome 2 3 Robert H. Millsa,b,c,d, Jacob M. Wozniaka,b, Alison Vrbanacc, Anaamika Campeaua,b, Benoit 4 Chassainge,f,g,h, Andrew Gewirtze, Rob Knightc,d, and David J. Gonzaleza,b,d,# 5 6 a Department of Pharmacology, University of California, San Diego, California, USA 7 b Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 8 California, USA 9 c Department of Pediatrics, and Department of Computer Science and Engineering, University of 10 California, San Diego California, USA 11 d Center for Microbiome Innovation, University of California, San Diego, California, USA 12 e Center for Inflammation, Immunity and Infection, Institute for Biomedical Sciences, Georgia State 13 University, Atlanta, GA, USA 14 f Neuroscience Institute, Georgia State University, Atlanta, GA, USA 15 g INSERM, U1016, Paris, France. 16 h Université de Paris, Paris, France. 17 18 Key words: Microbiota, Tandem Mass Tags, Organ Proteomics, Gnotobiotic Mice, Germ-free Mice, 19 Protein Networks, Proteomics 20 21 # Address Correspondence to: 22 David J. Gonzalez, PhD 23 Department of Pharmacology and Pharmacy 24 University of California, San Diego 25 La Jolla, CA 92093 26 E-mail: [email protected] 27 Phone: 858-822-1218 28 1 Downloaded from genome.cshlp.org on October 6, 2021 - Published by Cold Spring Harbor Laboratory Press 29 Abstract 30 Connections between the microbiome and health are rapidly emerging in a wide range of 31 diseases. -
Molecular Profile of Tumor-Specific CD8+ T Cell Hypofunction in a Transplantable Murine Cancer Model
Downloaded from http://www.jimmunol.org/ by guest on September 25, 2021 T + is online at: average * The Journal of Immunology , 34 of which you can access for free at: 2016; 197:1477-1488; Prepublished online 1 July from submission to initial decision 4 weeks from acceptance to publication 2016; doi: 10.4049/jimmunol.1600589 http://www.jimmunol.org/content/197/4/1477 Molecular Profile of Tumor-Specific CD8 Cell Hypofunction in a Transplantable Murine Cancer Model Katherine A. Waugh, Sonia M. Leach, Brandon L. Moore, Tullia C. Bruno, Jonathan D. Buhrman and Jill E. Slansky J Immunol cites 95 articles Submit online. Every submission reviewed by practicing scientists ? is published twice each month by Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts http://jimmunol.org/subscription Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html http://www.jimmunol.org/content/suppl/2016/07/01/jimmunol.160058 9.DCSupplemental This article http://www.jimmunol.org/content/197/4/1477.full#ref-list-1 Information about subscribing to The JI No Triage! Fast Publication! Rapid Reviews! 30 days* Why • • • Material References Permissions Email Alerts Subscription Supplementary The Journal of Immunology The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2016 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. This information is current as of September 25, 2021. The Journal of Immunology Molecular Profile of Tumor-Specific CD8+ T Cell Hypofunction in a Transplantable Murine Cancer Model Katherine A. -
Defining Functional Interactions During Biogenesis of Epithelial Junctions
ARTICLE Received 11 Dec 2015 | Accepted 13 Oct 2016 | Published 6 Dec 2016 | Updated 5 Jan 2017 DOI: 10.1038/ncomms13542 OPEN Defining functional interactions during biogenesis of epithelial junctions J.C. Erasmus1,*, S. Bruche1,*,w, L. Pizarro1,2,*, N. Maimari1,3,*, T. Poggioli1,w, C. Tomlinson4,J.Lees5, I. Zalivina1,w, A. Wheeler1,w, A. Alberts6, A. Russo2 & V.M.M. Braga1 In spite of extensive recent progress, a comprehensive understanding of how actin cytoskeleton remodelling supports stable junctions remains to be established. Here we design a platform that integrates actin functions with optimized phenotypic clustering and identify new cytoskeletal proteins, their functional hierarchy and pathways that modulate E-cadherin adhesion. Depletion of EEF1A, an actin bundling protein, increases E-cadherin levels at junctions without a corresponding reinforcement of cell–cell contacts. This unexpected result reflects a more dynamic and mobile junctional actin in EEF1A-depleted cells. A partner for EEF1A in cadherin contact maintenance is the formin DIAPH2, which interacts with EEF1A. In contrast, depletion of either the endocytic regulator TRIP10 or the Rho GTPase activator VAV2 reduces E-cadherin levels at junctions. TRIP10 binds to and requires VAV2 function for its junctional localization. Overall, we present new conceptual insights on junction stabilization, which integrate known and novel pathways with impact for epithelial morphogenesis, homeostasis and diseases. 1 National Heart and Lung Institute, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK. 2 Computing Department, Imperial College London, London SW7 2AZ, UK. 3 Bioengineering Department, Faculty of Engineering, Imperial College London, London SW7 2AZ, UK. 4 Department of Surgery & Cancer, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK. -
Apoptosis Induced by Proteasome Inhibition in Cancer Cells: Predominant Role of the P53/PUMA Pathway
Oncogene (2007) 26, 1681–1692 & 2007 Nature Publishing Group All rights reserved 0950-9232/07 $30.00 www.nature.com/onc ORIGINAL ARTICLE Apoptosis induced by proteasome inhibition in cancer cells: predominant role of the p53/PUMA pathway CG Concannon1, BF Koehler1,2, Claus Reimertz2, BM Murphy1, C Bonner1, N Thurow2, MW Ward1, AVillunger 3, AStrasser 4,DKo¨ gel2,5 and JHM Prehn1,5 1Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland; 2Experimental Neurosurgery, Centre for Neurology and Neurosurgery, Johann Wolfgang Goethe University Clinics, Theodor-Stern-Kai 7, Frankfurt/Main, Germany; 3Division of Experimental Pathophysiology and Immunology, Biocenter, Innsbruck Medical University, Innsbruck, Austria and 4The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia The proteasome has emerged as a novel target for Introduction antineoplastic treatment of hematological malignancies and solid tumors, including those of the central nervous The correct functioning of the ubiquitin-proteasome system. To identify cell death pathways activated in pathway is essential for the degradation of the majority response to inhibition of the proteasome system in cancer of intracellular proteins. Several key regulatory proteins cells, we treated human SH-SY5Y neuroblastoma cells involved in cell proliferation and differentiation are with the selective proteasome inhibitor (PI) epoxomicin regulated by proteasome-mediated proteolysis resulting (Epoxo). Prolonged exposure to Epoxo was associated in the activation or inhibition of specific cell signaling with increased levels of poly-ubiquitinylated proteins and pathways (Adams, 2004a). The proteasome is also p53, release of cytochrome c from the mitochondria, and central to the regulation of cell death and apoptosis. -
University of Groningen the Human HSP70/HSP40 Chaperone Family
University of Groningen The human HSP70/HSP40 chaperone family Hageman, Jurre IMPORTANT NOTE: You are advised to consult the publisher's version (publisher's PDF) if you wish to cite from it. Please check the document version below. Document Version Publisher's PDF, also known as Version of record Publication date: 2008 Link to publication in University of Groningen/UMCG research database Citation for published version (APA): Hageman, J. (2008). The human HSP70/HSP40 chaperone family: a study on its capacity to combat proteotoxic stress. s.n. Copyright Other than for strictly personal use, it is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), unless the work is under an open content license (like Creative Commons). The publication may also be distributed here under the terms of Article 25fa of the Dutch Copyright Act, indicated by the “Taverne” license. More information can be found on the University of Groningen website: https://www.rug.nl/library/open-access/self-archiving-pure/taverne- amendment. Take-down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. Downloaded from the University of Groningen/UMCG research database (Pure): http://www.rug.nl/research/portal. For technical reasons the number of authors shown on this cover page is limited to 10 maximum. Download date: 30-09-2021 CHAPTER 1 Introduction - Structural and functional diversities between members of the human HSPH, HSPA and DNAJ chaperone families Jurre Hageman and Harm H. -
Figure S1. DMD Module Network. the Network Is Formed by 260 Genes from Disgenet and 1101 Interactions from STRING. Red Nodes Are the Five Seed Candidate Genes
Figure S1. DMD module network. The network is formed by 260 genes from DisGeNET and 1101 interactions from STRING. Red nodes are the five seed candidate genes. Figure S2. DMD module network is more connected than a random module of the same size. It is shown the distribution of the largest connected component of 10.000 random modules of the same size of the DMD module network. The green line (x=260) represents the DMD largest connected component, obtaining a z-score=8.9. Figure S3. Shared genes between BMD and DMD signature. A) A meta-analysis of three microarray datasets (GSE3307, GSE13608 and GSE109178) was performed for the identification of differentially expressed genes (DEGs) in BMD muscle biopsies as compared to normal muscle biopsies. Briefly, the GSE13608 dataset included 6 samples of skeletal muscle biopsy from healthy people and 5 samples from BMD patients. Biopsies were taken from either biceps brachii, triceps brachii or deltoid. The GSE3307 dataset included 17 samples of skeletal muscle biopsy from healthy people and 10 samples from BMD patients. The GSE109178 dataset included 14 samples of controls and 11 samples from BMD patients. For both GSE3307 and GSE10917 datasets, biopsies were taken at the time of diagnosis and from the vastus lateralis. For the meta-analysis of GSE13608, GSE3307 and GSE109178, a random effects model of effect size measure was used to integrate gene expression patterns from the two datasets. Genes with an adjusted p value (FDR) < 0.05 and an │effect size│>2 were identified as DEGs and selected for further analysis. A significant number of DEGs (p<0.001) were in common with the DMD signature genes (blue nodes), as determined by a hypergeometric test assessing the significance of the overlap between the BMD DEGs and the number of DMD signature genes B) MCODE analysis of the overlapping genes between BMD DEGs and DMD signature genes. -
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. -
Mitochondrial Quality Control in Neurodegenerative Diseases: Focus on Parkinson’S Disease and Huntington’S Disease
ADVERTIMENT. Lʼaccés als continguts dʼaquesta tesi queda condicionat a lʼacceptació de les condicions dʼús establertes per la següent llicència Creative Commons: http://cat.creativecommons.org/?page_id=184 ADVERTENCIA. El acceso a los contenidos de esta tesis queda condicionado a la aceptación de las condiciones de uso establecidas por la siguiente licencia Creative Commons: http://es.creativecommons.org/blog/licencias/ WARNING. The access to the contents of this doctoral thesis it is limited to the acceptance of the use conditions set by the following Creative Commons license: https://creativecommons.org/licenses/?lang=en Mitochondrial quality control in neurodegenerative diseases: focus on Parkinson’s disease and Huntington’s disease TESI DOCTORAL 2018 Programa de Doctorat en Neurociències Institut de Neurociències Tesi realitzada al laboratori de Malalties Neurodegeenratives de l’Institut de Recerca de la Vall d’Hebron (VHIR) Doctorand Director Tutor Sandra Franco Iborra Miquel Vila Bover José Rodríguez Álvarez Co-directora Co-directora Celine Perier Marta Martínez Vicente i AGRAÏMENTS En primer lloc vull agraïr al Miquel Vila per l’oportunitat que em va donar de començar a fer la tesi doctoral al seu lab. Gràcies per tenir sempre la porta oberta del teu despatx, per la confiança dipositada en mi i per tot el que m’has ensenyat durant tots aquests anys. A més, he tingut la sort de tenir no només un director de tesis sinó tres! Celine muchas gracias por estar siempre ahí, por ensenyarme tu manera de hacer ciencia (que me encanta!) y por ser siempre tan positiva. En mi manera de trabajar hay un poquito de ti y espero ir pasando este conocimiento a los demás porque en todo laboratorio debería ser obligatorio que hubiera alguien como tu. -
The Hsp70/Hsp90 Chaperone Machinery in Neurodegenerative Diseases
REVIEW published: 16 May 2017 doi: 10.3389/fnins.2017.00254 The Hsp70/Hsp90 Chaperone Machinery in Neurodegenerative Diseases Rachel E. Lackie 1, 2, Andrzej Maciejewski 1, 3, Valeriy G. Ostapchenko 1, Jose Marques-Lopes 1, Wing-Yiu Choy 3, Martin L. Duennwald 4, Vania F. Prado 1, 2, 5, 6 and Marco A. M. Prado 1, 2, 5, 6* 1 Molecular Medicine, Robarts Research Institute, University of Western Ontario, London, ON, Canada, 2 Program in Neuroscience, University of Western Ontario, London, ON, Canada, 3 Department of Biochemistry, University of Western Ontario, London, ON, Canada, 4 Department of Pathology and Laboratory Medicine, University of Western Ontario, London, ON, Canada, 5 Department of Physiology and Pharmacology, University of Western Ontario, London, ON, Canada, 6 Department of Anatomy and Cell Biology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, Canada The accumulation of misfolded proteins in the human brain is one of the critical features of many neurodegenerative diseases, including Alzheimer’s disease (AD). Assembles of beta-amyloid (Aβ) peptide—either soluble (oligomers) or insoluble (plaques) and Edited by: Cintia Roodveldt, of tau protein, which form neurofibrillary tangles, are the major hallmarks of AD. Centro Andaluz de Biología Molecular Chaperones and co-chaperones regulate protein folding and client maturation, but they y Medicina Regenerativa, Spain also target misfolded or aggregated proteins for refolding or for degradation, mostly Reviewed by: Toshihide Takeuchi, by the proteasome. They form an important line of defense against misfolded proteins Osaka University, Japan and are part of the cellular quality control system. The heat shock protein (Hsp) family, Janine Kirstein, particularly Hsp70 and Hsp90, plays a major part in this process and it is well-known to Leibniz Institute for Molecular Pharmacology (FMP), Germany regulate protein misfolding in a variety of diseases, including tau levels and toxicity in AD. -
Mitochondrial Protein Quality Control Mechanisms
G C A T T A C G G C A T genes Review Mitochondrial Protein Quality Control Mechanisms Pooja Jadiya * and Dhanendra Tomar * Center for Translational Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA * Correspondence: [email protected] (P.J.); [email protected] (D.T.); Tel.: +1-215-707-9144 (D.T.) Received: 29 April 2020; Accepted: 15 May 2020; Published: 18 May 2020 Abstract: Mitochondria serve as a hub for many cellular processes, including bioenergetics, metabolism, cellular signaling, redox balance, calcium homeostasis, and cell death. The mitochondrial proteome includes over a thousand proteins, encoded by both the mitochondrial and nuclear genomes. The majority (~99%) of proteins are nuclear encoded that are synthesized in the cytosol and subsequently imported into the mitochondria. Within the mitochondria, polypeptides fold and assemble into their native functional form. Mitochondria health and integrity depend on correct protein import, folding, and regulated turnover termed as mitochondrial protein quality control (MPQC). Failure to maintain these processes can cause mitochondrial dysfunction that leads to various pathophysiological outcomes and the commencement of diseases. Here, we summarize the current knowledge about the role of different MPQC regulatory systems such as mitochondrial chaperones, proteases, the ubiquitin-proteasome system, mitochondrial unfolded protein response, mitophagy, and mitochondria-derived vesicles in the maintenance of mitochondrial proteome and health. The proper understanding of mitochondrial protein quality control mechanisms will provide relevant insights to treat multiple human diseases. Keywords: mitochondria; proteome; ubiquitin; proteasome; chaperones; protease; mitophagy; mitochondrial protein quality control; mitochondria-associated degradation; mitochondrial unfolded protein response 1. Introduction Mitochondria are double membrane, dynamic, and semiautonomous organelles which have several critical cellular functions. -
CLN8 Mutations Presenting with a Phenotypic Continuum of Neuronal Ceroid Lipofuscinosis—Literature Review and Case Report
G C A T T A C G G C A T genes Article CLN8 Mutations Presenting with a Phenotypic Continuum of Neuronal Ceroid Lipofuscinosis—Literature Review and Case Report Magdalena Badura-Stronka 1,*,†, Anna Winczewska-Wiktor 2,†, Anna Pietrzak 3,†, Adam Sebastian Hirschfeld 1, Tomasz Zemojtel 4, Katarzyna Woły ´nska 1, Katarzyna Bednarek-Rajewska 5, Monika Seget-Dubaniewicz 5, Agnieszka Matheisel 6, Anna Latos-Bielenska 1 and Barbara Steinborn 2 1 Chair and Department of Medical Genetics, Poznan University of Medical Sciences, 60-352 Poznan, Poland; [email protected] (A.S.H.); [email protected] (K.W.); [email protected] (A.L.-B.) 2 Chair and Department of Developmental Neurology, Poznan University of Medical Sciences, 60-355 Poznan, Poland; [email protected] (A.W.-W.); [email protected] (B.S.) 3 Department of Neurology, 10th Military Research Hospital and Polyclinic, 85-681 Bydgoszcz, Poland; [email protected] 4 BIH Genomics Core Unit, Campus Mitte, Charite University Medicine, 13353 Berlin, Germany; [email protected] 5 Department of Clinical Pathology, Poznan University of Medical Sciences, 60-355 Poznan, Poland; [email protected] (K.B.-R.); [email protected] (M.S.-D.) 6 Citation: Badura-Stronka, M.; Department of Developmental Neurology, Gdansk Medical University, 80-307 Gdansk, Poland; Winczewska-Wiktor, A.; Pietrzak, A.; [email protected] * Correspondence: [email protected] Hirschfeld, A.S.; Zemojtel, T.; † These authors contributed equally to this work. Woły´nska,K.; Bednarek-Rajewska, K.; Seget-Dubaniewicz, M.; Matheisel, A.; Latos-Bielenska, A.; Steinborn, B. Abstract: CLN8 is a ubiquitously expressed membrane-spanning protein that localizes primarily CLN8 Mutations Presenting with a in the ER, with partial localization in the ER-Golgi intermediate compartment.