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  • I HIGH MASS ACCURACY COUPLED to SPATIALLY-DIRECTED
    HIGH MASS ACCURACY COUPLED TO SPATIALLY-DIRECTED PROTEOMICS FOR IMPROVED PROTEIN IDENTIFICATIONS IN IMAGING MASS SPECTROMETRY EXPERIMENTS By David Geoffrey Rizzo Dissertation Submitted to the Faculty of the Graduate School of Vanderbilt University in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY in Chemistry August, 2016 Nashville, Tennessee Approved: Richard M. Caprioli, Ph.D. Kevin L. Schey, Ph.D. John A. McLean, Ph.D. Michael P. Stone, Ph.D. i Copyright © 2016 by David Geoffrey Rizzo All Rights Reserved ii This work is dedicated to my family and friends, who have shown nothing but support for me in all of life’s endeavors. iii ACKNOWLEDGEMENTS “As we express our gratitude, we must never forget that the highest appreciation is not to utter words, but to live by them.” - John F. Kennedy – There are many people I must thank for showing kindness, encouragement, and support for me during my tenure as a graduate student. First and foremost, I would like to thank my research advisor, Richard Caprioli, for providing both ample resources and guidance that allowed me to grow as a scientist. Our discussions about my research and science in general have helped me become a much more focused and discerning analytical chemist. I must also thank my Ph.D. committee members, Drs. Kevin Schey, John McLean, and Michael Stone, who have brought valuable insight into my research and provided direction along the way. My undergraduate advisor, Dr. Facundo Fernández, encouraged me to begin research in his lab and introduced me to the world of mass spectrometry.
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  • 1 Metabolic Dysfunction Is Restricted to the Sciatic Nerve in Experimental
    Page 1 of 255 Diabetes Metabolic dysfunction is restricted to the sciatic nerve in experimental diabetic neuropathy Oliver J. Freeman1,2, Richard D. Unwin2,3, Andrew W. Dowsey2,3, Paul Begley2,3, Sumia Ali1, Katherine A. Hollywood2,3, Nitin Rustogi2,3, Rasmus S. Petersen1, Warwick B. Dunn2,3†, Garth J.S. Cooper2,3,4,5* & Natalie J. Gardiner1* 1 Faculty of Life Sciences, University of Manchester, UK 2 Centre for Advanced Discovery and Experimental Therapeutics (CADET), Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester, UK 3 Centre for Endocrinology and Diabetes, Institute of Human Development, Faculty of Medical and Human Sciences, University of Manchester, UK 4 School of Biological Sciences, University of Auckland, New Zealand 5 Department of Pharmacology, Medical Sciences Division, University of Oxford, UK † Present address: School of Biosciences, University of Birmingham, UK *Joint corresponding authors: Natalie J. Gardiner and Garth J.S. Cooper Email: [email protected]; [email protected] Address: University of Manchester, AV Hill Building, Oxford Road, Manchester, M13 9PT, United Kingdom Telephone: +44 161 275 5768; +44 161 701 0240 Word count: 4,490 Number of tables: 1, Number of figures: 6 Running title: Metabolic dysfunction in diabetic neuropathy 1 Diabetes Publish Ahead of Print, published online October 15, 2015 Diabetes Page 2 of 255 Abstract High glucose levels in the peripheral nervous system (PNS) have been implicated in the pathogenesis of diabetic neuropathy (DN). However our understanding of the molecular mechanisms which cause the marked distal pathology is incomplete. Here we performed a comprehensive, system-wide analysis of the PNS of a rodent model of DN.
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  • Cellular and Molecular Signatures in the Disease Tissue of Early
    Cellular and Molecular Signatures in the Disease Tissue of Early Rheumatoid Arthritis Stratify Clinical Response to csDMARD-Therapy and Predict Radiographic Progression Frances Humby1,* Myles Lewis1,* Nandhini Ramamoorthi2, Jason Hackney3, Michael Barnes1, Michele Bombardieri1, Francesca Setiadi2, Stephen Kelly1, Fabiola Bene1, Maria di Cicco1, Sudeh Riahi1, Vidalba Rocher-Ros1, Nora Ng1, Ilias Lazorou1, Rebecca E. Hands1, Desiree van der Heijde4, Robert Landewé5, Annette van der Helm-van Mil4, Alberto Cauli6, Iain B. McInnes7, Christopher D. Buckley8, Ernest Choy9, Peter Taylor10, Michael J. Townsend2 & Costantino Pitzalis1 1Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK. Departments of 2Biomarker Discovery OMNI, 3Bioinformatics and Computational Biology, Genentech Research and Early Development, South San Francisco, California 94080 USA 4Department of Rheumatology, Leiden University Medical Center, The Netherlands 5Department of Clinical Immunology & Rheumatology, Amsterdam Rheumatology & Immunology Center, Amsterdam, The Netherlands 6Rheumatology Unit, Department of Medical Sciences, Policlinico of the University of Cagliari, Cagliari, Italy 7Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow G12 8TA, UK 8Rheumatology Research Group, Institute of Inflammation and Ageing (IIA), University of Birmingham, Birmingham B15 2WB, UK 9Institute of
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  • Human Induced Pluripotent Stem Cell–Derived Podocytes Mature Into Vascularized Glomeruli Upon Experimental Transplantation
    BASIC RESEARCH www.jasn.org Human Induced Pluripotent Stem Cell–Derived Podocytes Mature into Vascularized Glomeruli upon Experimental Transplantation † Sazia Sharmin,* Atsuhiro Taguchi,* Yusuke Kaku,* Yasuhiro Yoshimura,* Tomoko Ohmori,* ‡ † ‡ Tetsushi Sakuma, Masashi Mukoyama, Takashi Yamamoto, Hidetake Kurihara,§ and | Ryuichi Nishinakamura* *Department of Kidney Development, Institute of Molecular Embryology and Genetics, and †Department of Nephrology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan; ‡Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Hiroshima, Japan; §Division of Anatomy, Juntendo University School of Medicine, Tokyo, Japan; and |Japan Science and Technology Agency, CREST, Kumamoto, Japan ABSTRACT Glomerular podocytes express proteins, such as nephrin, that constitute the slit diaphragm, thereby contributing to the filtration process in the kidney. Glomerular development has been analyzed mainly in mice, whereas analysis of human kidney development has been minimal because of limited access to embryonic kidneys. We previously reported the induction of three-dimensional primordial glomeruli from human induced pluripotent stem (iPS) cells. Here, using transcription activator–like effector nuclease-mediated homologous recombination, we generated human iPS cell lines that express green fluorescent protein (GFP) in the NPHS1 locus, which encodes nephrin, and we show that GFP expression facilitated accurate visualization of nephrin-positive podocyte formation in
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  • Discovery of a Molecular Glue That Enhances Uprmt to Restore
    bioRxiv preprint doi: https://doi.org/10.1101/2021.02.17.431525; this version posted February 17, 2021. 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. Title: Discovery of a molecular glue that enhances UPRmt to restore proteostasis via TRKA-GRB2-EVI1-CRLS1 axis Authors: Li-Feng-Rong Qi1, 2 †, Cheng Qian1, †, Shuai Liu1, 2†, Chao Peng3, 4, Mu Zhang1, Peng Yang1, Ping Wu3, 4, Ping Li1 and Xiaojun Xu1, 2 * † These authors share joint first authorship Running title: Ginsenoside Rg3 reverses Parkinson’s disease model by enhancing mitochondrial UPR Affiliations: 1 State Key Laboratory of Natural Medicines, China Pharmaceutical University, 210009, Nanjing, Jiangsu, China. 2 Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases, China Pharmaceutical University, 210009, Nanjing, Jiangsu, China. 3. National Facility for Protein Science in Shanghai, Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Science, Shanghai 201210, China 4. Shanghai Science Research Center, Chinese Academy of Sciences, Shanghai, 201204, China. Corresponding author: Ping Li, State Key Laboratory of Natural Medicines, China Pharmaceutical University, 210009, Nanjing, Jiangsu, China. Email: [email protected], Xiaojun Xu, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases, China Pharmaceutical University, 210009, Nanjing, Jiangsu, China. Telephone number: +86-2583271203, E-mail: [email protected]. bioRxiv preprint doi: https://doi.org/10.1101/2021.02.17.431525; this version posted February 17, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder.
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  • A Genome-Wide Rnai Screen Identifies Multiple Synthetic Lethal
    A Genome-wide RNAi Screen Identifies Multiple Synthetic Lethal Interactions with the Ras Oncogene Ji Luo,1 Michael J. Emanuele,1 Danan Li,2 Chad J. Creighton,3 Michael R. Schlabach,1 Thomas F. Westbrook,4 Kwok-Kin Wong,2 and Stephen J. Elledge1,* 1Howard Hughes Medical Institute and Department of Genetics, Harvard Medical School, Division of Genetics, Brigham and Women’s Hospital 2Department of Medicine, Harvard Medical School and Department of Medical Oncology, Dana Farber Cancer Center, Ludwig Center at Dana-Farber/Harvard Cancer Center Boston, MA 02115, USA 3Dan L. Duncan Cancer Center Division of Biostatistics 4Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Department of Molecular and Human Genetics, Dan L. Duncan Cancer Center Baylor College of Medicine, Houston, TX 77030, USA *Correspondence: [email protected] DOI 10.1016/j.cell.2009.05.006 SUMMARY (Ngo et al., 2006; Schlabach et al., 2008; Silva et al., 2008). We have developed barcoded, retroviral/lentiviral-based short Oncogenic mutations in the small GTPase Ras are hairpin RNA (shRNA) libraries targeting the entire human genome highly prevalent in cancer, but an understanding of to enable genome-wide loss-of-function analysis through stable the vulnerabilities of these cancers is lacking. We gene knockdown (Silva et al., 2005). Our design also allowed undertook a genome-wide RNAi screen to identify us to use microarray deconvolution to develop a multiplex synthetic lethal interactions with the KRAS onco- screening platform that enables the highly parallel screening gene. We discovered a diverse set of proteins whose of >10,000 shRNAs in a pool-based format (Schlabach et al., 2008; Silva et al., 2008).
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  • The Ubiquitin-Proteasome System
    Review The ubiquitin-proteasome system DIPANKAR NANDI*, PANKAJ TAHILIANI, ANUJITH KUMAR and DILIP CHANDU Department of Biochemistry, Indian Institute of Science, Bangalore 560 012, India *Corresponding author (Fax, 91-80-23600814; Email, [email protected]) The 2004 Nobel Prize in chemistry for the discovery of protein ubiquitination has led to the recognition of cellular proteolysis as a central area of research in biology. Eukaryotic proteins targeted for degradation by this pathway are first ‘tagged’ by multimers of a protein known as ubiquitin and are later proteolyzed by a giant enzyme known as the proteasome. This article recounts the key observations that led to the discovery of ubiquitin-proteasome system (UPS). In addition, different aspects of proteasome biology are highlighted. Finally, some key roles of the UPS in different areas of biology and the use of inhibitors of this pathway as possible drug targets are discussed. [Nandi D, Tahiliani P, Kumar A and Chandu D 2006 The ubiquitin-proteasome system; J. Biosci. 31 137–155] 1. Introduction biological processes, e.g. transcription, cell cycle, antigen processing, cellular defense, signalling etc. is now well In an incisive article, J Goldstein, the 1985 Nobel laureate established (Ciechanover and Iwai 2004; Varshavsky 2005). for the regulation of cholesterol metabolism (together with During the early days in the field of cytosolic protein M Brown) and Chair for the Jury for the Lasker awards, degradation, cell biologists were intrigued by the requirement laments the fact that it is hard to pick out truly original dis- of ATP in this process as it is well known that peptide bond coveries among the plethora of scientific publications hydrolysis does not require metabolic energy.
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  • Structural Insights Into Substrate Recognition and Processing by the 20S Proteasome
    biomolecules Review Structural Insights into Substrate Recognition and Processing by the 20S Proteasome Indrajit Sahu * and Michael H. Glickman * Faculty of Biology, Technion-Israel Institute of Technology, 32000 Haifa, Israel * Correspondence: [email protected] (I.S.); [email protected] (M.H.G.); Tel.: +972-0586747499 (I.S.); +972-4-829-4552 (M.H.G.) Abstract: Four decades of proteasome research have yielded extensive information on ubiquitin- dependent proteolysis. The archetype of proteasomes is a 20S barrel-shaped complex that does not rely on ubiquitin as a degradation signal but can degrade substrates with a considerable unstructured stretch. Since roughly half of all proteasomes in most eukaryotic cells are free 20S complexes, ubiquitin-independent protein degradation may coexist with ubiquitin-dependent degradation by the highly regulated 26S proteasome. This article reviews recent advances in our understanding of the biochemical and structural features that underlie the proteolytic mechanism of 20S proteasomes. The two outer α-rings of 20S proteasomes provide a number of potential docking sites for loosely folded polypeptides. The binding of a substrate can induce asymmetric conformational changes, trigger gate opening, and initiate its own degradation through a protease-driven translocation mechanism. Consequently, the substrate translocates through two additional narrow apertures augmented by the β-catalytic active sites. The overall pulling force through the two annuli results in a protease-like unfolding of the substrate and subsequent proteolysis in the catalytic chamber. Although both proteasomes contain identical β-catalytic active sites, the differential translocation mechanisms yield distinct peptide products. Nonoverlapping substrate repertoires and product outcomes rationalize cohabitation of both proteasome complexes in cells.
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  • The Role of the COP9 Signalosome and Neddylation in DNA Damage Signaling and Repair
    Biomolecules 2015, 5, 2388-2416; doi:10.3390/biom5042388 OPEN ACCESS biomolecules ISSN 2218-273X www.mdpi.com/journal/biomolecules/ Review The Role of the COP9 Signalosome and Neddylation in DNA Damage Signaling and Repair Dudley Chung 1,† and Graham Dellaire 1,2,†,* 1 Department of Pathology, Dalhousie University, Halifax, NS B3H 4R2, Canada; E-Mail: [email protected] 2 Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada † These authors contributed equally to this work. * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +1-902-494-4730. Academic Editors: Wolf-Dietrich Heyer, Thomas Helleday and Fumio Hanaoka Received: 30 June 2015 / Accepted: 21 September 2015 / Published: 30 September 2015 Abstract: The maintenance of genomic integrity is an important process in organisms as failure to sense and repair damaged DNA can result in a variety of diseases. Eukaryotic cells have developed complex DNA repair response (DDR) mechanisms to accurately sense and repair damaged DNA. Post-translational modifications by ubiquitin and ubiquitin-like proteins, such as SUMO and NEDD8, have roles in coordinating the progression of DDR. Proteins in the neddylation pathway have also been linked to regulating DDR. Of interest is the COP9 signalosome (CSN), a multi-subunit metalloprotease present in eukaryotes that removes NEDD8 from cullins and regulates the activity of cullin-RING ubiquitin ligases (CRLs). This in turn regulates the stability and turnover of a host of CRL-targeted proteins, some of which have established roles in DDR. This review will summarize the current knowledge on the role of the CSN and neddylation in DNA repair.
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  • COP9 Signalosome Subunit 8 Is Required for Postnatal Hepatocyte Survival and Effective Proliferation
    Cell Death and Differentiation (2011) 18, 259–270 & 2011 Macmillan Publishers Limited All rights reserved 1350-9047/11 $32.00 www.nature.com/cdd COP9 signalosome subunit 8 is required for postnatal hepatocyte survival and effective proliferation D Lei1,2,FLi2,3,HSu1,2, Z Tian1,BYe3, N Wei4 and X Wang*,1,2 Studies using lower organisms and cultured mammalian cells have revealed that the COP9 signalosome (CSN) has important roles in multiple cellular processes. Conditional gene targeting was recently used to study CSN function in murine T-cell development and activation. Using the Cre-loxP system, here we have achieved postnatal hepatocyte-restricted knockout of the csn8 gene (HR-Csn8KO) in mice. The protein abundance of other seven CSN subunits was differentially downregulated by HR-Csn8KO and the deneddylation of all cullins examined was significantly impaired. Moreover, HR-Csn8KO-induced massive hepatocyte apoptosis and evoked extensive reparative responses in the liver, including marked intralobular proliferation of biliary lineage cells and trans-differentiation and proliferation of the oval cells. However, division of pre-existing hepatocytes was significantly diminished in HR-Csn8KO livers. These findings indicate that Csn8 is essential to the ability of mature hepatocytes to proliferate effectively in response to hepatic injury. The histopathological examinations revealed striking hepatocytomegaly in Csn8-deficient livers. The hepatocyte nuclei were dramatically enlarged and pleomorphic with hyperchromasia and prominent nucleoli, consistent with dysplasia or preneoplastic cellular alteration in HR-Csn8KO mice at 6 weeks. Pericellular and perisinusoid fibrosis with distorted architecture was also evident at 6 weeks. It is concluded that CSN8/CSN is essential to postnatal hepatocyte survival and effective proliferation.
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  • Electronic Supplementary Material (ESI) for Metallomics
    Electronic Supplementary Material (ESI) for Metallomics. This journal is © The Royal Society of Chemistry 2020 Manganese-induced neurotoxicity in cerebellar granule neurons due to perturbation of cell network pathways with potential implications for neurodegenerative disorders Raúl Bonne Hernández1,6,7*@, Montserrat Carrascal2*, Joaquin Abian2, Bernhard Michalke3, Marcelo Farina4, Yasmilde Rodriguez Gonzalez5, Grace O. Iyirhiaro5, Houman Moteshareie6 Daniel Burnside6 Ashkan Golshani6, Cristina Suñol7@ 1Laboratory of Bioinorganic and Environmental Toxicology – LABITA. Department of Exact and Earth Sciences. Federal University of São Paulo. Rua Prof. Artur Riedel, 275, CEP: 09972-270. Diadema-SP, Brazil. 2CSIC/UAB Proteomics Laboratory, Institut d’Investigacions Biomèdiques de Barcelona, IIBB-CSIC, IDIBAPS, Barcelona, Spain. 3Helmholtz Zentrum München GmbH, German Research Center for Environmental Health, Research Unit Analytical BioGeoChemistry, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany. 4 Departamento de Bioquímica, Centro de Ciências Biológicas, Campus Universitário, Trindade, Bloco C. Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, CEP 88040-900, Brazil. 5Department of Cellular and Molecular Medicine, Faculty of Medicine. University of Ottawa 451 Smyth Road, Ottawa, ON, K1H 8M5 6Department of Biology. Carleton University. 209 Nesbitt Biology Building. 1125 Colonel by Drive. Ottawa, ON, K1S 5B6 7Department of Neurochemistry and Neuropharmacology. Institut d’Investigacions Biomèdiques de Barcelona, IIBB-CSIC,
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  • An Organelle-Specific Protein Landscape Identifies
    ARTICLE Received 15 Feb 2016 | Accepted 1 Apr 2016 | Published 13 May 2016 DOI: 10.1038/ncomms11491 OPEN An organelle-specific protein landscape identifies novel diseases and molecular mechanisms Karsten Boldt1,*, Jeroen van Reeuwijk2,*, Qianhao Lu3,4,*, Konstantinos Koutroumpas5,*, Thanh-Minh T. Nguyen2, Yves Texier1,6, Sylvia E.C. van Beersum2, Nicola Horn1, Jason R. Willer7, Dorus A. Mans2, Gerard Dougherty8, Ideke J.C. Lamers2, Karlien L.M. Coene2, Heleen H. Arts2, Matthew J. Betts3,4, Tina Beyer1, Emine Bolat2, Christian Johannes Gloeckner9, Khatera Haidari10, Lisette Hetterschijt11, Daniela Iaconis12, Dagan Jenkins13, Franziska Klose1, Barbara Knapp14, Brooke Latour2, Stef J.F. Letteboer2, Carlo L. Marcelis2, Dragana Mitic15, Manuela Morleo12,16, Machteld M. Oud2, Moniek Riemersma2, Susan Rix13, Paulien A. Terhal17, Grischa Toedt18, Teunis J.P. van Dam19, Erik de Vrieze11, Yasmin Wissinger1, Ka Man Wu2, UK10K Rare Diseases Group#, Gordana Apic15, Philip L. Beales13, Oliver E. Blacque20, Toby J. Gibson18, Martijn A. Huynen19, Nicholas Katsanis7, Hannie Kremer11, Heymut Omran8, Erwin van Wijk11, Uwe Wolfrum14, Franc¸ois Kepes5, Erica E. Davis7, Brunella Franco12,16, Rachel H. Giles10, Marius Ueffing1,*, Robert B. Russell3,4,* & Ronald Roepman2,* Cellular organelles provide opportunities to relate biological mechanisms to disease. Here we use affinity proteomics, genetics and cell biology to interrogate cilia: poorly understood organelles, where defects cause genetic diseases. Two hundred and seventeen tagged human ciliary proteins create a final landscape of 1,319 proteins, 4,905 interactions and 52 complexes. Reverse tagging, repetition of purifications and statistical analyses, produce a high-resolution network that reveals organelle- specific interactions and complexes not apparent in larger studies, and links vesicle transport, the cytoskeleton, signalling and ubiquitination to ciliary signalling and proteostasis.
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