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Klaudel J, Trenkner W, Pawłowski K, Radowski P, Surman D, Ziniewicz B, Smolarczyk M, Kossakowska-Jemioło U, Krasowski W. Large-bore SOFIA catheter for bailout thrombus aspiration in STEMI. Cardiol J 2024; 31:352-354. [PMID: 38686985 DOI: 10.5603/cj.95375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 01/14/2024] [Accepted: 04/10/2024] [Indexed: 05/02/2024] Open
Affiliation(s)
- Jacek Klaudel
- Department of Cardiology, St. Adalbert's Hospital in Gdansk, Copernicus PL, Gdansk, Poland.
| | - Wojciech Trenkner
- Department of Cardiology, St. Adalbert's Hospital in Gdansk, Copernicus PL, Gdansk, Poland
| | - Krzysztof Pawłowski
- Department of Cardiology, St. Adalbert's Hospital in Gdansk, Copernicus PL, Gdansk, Poland
- Department of Cardiology and Interventional Angiology, Kashubian Center for Heart and Vascular Diseases in Wejherowo, Poland
| | - Piotr Radowski
- Department of Cardiology, St. Adalbert's Hospital in Gdansk, Copernicus PL, Gdansk, Poland
| | - Dariusz Surman
- Department of Cardiology, St. Adalbert's Hospital in Gdansk, Copernicus PL, Gdansk, Poland
| | - Bartłomiej Ziniewicz
- Department of Cardiology, St. Adalbert's Hospital in Gdansk, Copernicus PL, Gdansk, Poland
| | - Michał Smolarczyk
- Department of Cardiology, St. Adalbert's Hospital in Gdansk, Copernicus PL, Gdansk, Poland
| | | | - Włodzimierz Krasowski
- Department of Cardiology, St. Adalbert's Hospital in Gdansk, Copernicus PL, Gdansk, Poland
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2
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Baranowski B, Pawłowski K. Protein family neighborhood analyzer-ProFaNA. PeerJ 2023; 11:e15715. [PMID: 37492397 PMCID: PMC10364804 DOI: 10.7717/peerj.15715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 06/16/2023] [Indexed: 07/27/2023] Open
Abstract
Background Functionally related genes are well known to be often grouped in close vicinity in the genomes, particularly in prokaryotes. Notwithstanding the diverse evolutionary mechanisms leading to this phenomenon, it can be used to predict functions of uncharacterized genes. Methods Here, we provide a simple but robust statistical approach that leverages the vast amounts of genomic data available today. Considering a protein domain as a functional unit, one can explore other functional units (domains) that significantly often occur within the genomic neighborhoods of the queried domain. This analysis can be performed across different taxonomic levels. Provisions can also be made to correct for the uneven sampling of the taxonomic space by genomic sequencing projects that often focus on large numbers of very closely related strains, e.g., pathogenic ones. To this end, an optional procedure for averaging occurrences within subtaxa is available. Results Several examples show this approach can provide useful functional predictions for uncharacterized gene families, and how to combine this information with other approaches. The method is made available as a web server at http://bioinfo.sggw.edu.pl/neighborhood_analysis.
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Affiliation(s)
- Bartosz Baranowski
- Department of Biochemistry and Microbiology, Warsaw University of Life Sciences, Warszawa, Poland
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warszawa, Poland
| | - Krzysztof Pawłowski
- Department of Biochemistry and Microbiology, Warsaw University of Life Sciences, Warszawa, Poland
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas, United States
- Department of Translational Sciences, Lund University, Lund, Sweden
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3
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Torosyan H, Paul MD, Forget A, Lo M, Diwanji D, Pawłowski K, Krogan NJ, Jura N, Verba KA. Structural insights into regulation of the PEAK3 pseudokinase scaffold by 14-3-3. Nat Commun 2023; 14:3543. [PMID: 37336883 PMCID: PMC10279700 DOI: 10.1038/s41467-023-38864-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 05/16/2023] [Indexed: 06/21/2023] Open
Abstract
PEAK pseudokinases are molecular scaffolds which dimerize to regulate cell migration, morphology, and proliferation, as well as cancer progression. The mechanistic role dimerization plays in PEAK scaffolding remains unclear, as there are no structures of PEAKs in complex with their interactors. Here, we report the cryo-EM structure of dimeric PEAK3 in complex with an endogenous 14-3-3 heterodimer. Our structure reveals an asymmetric binding mode between PEAK3 and 14-3-3 stabilized by one pseudokinase domain and the SHED domain of the PEAK3 dimer. The binding interface contains a canonical phosphosite-dependent primary interaction and a unique secondary interaction not observed in previous structures of 14-3-3/client complexes. Additionally, we show that PKD regulates PEAK3/14-3-3 binding, which when prevented leads to PEAK3 nuclear enrichment and distinct protein-protein interactions. Altogether, our data demonstrate that PEAK3 dimerization forms an unusual secondary interface for 14-3-3 binding, facilitating 14-3-3 regulation of PEAK3 localization and interactome diversity.
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Affiliation(s)
- Hayarpi Torosyan
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, 94158, USA
- Biophysics Graduate Program, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Michael D Paul
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Antoine Forget
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Megan Lo
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Devan Diwanji
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, 94158, USA
- Medical Scientist Training Program, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Krzysztof Pawłowski
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- Department of Biochemistry and Microbiology, Warsaw University of Life Sciences, 02-787, Warszawa, Poland
| | - Nevan J Krogan
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
| | - Natalia Jura
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, 94158, USA.
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA.
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA.
| | - Kliment A Verba
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA.
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA.
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4
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Shekhar S, Moehlman AT, Park B, Ewnetu M, Tracy C, Titos I, Pawłowski K, Tagliabracci VS, Krämer H. Allnighter pseudokinase-mediated feedback links proteostasis and sleep in Drosophila. Nat Commun 2023; 14:2932. [PMID: 37217484 DOI: 10.1038/s41467-023-38485-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 05/04/2023] [Indexed: 05/24/2023] Open
Abstract
In nervous systems, retrograde signals are key for organizing circuit activity and maintaining neuronal homeostasis. We identify the conserved Allnighter (Aln) pseudokinase as a cell non-autonomous regulator of proteostasis responses necessary for normal sleep and structural plasticity of Drosophila photoreceptors. In aln mutants exposed to extended ambient light, proteostasis is dysregulated and photoreceptors develop striking, but reversible, dysmorphology. The aln gene is widely expressed in different neurons, but not photoreceptors. However, secreted Aln protein is retrogradely endocytosed by photoreceptors. Inhibition of photoreceptor synaptic release reduces Aln levels in lamina neurons, consistent with secreted Aln acting in a feedback loop. In addition, aln mutants exhibit reduced night time sleep, providing a molecular link between dysregulated proteostasis and sleep, two characteristics of ageing and neurodegenerative diseases.
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Affiliation(s)
- Shashank Shekhar
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX; O'Donnell Brain Institute, Dallas, USA.
| | - Andrew T Moehlman
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX; O'Donnell Brain Institute, Dallas, USA
- Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Brenden Park
- Department of Molecular Biology UT Southwestern Medical Center, Dallas, TX, USA
| | - Michael Ewnetu
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX; O'Donnell Brain Institute, Dallas, USA
| | - Charles Tracy
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX; O'Donnell Brain Institute, Dallas, USA
| | - Iris Titos
- Molecular Medicine Program, University of Utah, School of Medicine, Salt Lake City, UT, USA
| | - Krzysztof Pawłowski
- Department of Molecular Biology UT Southwestern Medical Center, Dallas, TX, USA
- Department of Biochemistry and Microbiology, Institute of Biology, Warsaw University of Life Sciences, Warsaw, 02-776, Poland
| | - Vincent S Tagliabracci
- Department of Molecular Biology UT Southwestern Medical Center, Dallas, TX, USA
- Howard Hughes Medical Institute, Maryland, USA
| | - Helmut Krämer
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX; O'Donnell Brain Institute, Dallas, USA.
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX, USA.
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5
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Kopyciński J, Łebek M, Górecki W, Pawłowski K. Ultrawide Dark Solitons and Droplet-Soliton Coexistence in a Dipolar Bose Gas with Strong Contact Interactions. Phys Rev Lett 2023; 130:043401. [PMID: 36763437 DOI: 10.1103/physrevlett.130.043401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 11/10/2022] [Accepted: 12/19/2022] [Indexed: 06/18/2023]
Abstract
We look into dark solitons in a quasi-1D dipolar Bose gas and in a quantum droplet. We derive the analytical solitonic solution of a Gross-Pitaevskii-like equation accounting for beyond mean-field effects. The results show there is a certain critical value of the dipolar interactions, for which the width of a motionless soliton diverges. Moreover, there is a peculiar solution of the motionless soliton with a nonzero density minimum. We also present the energy spectrum of these solitons with an additional excitation subbranch appearing. Finally, we perform a series of numerical experiments revealing the coexistence of a dark soliton inside a quantum droplet.
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Affiliation(s)
- Jakub Kopyciński
- Center for Theoretical Physics, Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw, Poland
| | - Maciej Łebek
- Center for Theoretical Physics, Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw, Poland
| | - Wojciech Górecki
- Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland
| | - Krzysztof Pawłowski
- Center for Theoretical Physics, Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw, Poland
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6
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Pawłowski K, Dziadkiewicz A, Podlasek A, Klaudel J, Mączkowiak A, Szołkiewicz M. Thrombectomy-Capable Stroke Centre-A Key to Acute Stroke Care System Improvement? Retrospective Analysis of Safety and Efficacy of Endovascular Treatment in Cardiac Cathlab. Int J Environ Res Public Health 2023; 20:2232. [PMID: 36767599 PMCID: PMC9915992 DOI: 10.3390/ijerph20032232] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/16/2023] [Accepted: 01/24/2023] [Indexed: 06/18/2023]
Abstract
The optimal structure of the acute ischaemic stroke treatment network is unknown and eagerly sought. To make it most effective, different treatment and transportation strategies have been developed and investigated worldwide. Since only a fraction of acute stroke patients with large vessel occlusion are treated, a new entity-thrombectomy-capable stroke centre (TCSC)-was introduced to respond to the growing demand for timely endovascular treatment. The purpose of this study was to present the early experience of the first 70 patients treated by mechanical means in a newly developed cardiac Cathlab-based TCSC. The essential safety and efficacy measures were recorded and compared with those reported in the invasive arm of the HERMES meta-analysis-the largest published dataset on the subject. We found no significant differences in terms of clinical and safety outcomes, such as early neurological recovery, level of functional independence at 90 days, symptomatic intracranial haemorrhage, parenchymal haematoma type 2, and mortality. These encouraging results obtained in the small endovascular centre may be an argument for the introduction of the TCSC into operating stroke networks to increase patient access to timely treatment and to improve clinical outcomes.
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Affiliation(s)
- Krzysztof Pawłowski
- Department of Cardiology and Interventional Angiology, Kashubian Center for Heart and Vascular Diseases, Pomeranian Hospitals, 84-200 Wejherowo, Poland
| | - Artur Dziadkiewicz
- Department of Neurology and Stroke, Pomeranian Hospitals, 84-200 Wejherowo, Poland
| | - Anna Podlasek
- Tayside Innovation Medtech Ecosystem (TIME), University of Dundee, Dundee DD1 4HN, UK
- Precision Imaging Beacon, Radiological Sciences, University of Nottingham, Nottingham NG7 2RD, UK
| | - Jacek Klaudel
- Department of Invasive Cardiology, St. Adalbert’s Hospital, Copernicus PL, 80-070 Gdansk, Poland
| | - Alicja Mączkowiak
- Department of Neurology and Stroke, Pomeranian Hospitals, 84-200 Wejherowo, Poland
| | - Marek Szołkiewicz
- Department of Cardiology and Interventional Angiology, Kashubian Center for Heart and Vascular Diseases, Pomeranian Hospitals, 84-200 Wejherowo, Poland
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7
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Krysińska M, Baranowski B, Deszcz B, Pawłowski K, Gradowski M. Pan-kinome of Legionella expanded by a bioinformatics survey. Sci Rep 2022; 12:21782. [PMID: 36526881 PMCID: PMC9758233 DOI: 10.1038/s41598-022-26109-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022] Open
Abstract
The pathogenic Legionella bacteria are notorious for delivering numerous effector proteins into the host cell with the aim of disturbing and hijacking cellular processes for their benefit. Despite intensive studies, many effectors remain uncharacterized. Motivated by the richness of Legionella effector repertoires and their oftentimes atypical biochemistry, also by several known atypical Legionella effector kinases and pseudokinases discovered recently, we undertook an in silico survey and exploration of the pan-kinome of the Legionella genus, i.e., the union of the kinomes of individual species. In this study, we discovered 13 novel (pseudo)kinase families (all are potential effectors) with the use of non-standard bioinformatic approaches. Together with 16 known families, we present a catalog of effector and non-effector protein kinase-like families within Legionella, available at http://bioinfo.sggw.edu.pl/kintaro/ . We analyze and discuss the likely functional roles of the novel predicted kinases. Notably, some of the kinase families are also present in other bacterial taxa, including other pathogens, often phylogenetically very distant from Legionella. This work highlights Nature's ingeniousness in the pathogen-host arms race and offers a useful resource for the study of infection mechanisms.
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Affiliation(s)
- Marianna Krysińska
- grid.13276.310000 0001 1955 7966Department of Biochemistry and Microbiology, Warsaw University of Life Sciences — SGGW, Warsaw, Poland
| | - Bartosz Baranowski
- grid.413454.30000 0001 1958 0162Laboratory of Plant Pathogenesis, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Bartłomiej Deszcz
- grid.13276.310000 0001 1955 7966Department of Biochemistry and Microbiology, Warsaw University of Life Sciences — SGGW, Warsaw, Poland
| | - Krzysztof Pawłowski
- grid.13276.310000 0001 1955 7966Department of Biochemistry and Microbiology, Warsaw University of Life Sciences — SGGW, Warsaw, Poland ,grid.267313.20000 0000 9482 7121Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX USA ,grid.4514.40000 0001 0930 2361Department of Translational Medicine, Lund University, Lund, Sweden ,grid.413575.10000 0001 2167 1581Howard Hughes Medical Institute, Dallas, TX, USA
| | - Marcin Gradowski
- grid.13276.310000 0001 1955 7966Department of Biochemistry and Microbiology, Warsaw University of Life Sciences — SGGW, Warsaw, Poland
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8
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Lüscher B, Ahel I, Altmeyer M, Ashworth A, Bai P, Chang P, Cohen M, Corda D, Dantzer F, Daugherty MD, Dawson TM, Dawson VL, Deindl S, Fehr AR, Feijs KLH, Filippov DV, Gagné JP, Grimaldi G, Guettler S, Hoch NC, Hottiger MO, Korn P, Kraus WL, Ladurner A, Lehtiö L, Leung AKL, Lord CJ, Mangerich A, Matic I, Matthews J, Moldovan GL, Moss J, Natoli G, Nielsen ML, Niepel M, Nolte F, Pascal J, Paschal BM, Pawłowski K, Poirier GG, Smith S, Timinszky G, Wang ZQ, Yélamos J, Yu X, Zaja R, Ziegler M. ADP-ribosyltransferases, an update on function and nomenclature. FEBS J 2022; 289:7399-7410. [PMID: 34323016 PMCID: PMC9027952 DOI: 10.1111/febs.16142] [Citation(s) in RCA: 123] [Impact Index Per Article: 61.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/23/2021] [Accepted: 07/27/2021] [Indexed: 01/13/2023]
Abstract
ADP-ribosylation, a modification of proteins, nucleic acids, and metabolites, confers broad functions, including roles in stress responses elicited, for example, by DNA damage and viral infection and is involved in intra- and extracellular signaling, chromatin and transcriptional regulation, protein biosynthesis, and cell death. ADP-ribosylation is catalyzed by ADP-ribosyltransferases (ARTs), which transfer ADP-ribose from NAD+ onto substrates. The modification, which occurs as mono- or poly-ADP-ribosylation, is reversible due to the action of different ADP-ribosylhydrolases. Importantly, inhibitors of ARTs are approved or are being developed for clinical use. Moreover, ADP-ribosylhydrolases are being assessed as therapeutic targets, foremost as antiviral drugs and for oncological indications. Due to the development of novel reagents and major technological advances that allow the study of ADP-ribosylation in unprecedented detail, an increasing number of cellular processes and pathways are being identified that are regulated by ADP-ribosylation. In addition, characterization of biochemical and structural aspects of the ARTs and their catalytic activities have expanded our understanding of this protein family. This increased knowledge requires that a common nomenclature be used to describe the relevant enzymes. Therefore, in this viewpoint, we propose an updated and broadly supported nomenclature for mammalian ARTs that will facilitate future discussions when addressing the biochemistry and biology of ADP-ribosylation. This is combined with a brief description of the main functions of mammalian ARTs to illustrate the increasing diversity of mono- and poly-ADP-ribose mediated cellular processes.
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Affiliation(s)
- Bernhard Lüscher
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Germany
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, UK
| | - Matthias Altmeyer
- Department of Molecular Mechanisms of Disease, University of Zurich, Switzerland
| | - Alan Ashworth
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA
| | - Peter Bai
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, Hungary
| | | | - Michael Cohen
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, OR, USA
| | - Daniela Corda
- Department of Biomedical Sciences, National Research Council, Rome, Italy
| | | | - Matthew D Daugherty
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Ted M Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Valina L Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sebastian Deindl
- Department of Cell and Molecular Biology, Uppsala University, Sweden
| | - Anthony R Fehr
- Department of Molecular Biosciences, The University of Kansas, Lawrence, KS, USA
| | - Karla L H Feijs
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Germany
| | | | - Jean-Philippe Gagné
- Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Laval University, Quebec City, QC, Canada
| | | | - Sebastian Guettler
- Divisions of Structural Biology and Cancer Biology, The Institute of Cancer Research (ICR), London, UK
| | - Nicolas C Hoch
- Department of Biochemistry, University of São Paulo, Brazil
| | - Michael O Hottiger
- Department of Molecular Mechanisms of Disease, University of Zurich, Switzerland
| | - Patricia Korn
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Germany
| | - W Lee Kraus
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Andreas Ladurner
- Department of Physiological Chemistry, Ludwig-Maximilians-University of Munich, Planegg-Martinsried, Germany
| | - Lari Lehtiö
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Finland
| | - Anthony K L Leung
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Christopher J Lord
- CRUK Gene Function Laboratory, The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | | | - Ivan Matic
- Max Planck Institute for Biology of Ageing, Cologne, Germany
- Cologne Excellence Cluster for Stress Responses in Ageing-Associated Diseases (CECAD), University of Cologne, Germany
| | - Jason Matthews
- Institute of Basic Medical Sciences, University of Oslo, Norway
| | - George-Lucian Moldovan
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Joel Moss
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Gioacchino Natoli
- Department of Experimental Oncology, European Institute of Oncology (IEO), Milan, Italy
| | - Michael L Nielsen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | | | - Friedrich Nolte
- Institut für Immunologie, Universitätsklinikum Hamburg-Eppendorf, Germany
| | - John Pascal
- Biochemistry and Molecular Medicine, Université de Montréal, Canada
| | - Bryce M Paschal
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - Krzysztof Pawłowski
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Guy G Poirier
- Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Laval University, Quebec City, QC, Canada
| | - Susan Smith
- Department of Pathology, Kimmel Center for Biology and Medicine at the Skirball Institute, New York University School of Medicine, NY, USA
| | - Gyula Timinszky
- Lendület Laboratory of DNA Damage and Nuclear Dynamics, Institute of Genetics, Biological Research Centre, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Zhao-Qi Wang
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany
- Faculty of Biological Sciences, Friedrich-Schiller University of Jena, Germany
| | - José Yélamos
- Cancer Research Program, Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
| | - Xiaochun Yu
- School of Life Sciences, Westlake University, Hangzhou, China
| | - Roko Zaja
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Germany
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9
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Klaudel J, Trenkner W, Pawłowski K, Surman D, Radowski P, Krasowski W, Szołkiewicz M. Neurointerventional tools and techniques for coronary thrombus removal. A case-based review. J Cardiol Cases 2022; 26:407-411. [PMID: 36506496 PMCID: PMC9727564 DOI: 10.1016/j.jccase.2022.08.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 07/21/2022] [Accepted: 08/09/2022] [Indexed: 12/15/2022] Open
Abstract
Due to the negative results of randomized aspiration thrombectomy studies, its role in myocardial infarction has been limited to high thrombus burden and/or failed vessel recanalization, with little technological advancement over the last years. In contrast, there has been rapid progress in mechanical thrombectomy in stroke, which is understandable as most ischemic cerebrovascular accidents have an embolic etiology.We present three transradial procedures wherein neurointerventional catheters were used as a first-line device for en bloc removal of large clots lodged distally in tortuous coronary anatomy. First-pass reperfusion was achieved in all the cases, without dissection, distal embolization, or the no reflow phenomenon. Learning objective In the case of large clots, where coronary aspiration devices fail, neurointerventional catheters may be considered as a rescue strategy. They provide large aspiration lumen and excellent trackability with atraumatic design. Many other neurointerventional techniques can be easily adopted into the coronary armamentarium, possibly increasing the safety and efficacy of thrombus aspiration.
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Affiliation(s)
- Jacek Klaudel
- Department of Invasive Cardiology and Interventional Radiology, St. Adalbert's Hospital, Copernicus Podmiot Leczniczy Sp. z o.o., Gdansk, Poland
- Corresponding author at: Karłowicza 70, 80-275 Gdańsk, Poland.
| | - Wojciech Trenkner
- Department of Invasive Cardiology and Interventional Radiology, St. Adalbert's Hospital, Copernicus Podmiot Leczniczy Sp. z o.o., Gdansk, Poland
| | - Krzysztof Pawłowski
- Department of Cardiology and Interventional Angiology, Kashubian Center for Heart and Vascular Diseases, Pomeranian Hospitals, Wejherowo, Poland
| | - Dariusz Surman
- Department of Invasive Cardiology and Interventional Radiology, St. Adalbert's Hospital, Copernicus Podmiot Leczniczy Sp. z o.o., Gdansk, Poland
| | - Piotr Radowski
- Department of Invasive Cardiology and Interventional Radiology, St. Adalbert's Hospital, Copernicus Podmiot Leczniczy Sp. z o.o., Gdansk, Poland
| | - Włodzimierz Krasowski
- Department of Invasive Cardiology and Interventional Radiology, St. Adalbert's Hospital, Copernicus Podmiot Leczniczy Sp. z o.o., Gdansk, Poland
| | - Marek Szołkiewicz
- Department of Cardiology and Interventional Angiology, Kashubian Center for Heart and Vascular Diseases, Pomeranian Hospitals, Wejherowo, Poland
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10
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Park GJ, Osinski A, Hernandez G, Eitson JL, Majumdar A, Tonelli M, Henzler-Wildman K, Pawłowski K, Chen Z, Li Y, Schoggins JW, Tagliabracci VS. The mechanism of RNA capping by SARS-CoV-2. Nature 2022; 609:793-800. [PMID: 35944563 PMCID: PMC9492545 DOI: 10.1038/s41586-022-05185-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 08/03/2022] [Indexed: 11/29/2022]
Abstract
The RNA genome of SARS-CoV-2 contains a 5′ cap that facilitates the translation of viral proteins, protection from exonucleases and evasion of the host immune response1–4. How this cap is made in SARS-CoV-2 is not completely understood. Here we reconstitute the N7- and 2′-O-methylated SARS-CoV-2 RNA cap (7MeGpppA2′-O-Me) using virally encoded non-structural proteins (nsps). We show that the kinase-like nidovirus RdRp-associated nucleotidyltransferase (NiRAN) domain5 of nsp12 transfers the RNA to the amino terminus of nsp9, forming a covalent RNA–protein intermediate (a process termed RNAylation). Subsequently, the NiRAN domain transfers the RNA to GDP, forming the core cap structure GpppA-RNA. The nsp146 and nsp167 methyltransferases then add methyl groups to form functional cap structures. Structural analyses of the replication–transcription complex bound to nsp9 identified key interactions that mediate the capping reaction. Furthermore, we demonstrate in a reverse genetics system8 that the N terminus of nsp9 and the kinase-like active-site residues in the NiRAN domain are required for successful SARS-CoV-2 replication. Collectively, our results reveal an unconventional mechanism by which SARS-CoV-2 caps its RNA genome, thus exposing a new target in the development of antivirals to treat COVID-19. Reconstitution of the SARS-CoV-2 RNA 5′ cap reveals the unconventional mechanism by which SARS-CoV-2 caps its RNA genome, providing a new target in the development of antiviral agents to treat COVID-19.
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Affiliation(s)
- Gina J Park
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Adam Osinski
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Genaro Hernandez
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jennifer L Eitson
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Abir Majumdar
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Marco Tonelli
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Krzysztof Pawłowski
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Department of Biochemistry and Microbiology, Institute of Biology, Warsaw University of Life Sciences, Warsaw, Poland
| | - Zhe Chen
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yang Li
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - John W Schoggins
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Vincent S Tagliabracci
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA. .,Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas, USA. .,Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA. .,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas, USA.
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11
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Klaudel J, Glaza M, Klaudel B, Trenkner W, Pawłowski K, Szołkiewicz M. Catheter-induced coronary artery and aortic dissections. A study of the mechanisms, risk factors, and propagation causes. Cardiol J 2022:VM/OJS/J/86624. [PMID: 35762078 DOI: 10.5603/cj.a2022.0050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 02/06/2022] [Accepted: 05/10/2022] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Only the incidence, management, and prognosis of catheter-induced coronary artery and aortic dissections have been systematically studied until now. We sought to evaluate their mechanisms, risk factors, and propagation causes. METHODS Electronic databases containing 76,104 procedures and complication registries from 2000-2020 were searched and relevant cineangiographic studies adjudicated. RESULTS Ninety-six dissections were identified. The overall incidence was 0.126%, and 0.021% for aortic injuries. The in-hospital mortality rate was 4.2%, and 6.25% for aortic dissections. Compared to the non-complicated population, patients with dissection were more often female (48% vs. 34%, p = 0.004), with a higher prevalence of comorbidities such as hypertension (56% vs. 25%, p < 0.001) or chronic kidney disease (10% vs. 4%, p = 0.002). They more frequently presented with acute myocardial infarction (72% vs. 43%, p < 0.001), underwent percutaneous coronary intervention (85% vs. 39%, p < 0.001), and were examined with a radial approach (77% vs. 65%, p = 0.011). The most prevalent predisposing factor was small ostium diameter and/or atheroma. Deep intubation for support, catheter malalignment, and vessel prodding were the most frequent precipitating factors. Of the three dissection mechanisms, 'wedged contrast injection' was the commonest (the exclusive mechanism of aortic dissections). The propagation rate was 30.2% and led to doubling of coronary occlusions and aortic extensions. The most frequent progression triggers were repeat injections and unchanged catheter. In 94% of cases, dissections were inflicted by high-volume operators, with ≥ 5-year experience in 84% of procedures. The annual dissection rate increased over a 21-year timespan. CONCLUSIONS Catheter-induced dissection rarely came unheralded and typically occurred during urgent interventions performed in high-risk patients by experienced operators.
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Affiliation(s)
- Jacek Klaudel
- Department of Invasive Cardiology and Interventional Radiology, St. Adalbert's Hospital in Gdansk, Copernicus, Gdansk, Poland.
- Department of Cardiology, St. Vincent de Paul Hospital in Gdynia, Pomeranian Hospitals, Gdynia, Poland.
| | - Michał Glaza
- Department of Cardiology, St. Vincent de Paul Hospital in Gdynia, Pomeranian Hospitals, Gdynia, Poland
| | - Barbara Klaudel
- Faculty of Electronics, Telecommunications and Informatics, Department of Decision Systems and Robotics, Gdansk University of Technology, Gdansk, Poland
| | - Wojciech Trenkner
- Department of Invasive Cardiology and Interventional Radiology, St. Adalbert's Hospital in Gdansk, Copernicus, Gdansk, Poland
| | - Krzysztof Pawłowski
- Department of Cardiology and Interventional Angiology, Kashubian Center for Heart and Vascular Diseases in Wejherowo, Pomeranian Hospitals, Wejherowo, Poland
| | - Marek Szołkiewicz
- Department of Cardiology and Interventional Angiology, Kashubian Center for Heart and Vascular Diseases in Wejherowo, Pomeranian Hospitals, Wejherowo, Poland
- Department of Cardiology, St. Vincent de Paul Hospital in Gdynia, Pomeranian Hospitals, Gdynia, Poland
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12
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Black MH, Gradowski M, Pawłowski K, Tagliabracci VS. Methods for discovering catalytic activities for pseudokinases. Methods Enzymol 2022; 667:575-610. [PMID: 35525554 DOI: 10.1016/bs.mie.2022.03.047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Pseudoenzymes resemble active enzymes, but lack key catalytic residues believed to be required for activity. Many pseudoenzymes appear to be inactive in conventional enzyme assays. However, an alternative explanation for their apparent lack of activity is that pseudoenzymes are being assayed for the wrong reaction. We have discovered several new protein kinase-like families which have revealed how different binding orientations of adenosine triphosphate (ATP) and active site residue migration can generate a novel reaction from a common kinase scaffold. These results have exposed the catalytic versatility of the protein kinase fold and suggest that atypical kinases and pseudokinases should be analyzed for alternative transferase activities. In this chapter, we discuss a general approach for bioinformatically identifying divergent or atypical members of an enzyme superfamily, then present an experimental approach to characterize their catalytic activity.
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Affiliation(s)
- Miles H Black
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Marcin Gradowski
- Department of Biochemistry and Microbiology, Institute of Biology, Warsaw University of Life Sciences, Warsaw, Poland
| | - Krzysztof Pawłowski
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, United States; Department of Biochemistry and Microbiology, Institute of Biology, Warsaw University of Life Sciences, Warsaw, Poland.
| | - Vincent S Tagliabracci
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, United States; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, United States; Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, United States; Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, United States.
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13
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Ni C, Schmitz DA, Lee J, Pawłowski K, Wu J, Buszczak M. Labeling of heterochronic ribosomes reveals C1ORF109 and SPATA5 control a late step in human ribosome assembly. Cell Rep 2022; 38:110597. [PMID: 35354024 PMCID: PMC9004343 DOI: 10.1016/j.celrep.2022.110597] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 02/03/2022] [Accepted: 03/09/2022] [Indexed: 12/14/2022] Open
Abstract
Although features of ribosome assembly are shared between species, our understanding of the diversity, complexity, dynamics, and regulation of ribosome production in multicellular organisms remains incomplete. To gain insights into ribosome biogenesis in human cells, we perform a genome-wide loss-of-function screen combined with differential labeling of pre-existing and newly assembled ribosomes. These efforts identify two functionally uncharacterized genes, C1orf109 and SPATA5. We provide evidence that these factors, together with CINP and SPATA5L1, control a late step of human pre-60S maturation in the cytoplasm. Loss of either C1orf109 or SPATA5 impairs global protein synthesis. These results link ribosome assembly with neurodevelopmental disorders associated with recessive SPATA5 mutations. Based on these findings, we propose that the expanded repertoire of ribosome biogenesis factors likely enables multicellular organisms to coordinate multiple steps of ribosome production in response to different developmental and environmental stimuli. Ni et al. describe a live-cell labeling technique to track the production and movement of old and new ribosomes. Through a CRISPR screen, they identify C1ORF109 and SPATA5 as two ribosome biogenesis factors. They further reveal that SPATA5 allelic variants associated with neurodevelopmental defects impair ribosome maturation.
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Affiliation(s)
- Chunyang Ni
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA
| | - Daniel A Schmitz
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA
| | - Jeon Lee
- Lyda Hill-Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX 75390-9365, USA
| | - Krzysztof Pawłowski
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA
| | - Jun Wu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA; Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA
| | - Michael Buszczak
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA; Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA.
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14
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Park GJ, Osinski A, Hernandez G, Eitson JL, Majumdar A, Tonelli M, Henzler-Wildman K, Pawłowski K, Chen Z, Li Y, Schoggins JW, Tagliabracci VS. The mechanism of RNA capping by SARS-CoV-2. Res Sq 2022:rs.3.rs-1336910. [PMID: 35194601 PMCID: PMC8863163 DOI: 10.21203/rs.3.rs-1336910/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The SARS-CoV-2 RNA genome contains a 5'-cap that facilitates translation of viral proteins, protection from exonucleases and evasion of the host immune response1-4. How this cap is made is not completely understood. Here, we reconstitute the SARS-CoV-2 7MeGpppA2'-O-Me-RNA cap using virally encoded non-structural proteins (nsps). We show that the kinase-like NiRAN domain5 of nsp12 transfers RNA to the amino terminus of nsp9, forming a covalent RNA-protein intermediate (a process termed RNAylation). Subsequently, the NiRAN domain transfers RNA to GDP, forming the cap core structure GpppA-RNA. The nsp146 and nsp167 methyltransferases then add methyl groups to form functional cap structures. Structural analyses of the replication-transcription complex bound to nsp9 identified key interactions that mediate the capping reaction. Furthermore, we demonstrate in a reverse genetics system8 that the N-terminus of nsp9 and the kinase-like active site residues in the NiRAN domain are required for successful SARS-CoV-2 replication. Collectively, our results reveal an unconventional mechanism by which SARS-CoV-2 caps its RNA genome, thus exposing a new target in the development of antivirals to treat COVID-19.
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Affiliation(s)
- Gina J. Park
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Adam Osinski
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Genaro Hernandez
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jennifer L. Eitson
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Abir Majumdar
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Marco Tonelli
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | | | - Krzysztof Pawłowski
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Biochemistry and Microbiology, Institute of Biology, Warsaw University of Life Sciences, Warsaw 02-776, Poland
| | - Zhe Chen
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yang Li
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - John W. Schoggins
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Vincent S. Tagliabracci
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
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15
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Osinski A, Black MH, Pawłowski K, Chen Z, Li Y, Tagliabracci VS. Structural and mechanistic basis for protein glutamylation by the kinase fold. Mol Cell 2021; 81:4527-4539.e8. [PMID: 34407442 DOI: 10.1016/j.molcel.2021.08.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 08/02/2021] [Accepted: 08/03/2021] [Indexed: 12/12/2022]
Abstract
The kinase domain transfers phosphate from ATP to substrates. However, the Legionella effector SidJ adopts a kinase fold, yet catalyzes calmodulin (CaM)-dependent glutamylation to inactivate the SidE ubiquitin ligases. The structural and mechanistic basis in which the kinase domain catalyzes protein glutamylation is unknown. Here we present cryo-EM reconstructions of SidJ:CaM:SidE reaction intermediate complexes. We show that the kinase-like active site of SidJ adenylates an active-site Glu in SidE, resulting in the formation of a stable reaction intermediate complex. An insertion in the catalytic loop of the kinase domain positions the donor Glu near the acyl-adenylate for peptide bond formation. Our structural analysis led us to discover that the SidJ paralog SdjA is a glutamylase that differentially regulates the SidE ligases during Legionella infection. Our results uncover the structural and mechanistic basis in which the kinase fold catalyzes non-ribosomal amino acid ligations and reveal an unappreciated level of SidE-family regulation.
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Affiliation(s)
- Adam Osinski
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Miles H Black
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Krzysztof Pawłowski
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Institute of Biology, Warsaw University of Life Sciences, Warsaw 02-787, Poland
| | - Zhe Chen
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yang Li
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Vincent S Tagliabracci
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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16
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Tomchick DR, Black MH, Osinski A, Pawłowski K, Gradowski M, Chen Z, Li Y, Servage KA, Tagliabracci VS. Structural and mechanistic basis for protein glutamylation by the kinase fold. Acta Crystallogr A Found Adv 2021. [DOI: 10.1107/s010876732109111x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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17
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Betancourt LH, Gil J, Sanchez A, Doma V, Kuras M, Murillo JR, Velasquez E, Çakır U, Kim Y, Sugihara Y, Parada IP, Szeitz B, Appelqvist R, Wieslander E, Welinder C, de Almeida NP, Woldmar N, Marko‐Varga M, Eriksson J, Pawłowski K, Baldetorp B, Ingvar C, Olsson H, Lundgren L, Lindberg H, Oskolas H, Lee B, Berge E, Sjögren M, Eriksson C, Kim D, Kwon HJ, Knudsen B, Rezeli M, Malm J, Hong R, Horvath P, Szász AM, Tímár J, Kárpáti S, Horvatovich P, Miliotis T, Nishimura T, Kato H, Steinfelder E, Oppermann M, Miller K, Florindi F, Zhou Q, Domont GB, Pizzatti L, Nogueira FCS, Szadai L, Németh IB, Ekedahl H, Fenyö D, Marko‐Varga G. The Human Melanoma Proteome Atlas-Complementing the melanoma transcriptome. Clin Transl Med 2021; 11:e451. [PMID: 34323402 PMCID: PMC8299047 DOI: 10.1002/ctm2.451] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 05/17/2021] [Accepted: 05/20/2021] [Indexed: 12/12/2022] Open
Abstract
The MM500 meta-study aims to establish a knowledge basis of the tumor proteome to serve as a complement to genome and transcriptome studies. Somatic mutations and their effect on the transcriptome have been extensively characterized in melanoma. However, the effects of these genetic changes on the proteomic landscape and the impact on cellular processes in melanoma remain poorly understood. In this study, the quantitative mass-spectrometry-based proteomic analysis is interfaced with pathological tumor characterization, and associated with clinical data. The melanoma proteome landscape, obtained by the analysis of 505 well-annotated melanoma tumor samples, is defined based on almost 16 000 proteins, including mutated proteoforms of driver genes. More than 50 million MS/MS spectra were analyzed, resulting in approximately 13,6 million peptide spectrum matches (PSMs). Altogether 13 176 protein-coding genes, represented by 366 172 peptides, in addition to 52 000 phosphorylation sites, and 4 400 acetylation sites were successfully annotated. This data covers 65% and 74% of the predicted and identified human proteome, respectively. A high degree of correlation (Pearson, up to 0.54) with the melanoma transcriptome of the TCGA repository, with an overlap of 12 751 gene products, was found. Mapping of the expressed proteins with quantitation, spatiotemporal localization, mutations, splice isoforms, and PTM variants was proven not to be predicted by genome sequencing alone. The melanoma tumor molecular map was complemented by analysis of blood protein expression, including data on proteins regulated after immunotherapy. By adding these key proteomic pillars, the MM500 study expands the knowledge on melanoma disease.
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18
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Betancourt LH, Gil J, Kim Y, Doma V, Çakır U, Sanchez A, Murillo JR, Kuras M, Parada IP, Sugihara Y, Appelqvist R, Wieslander E, Welinder C, Velasquez E, de Almeida NP, Woldmar N, Marko‐Varga M, Pawłowski K, Eriksson J, Szeitz B, Baldetorp B, Ingvar C, Olsson H, Lundgren L, Lindberg H, Oskolas H, Lee B, Berge E, Sjögren M, Eriksson C, Kim D, Kwon HJ, Knudsen B, Rezeli M, Hong R, Horvatovich P, Miliotis T, Nishimura T, Kato H, Steinfelder E, Oppermann M, Miller K, Florindi F, Zhou Q, Domont GB, Pizzatti L, Nogueira FCS, Horvath P, Szadai L, Tímár J, Kárpáti S, Szász AM, Malm J, Fenyö D, Ekedahl H, Németh IB, Marko‐Varga G. The human melanoma proteome atlas-Defining the molecular pathology. Clin Transl Med 2021; 11:e473. [PMID: 34323403 PMCID: PMC8255060 DOI: 10.1002/ctm2.473] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 06/03/2021] [Accepted: 06/08/2021] [Indexed: 01/19/2023] Open
Abstract
The MM500 study is an initiative to map the protein levels in malignant melanoma tumor samples, focused on in-depth histopathology coupled to proteome characterization. The protein levels and localization were determined for a broad spectrum of diverse, surgically isolated melanoma tumors originating from multiple body locations. More than 15,500 proteoforms were identified by mass spectrometry, from which chromosomal and subcellular localization was annotated within both primary and metastatic melanoma. The data generated by global proteomic experiments covered 72% of the proteins identified in the recently reported high stringency blueprint of the human proteome. This study contributes to the NIH Cancer Moonshot initiative combining detailed histopathological presentation with the molecular characterization for 505 melanoma tumor samples, localized in 26 organs from 232 patients.
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19
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Hsieh TS, Lopez VA, Black MH, Osinski A, Pawłowski K, Tomchick DR, Liou J, Tagliabracci VS. Dynamic remodeling of host membranes by self-organizing bacterial effectors. Science 2021; 372:935-941. [PMID: 33927055 PMCID: PMC8543759 DOI: 10.1126/science.aay8118] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 02/17/2021] [Accepted: 04/14/2021] [Indexed: 01/09/2023]
Abstract
During infection, intracellular bacterial pathogens translocate a variety of effectors into host cells that modify host membrane trafficking for their benefit. We found a self-organizing system consisting of a bacterial phosphoinositide kinase and its opposing phosphatase that formed spatiotemporal patterns, including traveling waves, to remodel host cellular membranes. The Legionella effector MavQ, a phosphatidylinositol (PI) 3-kinase, was targeted to the endoplasmic reticulum (ER). MavQ and the Legionella PI 3-phosphatase SidP, even in the absence of other bacterial components, drove rapid PI 3-phosphate turnover on the ER and spontaneously formed traveling waves that spread along ER subdomains inducing vesicle and tubule budding. Thus, bacteria can exploit a self-organizing membrane-targeting mechanism to hijack host cellular structures for survival.
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Affiliation(s)
- Ting-Sung Hsieh
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Victor A Lopez
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Miles H Black
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Adam Osinski
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Krzysztof Pawłowski
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Biochemistry and Microbiology, Institute of Biology, Warsaw University of Life Sciences, Warsaw 02-776, Poland
| | - Diana R Tomchick
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jen Liou
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Vincent S Tagliabracci
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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20
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Pawłowski K, Klaudel J, Dziadkiewicz A, Mączkowiak A, Szołkiewicz M. Cardiac CathLab-based stroke thrombectomy routine service by the BRAIN team in a recently established Thrombectomy-Capable Stroke Center in Poland. Kardiol Pol 2021; 79:684-686. [PMID: 34002846 DOI: 10.33963/kp.a2021.0013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 05/18/2021] [Indexed: 11/23/2022]
Affiliation(s)
- Krzysztof Pawłowski
- Kashubian Center for Heart and Vascular Diseases, Pomeranian Hospitals, Wejherowo, Poland.
| | - Jacek Klaudel
- Department of Invasive Cardiology, St. Adalbert's Hospital, Copernicus PL, Gdańsk, Poland
| | - Artur Dziadkiewicz
- Department of Neurology and Stroke, Pomeranian Hospitals, Wejherowo, Poland
| | - Alicja Mączkowiak
- Department of Neurology and Stroke, Pomeranian Hospitals, Wejherowo, Poland
| | - Marek Szołkiewicz
- Kashubian Center for Heart and Vascular Diseases, Pomeranian Hospitals, Wejherowo, Poland
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21
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Christensen MB, Vibel T, Hilliard AJ, Kruk MB, Pawłowski K, Hryniuk D, Rzążewski K, Kristensen MA, Arlt JJ. Observation of Microcanonical Atom Number Fluctuations in a Bose-Einstein Condensate. Phys Rev Lett 2021; 126:153601. [PMID: 33929256 DOI: 10.1103/physrevlett.126.153601] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 03/11/2021] [Indexed: 06/12/2023]
Abstract
Quantum systems are typically characterized by the inherent fluctuation of their physical observables. Despite this fundamental importance, the investigation of the fluctuations in interacting quantum systems at finite temperature continues to pose considerable theoretical and experimental challenges. Here we report the characterization of atom number fluctuations in weakly interacting Bose-Einstein condensates. Technical fluctuations are mitigated through a combination of nondestructive detection and active stabilization of the cooling sequence. We observe fluctuations reduced by 27% below the canonical expectation for a noninteracting gas, revealing the microcanonical nature of our system. The peak fluctuations have near linear scaling with atom number ΔN_{0,p}^{2}∝N^{1.134} in an experimentally accessible transition region outside the thermodynamic limit. Our experimental results thus set a benchmark for theoretical calculations under typical experimental conditions.
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Affiliation(s)
- M B Christensen
- Center for Complex Quantum Systems, Department of Physics and Astronomy, Aarhus University, Ny Munkegade 120, DK-8000 Aarhus C, Denmark
| | - T Vibel
- Center for Complex Quantum Systems, Department of Physics and Astronomy, Aarhus University, Ny Munkegade 120, DK-8000 Aarhus C, Denmark
| | - A J Hilliard
- Center for Complex Quantum Systems, Department of Physics and Astronomy, Aarhus University, Ny Munkegade 120, DK-8000 Aarhus C, Denmark
| | - M B Kruk
- Center for Theoretical Physics, Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw, Poland
- Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw, Poland
| | - K Pawłowski
- Center for Theoretical Physics, Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw, Poland
| | - D Hryniuk
- Center for Theoretical Physics, Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw, Poland
| | - K Rzążewski
- Center for Theoretical Physics, Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw, Poland
| | - M A Kristensen
- Center for Complex Quantum Systems, Department of Physics and Astronomy, Aarhus University, Ny Munkegade 120, DK-8000 Aarhus C, Denmark
| | - J J Arlt
- Center for Complex Quantum Systems, Department of Physics and Astronomy, Aarhus University, Ny Munkegade 120, DK-8000 Aarhus C, Denmark
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22
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Wyżewski Z, Gradowski M, Krysińska M, Dudkiewicz M, Pawłowski K. A novel predicted ADP-ribosyltransferase-like family conserved in eukaryotic evolution. PeerJ 2021; 9:e11051. [PMID: 33854844 PMCID: PMC7955679 DOI: 10.7717/peerj.11051] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 02/11/2021] [Indexed: 01/12/2023] Open
Abstract
The presence of many completely uncharacterized proteins, even in well-studied organisms such as humans, seriously hampers full understanding of the functioning of the living cells. ADP-ribosylation is a common post-translational modification of proteins; also nucleic acids and small molecules can be modified by the covalent attachment of ADP-ribose. This modification, important in cellular signalling and infection processes, is usually executed by enzymes from the large superfamily of ADP-ribosyltransferases (ARTs). Here, using bioinformatics approaches, we identify a novel putative ADP-ribosyltransferase family, conserved in eukaryotic evolution, with a divergent active site. The hallmark of these proteins is the ART domain nestled between flanking leucine-rich repeat (LRR) domains. LRRs are typically involved in innate immune surveillance. The novel family appears as putative novel ADP-ribosylation-related actors, most likely pseudoenzymes. Sequence divergence and lack of clearly detectable “classical” ART active site suggests the novel domains are pseudoARTs, yet atypical ART activity, or alternative enzymatic activity cannot be excluded. We propose that this family, including its human member LRRC9, may be involved in an ancient defense mechanism, with analogies to the innate immune system, and coupling pathogen detection to ADP-ribosyltransfer or other signalling mechanisms.
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Affiliation(s)
- Zbigniew Wyżewski
- Institute of Biological Sciences, Cardinal Stefan Wyszynski University in Warsaw, Warszawa, Poland
| | - Marcin Gradowski
- Department of Biochemistry and Microbiology, Warsaw University of Life Sciences - SGGW, Warszawa, Poland
| | - Marianna Krysińska
- Department of Biochemistry and Microbiology, Warsaw University of Life Sciences - SGGW, Warszawa, Poland
| | - Małgorzata Dudkiewicz
- Department of Biochemistry and Microbiology, Warsaw University of Life Sciences - SGGW, Warszawa, Poland
| | - Krzysztof Pawłowski
- Department of Biochemistry and Microbiology, Warsaw University of Life Sciences - SGGW, Warszawa, Poland.,Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, United States.,Department of Translational Medicine, Lund University, Lund, Sweden
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23
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Black MH, Osinski A, Park GJ, Gradowski M, Servage KA, Pawłowski K, Tagliabracci VS. A Legionella effector ADP-ribosyltransferase inactivates glutamate dehydrogenase. J Biol Chem 2021; 296:100301. [PMID: 33476647 PMCID: PMC7949102 DOI: 10.1016/j.jbc.2021.100301] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 01/08/2021] [Accepted: 01/13/2021] [Indexed: 01/08/2023] Open
Abstract
ADP-ribosyltransferases (ARTs) are a widespread superfamily of enzymes frequently employed in pathogenic strategies of bacteria. Legionella pneumophila, the causative agent of a severe form of pneumonia known as Legionnaire's disease, has acquired over 330 translocated effectors that showcase remarkable biochemical and structural diversity. However, the ART effectors that influence L. pneumophila have not been well defined. Here, we took a bioinformatic approach to search the Legionella effector repertoire for additional divergent members of the ART superfamily and identified an ART domain in Legionella pneumophila gene0181, which we hereafter refer to as Legionella ADP-Ribosyltransferase 1 (Lart1) (Legionella ART 1). We show that L. pneumophila Lart1 targets a specific class of 120-kDa NAD+-dependent glutamate dehydrogenase (GDH) enzymes found in fungi and protists, including many natural hosts of Legionella. Lart1 targets a conserved arginine residue in the NAD+-binding pocket of GDH, thereby blocking oxidative deamination of glutamate. Therefore, Lart1 could be the first example of a Legionella effector which directly targets a host metabolic enzyme during infection.
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Affiliation(s)
- Miles H Black
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Adam Osinski
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Gina J Park
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Marcin Gradowski
- Institute of Biology, Warsaw University of Life Sciences, Warsaw, Poland
| | - Kelly A Servage
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas, USA; Department of Molecular Biology, University of Texas Southwestern Medical Center, Howard Hughes Medical Institute, Dallas, Texas, USA
| | - Krzysztof Pawłowski
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas, USA; Institute of Biology, Warsaw University of Life Sciences, Warsaw, Poland
| | - Vincent S Tagliabracci
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas, USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas, USA; Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA.
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24
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Li Y, Pawłowski K, Décamps B, Colciaghi P, Fadel M, Treutlein P, Zibold T. Fundamental Limit of Phase Coherence in Two-Component Bose-Einstein Condensates. Phys Rev Lett 2020; 125:123402. [PMID: 33016728 DOI: 10.1103/physrevlett.125.123402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 08/24/2020] [Indexed: 06/11/2023]
Abstract
We experimentally and theoretically study phase coherence in two-component Bose-Einstein condensates of ^{87}Rb atoms on an atom chip. Using Ramsey interferometry we determine the temporal decay of coherence between the |F=1,m_{F}=-1⟩ and |F=2,m_{F}=+1⟩ hyperfine ground states. We observe that the coherence is limited by random collisional phase shifts due to the stochastic nature of atom loss. The mechanism is confirmed quantitatively by a quantum trajectory method based on a master equation which takes into account collisional interactions, atom number fluctuations, and losses in the system. This decoherence process can be slowed down by reducing the density of the condensate. Our findings are relevant for experiments on quantum metrology and many-particle entanglement with Bose-Einstein condensates and the development of chip-based atomic clocks.
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Affiliation(s)
- Yifan Li
- Department of Physics, University of Basel, 4056 Basel, Switzerland
- Department of Engineering Physics, Tsinghua University, Beijing 100084, China
| | - Krzysztof Pawłowski
- Center for Theoretical Physics, Polish Academy of Sciences, 02-668 Warsaw, Poland
| | - Boris Décamps
- Department of Physics, University of Basel, 4056 Basel, Switzerland
| | - Paolo Colciaghi
- Department of Physics, University of Basel, 4056 Basel, Switzerland
| | - Matteo Fadel
- Department of Physics, University of Basel, 4056 Basel, Switzerland
| | | | - Tilman Zibold
- Department of Physics, University of Basel, 4056 Basel, Switzerland
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25
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Reiterer V, Pawłowski K, Desrochers G, Pause A, Sharpe HJ, Farhan H. The dead phosphatases society: a review of the emerging roles of pseudophosphatases. FEBS J 2020; 287:4198-4220. [PMID: 32484316 DOI: 10.1111/febs.15431] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 05/12/2020] [Accepted: 05/27/2020] [Indexed: 12/11/2022]
Abstract
Phosphatases are a diverse family of enzymes, comprising at least 10 distinct protein folds. Like most other enzyme families, many have sequence variations that predict an impairment or loss of catalytic activity classifying them as pseudophosphatases. Research on pseudoenzymes is an emerging area of interest, with new biological functions repurposed from catalytically active relatives. Here, we provide an overview of the pseudophosphatases identified to date in all major phosphatase families. We will highlight the degeneration of the various catalytic sequence motifs and discuss the challenges associated with the experimental determination of catalytic inactivity. We will also summarize the role of pseudophosphatases in various diseases and discuss the major challenges and future directions in this field.
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Affiliation(s)
| | | | - Guillaume Desrochers
- Department of Biochemistry, McGill University, Montréal, QC, Canada.,Goodman Cancer Research Centre, McGill University, Montréal, QC, Canada
| | - Arnim Pause
- Department of Biochemistry, McGill University, Montréal, QC, Canada.,Goodman Cancer Research Centre, McGill University, Montréal, QC, Canada
| | | | - Hesso Farhan
- Institute of Basic Medical Sciences, University of Oslo, Norway
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26
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Pla I, Sahlin KB, Pawłowski K, Appelqvist R, Marko-Varga G, Sanchez A, Malm J. A pilot proteomic study reveals different protein profiles related to testosterone and gonadotropin changes in a short-term controlled healthy human cohort. J Proteomics 2020; 220:103768. [PMID: 32240812 DOI: 10.1016/j.jprot.2020.103768] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 03/28/2020] [Indexed: 11/30/2022]
Affiliation(s)
- Indira Pla
- Section for Clinical Chemistry, Department of Translational Medicine, Lund University, Skåne University Hospital Malmö, 205 02 Malmö, Sweden; Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84 Lund, Sweden
| | - K Barbara Sahlin
- Section for Clinical Chemistry, Department of Translational Medicine, Lund University, Skåne University Hospital Malmö, 205 02 Malmö, Sweden; Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84 Lund, Sweden
| | - Krzysztof Pawłowski
- Section for Clinical Chemistry, Department of Translational Medicine, Lund University, Skåne University Hospital Malmö, 205 02 Malmö, Sweden; Department of Biochemistry and Microbiology, Institute of Biology, Warsaw University of Life Sciences - SGGW, Warszawa, Poland
| | - Roger Appelqvist
- Section for Clinical Chemistry, Department of Translational Medicine, Lund University, Skåne University Hospital Malmö, 205 02 Malmö, Sweden; Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84 Lund, Sweden
| | - György Marko-Varga
- Section for Clinical Chemistry, Department of Translational Medicine, Lund University, Skåne University Hospital Malmö, 205 02 Malmö, Sweden; Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84 Lund, Sweden; First Department of Surgery, Tokyo Medical University, 6-7-1 Nishishinjiku Shinjiku-ku, Japan
| | - Aniel Sanchez
- Section for Clinical Chemistry, Department of Translational Medicine, Lund University, Skåne University Hospital Malmö, 205 02 Malmö, Sweden; Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84 Lund, Sweden.
| | - Johan Malm
- Section for Clinical Chemistry, Department of Translational Medicine, Lund University, Skåne University Hospital Malmö, 205 02 Malmö, Sweden; Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84 Lund, Sweden
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27
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Sreelatha A, Nolan C, Park BC, Pawłowski K, Tomchick DR, Tagliabracci VS. A Legionella effector kinase is activated by host inositol hexakisphosphate. J Biol Chem 2020; 295:6214-6224. [PMID: 32229585 DOI: 10.1074/jbc.ra120.013067] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 03/26/2020] [Indexed: 12/18/2022] Open
Abstract
The transfer of a phosphate from ATP to a protein substrate, a modification known as protein phosphorylation, is catalyzed by protein kinases. Protein kinases play a crucial role in virtually every cellular activity. Recent studies of atypical protein kinases have highlighted the structural similarity of the kinase superfamily despite notable differences in primary amino acid sequence. Here, using a bioinformatics screen, we searched for putative protein kinases in the intracellular bacterial pathogen Legionella pneumophila and identified the type 4 secretion system effector Lpg2603 as a remote member of the protein kinase superfamily. Employing an array of biochemical and structural biology approaches, including in vitro kinase assays and isothermal titration calorimetry, we show that Lpg2603 is an active protein kinase with several atypical structural features. Importantly, we found that the eukaryote-specific host signaling molecule inositol hexakisphosphate (IP6) is required for Lpg2603 kinase activity. Crystal structures of Lpg2603 in the apo-form and when bound to IP6 revealed an active-site rearrangement that allows for ATP binding and catalysis. Our results on the structure and activity of Lpg2603 reveal a unique mode of regulation of a protein kinase, provide the first example of a bacterial kinase that requires IP6 for its activation, and may aid future work on the function of this effector during Legionella pathogenesis.
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Affiliation(s)
- Anju Sreelatha
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas 75390.
| | - Christine Nolan
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390
| | - Brenden C Park
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390
| | - Krzysztof Pawłowski
- Institute of Biology, Warsaw University of Life Sciences, Warsaw 02-787, Poland
| | - Diana R Tomchick
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas 75390; Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390
| | - Vincent S Tagliabracci
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas 75390; Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390.
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28
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Ołdziejewski R, Górecki W, Pawłowski K, Rzążewski K. Strongly Correlated Quantum Droplets in Quasi-1D Dipolar Bose Gas. Phys Rev Lett 2020; 124:090401. [PMID: 32202868 DOI: 10.1103/physrevlett.124.090401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 01/27/2020] [Indexed: 06/10/2023]
Abstract
We exploit a few- to many-body approach to study strongly interacting dipolar bosons in the quasi-one-dimensional system. The dipoles attract each other while the short range interactions are repulsive. Solving numerically the multiatom Schrödinger equation, we discover that such systems can exhibit not only the well-known bright soliton solutions but also novel quantum droplets for a strongly coupled case. For larger systems, basing on microscopic properties of the found few-body solution, we propose a new equation for a density amplitude of atoms. It accounts for fermionization for strongly repelling bosons by incorporating the Lieb-Liniger energy in a local density approximation and approaches the standard Gross-Pitaevskii equation (GPE) in the weakly interacting limit. Not only does such a framework provide an alternative mechanism of the droplet stability, but it also introduces means to further analyze this previously unexplored quantum phase. In the limiting strong repulsion case, yet another simple multiatom model is proposed. We stress that the celebrated Lee-Huang-Yang term in the GPE is not applicable in this case.
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Affiliation(s)
- Rafał Ołdziejewski
- Center for Theoretical Physics, Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw, Poland
| | - Wojciech Górecki
- Center for Theoretical Physics, Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw, Poland
| | - Krzysztof Pawłowski
- Center for Theoretical Physics, Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw, Poland
| | - Kazimierz Rzążewski
- Center for Theoretical Physics, Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw, Poland
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29
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Zhou Q, Bauden M, Andersson R, Hu D, Marko-Varga G, Xu J, Sasor A, Dai H, Pawłowski K, Said Hilmersson K, Chen X, Ansari D. YAP1 is an independent prognostic marker in pancreatic cancer and associated with extracellular matrix remodeling. J Transl Med 2020; 18:77. [PMID: 32054505 PMCID: PMC7017485 DOI: 10.1186/s12967-020-02254-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 02/01/2020] [Indexed: 12/19/2022] Open
Abstract
Background Pancreatic cancer is a major cause of cancer-related mortality. The identification of effective biomarkers is essential in order to improve management of the disease. Yes-associated protein 1 (YAP1) is a downstream effector of the Hippo pathway, a signal transduction system implicated in tissue repair and regeneration, as well as tumorigenesis. Here we evaluate the biomarker potential of YAP1 in pancreatic cancer tissue. Methods YAP1 was selected as a possible biomarker for pancreatic cancer from global protein sequencing of fresh frozen pancreatic cancer tissue samples and normal pancreas controls. The prognostic utility of YAP1 was evaluated using mRNA expression data from 176 pancreatic cancer patients in The Cancer Genome Atlas (TCGA), as well as protein expression data from immunohistochemistry analysis of a local tissue microarray (TMA) cohort comprising 140 pancreatic cancer patients. Ingenuity Pathway Analysis was applied to outline the interaction network for YAP1 in connection to the pancreatic tumor microenvironment. The expression of YAP1 target gene products was evaluated after treatment of the pancreatic cancer cell line Panc-1 with three substances interrupting YAP–TEAD interaction, including Super-TDU, Verteporfin and CA3. Results Mass spectrometry based proteomics showed that YAP1 is the top upregulated protein in pancreatic cancer tissue when compared to normal controls (log2 fold change 6.4; p = 5E−06). Prognostic analysis of YAP1 demonstrated a significant correlation between mRNA expression level data and reduced overall survival (p = 0.001). In addition, TMA and immunohistochemistry analysis suggested that YAP1 protein expression is an independent predictor of poor overall survival [hazard ratio (HR) 1.870, 95% confidence interval (CI) 1.224–2.855, p = 0.004], as well as reduced disease-free survival (HR 1.950, 95% CI 1.299–2.927, p = 0.001). Bioinformatic analyses coupled with in vitro assays indicated that YAP1 is involved in the transcriptional control of target genes, associated with extracellular matrix remodeling, which could be modified by selected substances disrupting the YAP1-TEAD interaction. Conclusions Our findings indicate that YAP1 is an important prognostic biomarker for pancreatic cancer and may play a regulatory role in the remodeling of the extracellular matrix.
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Affiliation(s)
- Qimin Zhou
- The Eye Hospital, School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang, China.,Department of Surgery, Clinical Sciences Lund, Lund University and Skåne University Hospital, 221 85, Lund, Sweden
| | - Monika Bauden
- Department of Surgery, Clinical Sciences Lund, Lund University and Skåne University Hospital, 221 85, Lund, Sweden
| | - Roland Andersson
- Department of Surgery, Clinical Sciences Lund, Lund University and Skåne University Hospital, 221 85, Lund, Sweden
| | - Dingyuan Hu
- Department of Surgery, Clinical Sciences Lund, Lund University and Skåne University Hospital, 221 85, Lund, Sweden
| | - György Marko-Varga
- Clinical Protein Science and Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, Lund, Sweden
| | - Jianfeng Xu
- Department of Surgery, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Agata Sasor
- Department of Pathology, Skåne University Hospital, Lund, Sweden
| | - Hua Dai
- Department of Pathology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Krzysztof Pawłowski
- Department of Experimental Design and Bioinformatics, Warsaw University of Life Sciences, Warsaw, Poland.,Department of Translational Medicine, Lund University, Malmö, Sweden
| | - Katarzyna Said Hilmersson
- Department of Surgery, Clinical Sciences Lund, Lund University and Skåne University Hospital, 221 85, Lund, Sweden
| | - Xi Chen
- The Eye Hospital, School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Daniel Ansari
- Department of Surgery, Clinical Sciences Lund, Lund University and Skåne University Hospital, 221 85, Lund, Sweden.
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30
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Black MH, Osinski A, Gradowski M, Servage KA, Pawłowski K, Tomchick DR, Tagliabracci VS. Bacterial pseudokinase catalyzes protein polyglutamylation to inhibit the SidE-family ubiquitin ligases. Science 2019; 364:787-792. [PMID: 31123136 DOI: 10.1126/science.aaw7446] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 05/01/2019] [Indexed: 12/11/2022]
Abstract
Enzymes with a protein kinase fold transfer phosphate from adenosine 5'-triphosphate (ATP) to substrates in a process known as phosphorylation. Here, we show that the Legionella meta-effector SidJ adopts a protein kinase fold, yet unexpectedly catalyzes protein polyglutamylation. SidJ is activated by host-cell calmodulin to polyglutamylate the SidE family of ubiquitin (Ub) ligases. Crystal structures of the SidJ-calmodulin complex reveal a protein kinase fold that catalyzes ATP-dependent isopeptide bond formation between the amino group of free glutamate and the γ-carboxyl group of an active-site glutamate in SidE. We show that SidJ polyglutamylation of SidE, and the consequent inactivation of Ub ligase activity, is required for successful Legionella replication in a viable eukaryotic host cell.
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Affiliation(s)
- Miles H Black
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Adam Osinski
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | | | - Kelly A Servage
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Howard Hughes Medical Institute, Dallas, TX 75390, USA
| | - Krzysztof Pawłowski
- Warsaw University of Life Sciences, Warsaw, Poland.,Lund University, Lund, Sweden
| | - Diana R Tomchick
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Vincent S Tagliabracci
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA. .,Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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31
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Betancourt LH, Szasz AM, Kuras M, Rodriguez Murillo J, Sugihara Y, Pla I, Horvath Z, Pawłowski K, Rezeli M, Miharada K, Gil J, Eriksson J, Appelqvist R, Miliotis T, Baldetorp B, Ingvar C, Olsson H, Lundgren L, Horvatovich P, Welinder C, Wieslander E, Kwon HJ, Malm J, Nemeth IB, Jönsson G, Fenyö D, Sanchez A, Marko-Varga G. The Hidden Story of Heterogeneous B-raf V600E Mutation Quantitative Protein Expression in Metastatic Melanoma-Association with Clinical Outcome and Tumor Phenotypes. Cancers (Basel) 2019; 11:E1981. [PMID: 31835364 PMCID: PMC6966659 DOI: 10.3390/cancers11121981] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 11/23/2019] [Accepted: 12/03/2019] [Indexed: 02/07/2023] Open
Abstract
In comparison to other human cancer types, malignant melanoma exhibits the greatest amount of heterogeneity. After DNA-based detection of the BRAF V600E mutation in melanoma patients, targeted inhibitor treatment is the current recommendation. This approach, however, does not take the abundance of the therapeutic target, i.e., the B-raf V600E protein, into consideration. As shown by immunohistochemistry, the protein expression profiles of metastatic melanomas clearly reveal the existence of inter- and intra-tumor variability. Nevertheless, the technique is only semi-quantitative. To quantitate the mutant protein there is a fundamental need for more precise techniques that are aimed at defining the currently non-existent link between the levels of the target protein and subsequent drug efficacy. Using cutting-edge mass spectrometry combined with DNA and mRNA sequencing, the mutated B-raf protein within metastatic tumors was quantitated for the first time. B-raf V600E protein analysis revealed a subjacent layer of heterogeneity for mutation-positive metastatic melanomas. These were characterized into two distinct groups with different tumor morphologies, protein profiles and patient clinical outcomes. This study provides evidence that a higher level of expression in the mutated protein is associated with a more aggressive tumor progression. Our study design, comprised of surgical isolation of tumors, histopathological characterization, tissue biobanking, and protein analysis, may enable the eventual delineation of patient responders/non-responders and subsequent therapy for malignant melanoma.
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Affiliation(s)
- Lazaro Hiram Betancourt
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical, Engineering, Lund University, BMC D13, 221 84 Lund, Sweden; (L.H.B.); (Z.H.); (M.R.); (J.G.); (J.E.); (R.A.); (G.M.-V.)
| | - A. Marcell Szasz
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical, Engineering, Lund University, BMC D13, 221 84 Lund, Sweden; (L.H.B.); (Z.H.); (M.R.); (J.G.); (J.E.); (R.A.); (G.M.-V.)
- Cancer Center, Semmelweis University, Budapest 1083, Hungary
| | - Magdalena Kuras
- Section for Clinical Chemistry, Department of Translational Medicine, Lund University, Skåne University Hospital Malmö, 205 02 Malmö, Sweden; (M.K.); (I.P.); (K.P.); (J.M.); (A.S.)
| | - Jimmy Rodriguez Murillo
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17 177 Stockholm, Sweden; (J.R.M.); (Y.S.)
| | - Yutaka Sugihara
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17 177 Stockholm, Sweden; (J.R.M.); (Y.S.)
| | - Indira Pla
- Section for Clinical Chemistry, Department of Translational Medicine, Lund University, Skåne University Hospital Malmö, 205 02 Malmö, Sweden; (M.K.); (I.P.); (K.P.); (J.M.); (A.S.)
| | - Zsolt Horvath
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical, Engineering, Lund University, BMC D13, 221 84 Lund, Sweden; (L.H.B.); (Z.H.); (M.R.); (J.G.); (J.E.); (R.A.); (G.M.-V.)
| | - Krzysztof Pawłowski
- Section for Clinical Chemistry, Department of Translational Medicine, Lund University, Skåne University Hospital Malmö, 205 02 Malmö, Sweden; (M.K.); (I.P.); (K.P.); (J.M.); (A.S.)
- Department of Biochemistry and Microbiology, Warsaw University of Life Sciences, 02-787 Warsaw, Poland
| | - Melinda Rezeli
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical, Engineering, Lund University, BMC D13, 221 84 Lund, Sweden; (L.H.B.); (Z.H.); (M.R.); (J.G.); (J.E.); (R.A.); (G.M.-V.)
| | - Kenichi Miharada
- Department of Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, BMC A12, Sölvegatan 17, 221 84 Lund, Sweden;
| | - Jeovanis Gil
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical, Engineering, Lund University, BMC D13, 221 84 Lund, Sweden; (L.H.B.); (Z.H.); (M.R.); (J.G.); (J.E.); (R.A.); (G.M.-V.)
| | - Jonatan Eriksson
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical, Engineering, Lund University, BMC D13, 221 84 Lund, Sweden; (L.H.B.); (Z.H.); (M.R.); (J.G.); (J.E.); (R.A.); (G.M.-V.)
| | - Roger Appelqvist
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical, Engineering, Lund University, BMC D13, 221 84 Lund, Sweden; (L.H.B.); (Z.H.); (M.R.); (J.G.); (J.E.); (R.A.); (G.M.-V.)
| | - Tasso Miliotis
- Translational Science, Cardiovascular Renal and Metabolism, IMED Biotech Unit, AstraZeneca, 431 50 Gothenburg, Sweden;
| | - Bo Baldetorp
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85 Lund, Sweden; (B.B.); (H.O.); (L.L.); (C.W.); (E.W.); (G.J.)
| | - Christian Ingvar
- Department of Surgery, Clinical Sciences, Lund University, Skåne University Hospital, 222 42 Lund, Sweden;
| | - Håkan Olsson
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85 Lund, Sweden; (B.B.); (H.O.); (L.L.); (C.W.); (E.W.); (G.J.)
| | - Lotta Lundgren
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85 Lund, Sweden; (B.B.); (H.O.); (L.L.); (C.W.); (E.W.); (G.J.)
| | - Peter Horvatovich
- Department of Analytical Biochemistry, Faculty of Science and Engineering, University of Groningen, 9712 CP Groningen, The Netherlands;
| | - Charlotte Welinder
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85 Lund, Sweden; (B.B.); (H.O.); (L.L.); (C.W.); (E.W.); (G.J.)
| | - Elisabet Wieslander
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85 Lund, Sweden; (B.B.); (H.O.); (L.L.); (C.W.); (E.W.); (G.J.)
| | - Ho Jeong Kwon
- Department of Biotechnology, Yonsei University, Seoul 03722, Korea;
| | - Johan Malm
- Section for Clinical Chemistry, Department of Translational Medicine, Lund University, Skåne University Hospital Malmö, 205 02 Malmö, Sweden; (M.K.); (I.P.); (K.P.); (J.M.); (A.S.)
| | - Istvan Balazs Nemeth
- Department of Dermatology and Allergology, University of Szeged, H-6720 Szeged, Hungary;
| | - Göran Jönsson
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85 Lund, Sweden; (B.B.); (H.O.); (L.L.); (C.W.); (E.W.); (G.J.)
| | - David Fenyö
- Institute for Systems Genetics, NYU School of Medicine, 550 1st Ave, New York, NY 10016, USA;
| | - Aniel Sanchez
- Section for Clinical Chemistry, Department of Translational Medicine, Lund University, Skåne University Hospital Malmö, 205 02 Malmö, Sweden; (M.K.); (I.P.); (K.P.); (J.M.); (A.S.)
| | - György Marko-Varga
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical, Engineering, Lund University, BMC D13, 221 84 Lund, Sweden; (L.H.B.); (Z.H.); (M.R.); (J.G.); (J.E.); (R.A.); (G.M.-V.)
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Sahlin KB, Pla I, Sanchez A, Pawłowski K, Leijonhufvud I, Appelqvist R, Marko-Varga G, Giwercman A, Malm J. Short-term effect of pharmacologically induced alterations in testosterone levels on common blood biomarkers in a controlled healthy human model. Scand J Clin Lab Invest 2019; 80:25-31. [PMID: 31738571 DOI: 10.1080/00365513.2019.1689429] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Testosterone deficiency in males is associated with serious comorbidities such as cardiovascular disease, diabetes type two, and also an increased risk of premature death. The pathogenetic mechanism behind this association, however, has not yet been clarified and is potentially bidirectional. The aim of this clinical trial was to gain insight into the short-term effect of changes in testosterone on blood analytes in healthy young men. Thirty healthy young male volunteers were recruited and monitored in our designed human model. Blood sampling was performed prior to and 3 weeks after pharmacological castration with a gonadotropin-releasing hormone antagonist. Subsequently, testosterone replacement with 1000 mg testosterone undecanoate was given and additional blood samples were collected 2 weeks later. The alterations in the levels of 37 routine biomarkers were statistically analysed. Eight biomarkers changed significantly in a similar manner as testosterone between the time points (e.g. prostate specific antigen, creatinine and magnesium), whereas seven other markers changed in the inverse manner as testosterone, including sexual hormone-binding globulin, urea, aspartate aminotransferase and alanine aminotransferase. Most of our results were supported by data from other studies. The designed controlled human model yielded changes in known biomarkers suggesting that low testosterone has a negative effect on health in young healthy men.
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Affiliation(s)
- K Barbara Sahlin
- Section for Clinical Chemistry, Department of Translational Medicine, Lund University, Skåne University Hospital Malmö, Malmö, Sweden.,Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, Lund, Sweden
| | - Indira Pla
- Section for Clinical Chemistry, Department of Translational Medicine, Lund University, Skåne University Hospital Malmö, Malmö, Sweden.,Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, Lund, Sweden
| | - Aniel Sanchez
- Section for Clinical Chemistry, Department of Translational Medicine, Lund University, Skåne University Hospital Malmö, Malmö, Sweden.,Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, Lund, Sweden
| | - Krzysztof Pawłowski
- Section for Clinical Chemistry, Department of Translational Medicine, Lund University, Skåne University Hospital Malmö, Malmö, Sweden.,Department of Biochemistry and Microbiology, Institute of Biology, Warsaw University of Life Sciences - SGGW, Warszawa, Poland
| | - Irene Leijonhufvud
- Molecular Reproductive Medicine, Department of Translational Medicine, Lund University, Skåne University Hospital Malmö, Malmö, Sweden
| | - Roger Appelqvist
- Section for Clinical Chemistry, Department of Translational Medicine, Lund University, Skåne University Hospital Malmö, Malmö, Sweden.,Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, Lund, Sweden
| | - György Marko-Varga
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, Lund, Sweden
| | - Aleksander Giwercman
- Molecular Reproductive Medicine, Department of Translational Medicine, Lund University, Skåne University Hospital Malmö, Malmö, Sweden
| | - Johan Malm
- Section for Clinical Chemistry, Department of Translational Medicine, Lund University, Skåne University Hospital Malmö, Malmö, Sweden.,Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, Lund, Sweden
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33
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Gil J, Betancourt LH, Pla I, Sanchez A, Appelqvist R, Miliotis T, Kuras M, Oskolas H, Kim Y, Horvath Z, Eriksson J, Berge E, Burestedt E, Jönsson G, Baldetorp B, Ingvar C, Olsson H, Lundgren L, Horvatovich P, Murillo JR, Sugihara Y, Welinder C, Wieslander E, Lee B, Lindberg H, Pawłowski K, Kwon HJ, Doma V, Timar J, Karpati S, Szasz AM, Németh IB, Nishimura T, Corthals G, Rezeli M, Knudsen B, Malm J, Marko-Varga G. Clinical protein science in translational medicine targeting malignant melanoma. Cell Biol Toxicol 2019; 35:293-332. [PMID: 30900145 PMCID: PMC6757020 DOI: 10.1007/s10565-019-09468-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 02/13/2019] [Indexed: 02/06/2023]
Abstract
Melanoma of the skin is the sixth most common type of cancer in Europe and accounts for 3.4% of all diagnosed cancers. More alarming is the degree of recurrence that occurs with approximately 20% of patients lethally relapsing following treatment. Malignant melanoma is a highly aggressive skin cancer and metastases rapidly extend to the regional lymph nodes (stage 3) and to distal organs (stage 4). Targeted oncotherapy is one of the standard treatment for progressive stage 4 melanoma, and BRAF inhibitors (e.g. vemurafenib, dabrafenib) combined with MEK inhibitor (e.g. trametinib) can effectively counter BRAFV600E-mutated melanomas. Compared to conventional chemotherapy, targeted BRAFV600E inhibition achieves a significantly higher response rate. After a period of cancer control, however, most responsive patients develop resistance to the therapy and lethal progression. The many underlying factors potentially causing resistance to BRAF inhibitors have been extensively studied. Nevertheless, the remaining unsolved clinical questions necessitate alternative research approaches to address the molecular mechanisms underlying metastatic and treatment-resistant melanoma. In broader terms, proteomics can address clinical questions far beyond the reach of genomics, by measuring, i.e. the relative abundance of protein products, post-translational modifications (PTMs), protein localisation, turnover, protein interactions and protein function. More specifically, proteomic analysis of body fluids and tissues in a given medical and clinical setting can aid in the identification of cancer biomarkers and novel therapeutic targets. Achieving this goal requires the development of a robust and reproducible clinical proteomic platform that encompasses automated biobanking of patient samples, tissue sectioning and histological examination, efficient protein extraction, enzymatic digestion, mass spectrometry-based quantitative protein analysis by label-free or labelling technologies and/or enrichment of peptides with specific PTMs. By combining data from, e.g. phosphoproteomics and acetylomics, the protein expression profiles of different melanoma stages can provide a solid framework for understanding the biology and progression of the disease. When complemented by proteogenomics, customised protein sequence databases generated from patient-specific genomic and transcriptomic data aid in interpreting clinical proteomic biomarker data to provide a deeper and more comprehensive molecular characterisation of cellular functions underlying disease progression. In parallel to a streamlined, patient-centric, clinical proteomic pipeline, mass spectrometry-based imaging can aid in interrogating the spatial distribution of drugs and drug metabolites within tissues at single-cell resolution. These developments are an important advancement in studying drug action and efficacy in vivo and will aid in the development of more effective and safer strategies for the treatment of melanoma. A collaborative effort of gargantuan proportions between academia and healthcare professionals has led to the initiation, establishment and development of a cutting-edge cancer research centre with a specialisation in melanoma and lung cancer. The primary research focus of the European Cancer Moonshot Lund Center is to understand the impact that drugs have on cancer at an individualised and personalised level. Simultaneously, the centre increases awareness of the relentless battle against cancer and attracts global interest in the exceptional research performed at the centre.
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Affiliation(s)
- Jeovanis Gil
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden.
| | - Lazaro Hiram Betancourt
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden.
| | - Indira Pla
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
- Section for Clinical Chemistry, Department of Translational Medicine, Lund University, Skåne University Hospital Malmö, 205 02, Malmö, Sweden
| | - Aniel Sanchez
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
- Section for Clinical Chemistry, Department of Translational Medicine, Lund University, Skåne University Hospital Malmö, 205 02, Malmö, Sweden
| | - Roger Appelqvist
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Tasso Miliotis
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
- Translational Science, Cardiovascular Renal and Metabolism, IMED Biotech Unit, AstraZeneca, Gothenburg, Sweden
| | - Magdalena Kuras
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Henriette Oskolas
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Yonghyo Kim
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Zsolt Horvath
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Jonatan Eriksson
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Ethan Berge
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Elisabeth Burestedt
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Göran Jönsson
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85, Lund, Sweden
| | - Bo Baldetorp
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85, Lund, Sweden
| | - Christian Ingvar
- Department of Surgery, Clinical Sciences, Lund University, SUS, Lund, Sweden
| | - Håkan Olsson
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85, Lund, Sweden
| | - Lotta Lundgren
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85, Lund, Sweden
- Department of Haematology, Oncology and Radiation Physics, Skåne University Hospital, Lund, Sweden
| | - Peter Horvatovich
- Department of Analytical Biochemistry, Faculty of Science and Engineering, University of Groningen, Groningen, The Netherlands
| | - Jimmy Rodriguez Murillo
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Yutaka Sugihara
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Charlotte Welinder
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85, Lund, Sweden
| | - Elisabet Wieslander
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85, Lund, Sweden
| | - Boram Lee
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Henrik Lindberg
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Krzysztof Pawłowski
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
- Department of Experimental Design and Bioinformatics, Faculty of Agriculture and Biology, Warsaw University of Life Sciences, Warsaw, Poland
| | - Ho Jeong Kwon
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
- Chemical Genomics Global Research Lab, Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Viktoria Doma
- Second Department of Pathology, Semmelweis University, Budapest, Hungary
| | - Jozsef Timar
- Second Department of Pathology, Semmelweis University, Budapest, Hungary
| | - Sarolta Karpati
- Department of Dermatology, Semmelweis University, Budapest, Hungary
| | - A Marcell Szasz
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85, Lund, Sweden
- Cancer Center, Semmelweis University, Budapest, 1083, Hungary
- MTA-TTK Momentum Oncology Biomarker Research Group, Hungarian Academy of Sciences, Budapest, 1117, Hungary
| | - István Balázs Németh
- Department of Dermatology and Allergology, University of Szeged, Szeged, H-6720, Hungary
| | - Toshihide Nishimura
- Clinical Translational Medicine Informatics, St. Marianna University School of Medicine, Kawasaki, Kanagawa, Japan
- Department of Surgery, Tokyo Medical University, 6-7-1 Nishishinjiku Shinjiku-ku, Tokyo, Japan
| | - Garry Corthals
- Van't Hoff Institute of Molecular Sciences, 1090 GS, Amsterdam, The Netherlands
| | - Melinda Rezeli
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Beatrice Knudsen
- Biomedical Sciences and Pathology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Johan Malm
- Section for Clinical Chemistry, Department of Translational Medicine, Lund University, Skåne University Hospital Malmö, 205 02, Malmö, Sweden
| | - György Marko-Varga
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
- Chemical Genomics Global Research Lab, Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
- Department of Surgery, Tokyo Medical University, 6-7-1 Nishishinjiku Shinjiku-ku, Tokyo, Japan
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34
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Tomchick DR, Sreelatha A, Yee SS, Lopez VA, Park BC, Kinch LN, Pilch S, Servage KA, Zhang J, Jiou J, Karasiewicz-Urbańska M, Łobocka M, Grishin NV, Orth K, Kucharczyk R, Pawłowski K, Tagliabracci VS. Protein AMPylation by an evolutionarily conserved pseudokinase. Acta Crystallogr A Found Adv 2019. [DOI: 10.1107/s0108767319096922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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35
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Walden M, Tian L, Ross RL, Sykora UM, Byrne DP, Hesketh EL, Masandi SK, Cassel J, George R, Ault JR, El Oualid F, Pawłowski K, Salvino JM, Eyers PA, Ranson NA, Del Galdo F, Greenberg RA, Zeqiraj E. Metabolic control of BRISC-SHMT2 assembly regulates immune signalling. Nature 2019; 570:194-199. [PMID: 31142841 PMCID: PMC6914362 DOI: 10.1038/s41586-019-1232-1] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 04/29/2019] [Indexed: 02/04/2023]
Abstract
SHMT2 regulates one-carbon transfer reactions essential for amino acid and nucleotide metabolism, using PLP as a cofactor. Apo SHMT2 exists as a dimer with unknown functions, whereas PLP binding stabilizes the active, tetrameric state. SHMT2 also promotes inflammatory cytokine signaling by interacting with the BRISC deubiquitylase (DUB) complex, although it is unclear if this function relates to metabolism. We reveal the cryo-EM structure of human BRISC-SHMT2 complex at 3.8 Å resolution. The BRISC complex is a U-shaped dimer of four subunits and SHMT2 sterically blocks the BRCC36 active site and inhibits DUB activity. Only the inactive SHMT2 dimer, but not the active, PLP-bound tetramer binds and inhibits BRISC. BRISC mutations that disrupt SHMT2 binding impaired type I interferon signaling in response to inflammatory stimuli. Intracellular PLP levels regulated BRISC-SHMT2 interaction and inflammatory cytokine responses. These data reveal a new mechanism of metabolite regulation of DUB activity and inflammatory signaling.
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Affiliation(s)
- Miriam Walden
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Lei Tian
- Department of Cancer Biology, Basser Center for BRCA, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Rebecca L Ross
- Leeds Institute of Rheumatic and Musculoskeletal Medicine and NIHR Biomedical Research Centre, University of Leeds, Leeds, UK
| | - Upasana M Sykora
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Dominic P Byrne
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Emma L Hesketh
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Safi K Masandi
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Joel Cassel
- The Wistar Cancer Center for Molecular Screening, The Wistar Institute, Philadelphia, PA, USA
| | - Rachel George
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - James R Ault
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | | | - Krzysztof Pawłowski
- Warsaw University of Life Sciences, Warsaw, Poland.,Department of Translational Medicine, Clinical Sciences, Lund University, Lund, Sweden
| | - Joseph M Salvino
- The Wistar Cancer Center for Molecular Screening, The Wistar Institute, Philadelphia, PA, USA
| | - Patrick A Eyers
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Neil A Ranson
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Francesco Del Galdo
- Leeds Institute of Rheumatic and Musculoskeletal Medicine and NIHR Biomedical Research Centre, University of Leeds, Leeds, UK
| | - Roger A Greenberg
- Department of Cancer Biology, Basser Center for BRCA, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Elton Zeqiraj
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK.
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Dudkiewicz M, Pawłowski K. A novel conserved family of Macro-like domains-putative new players in ADP-ribosylation signaling. PeerJ 2019; 7:e6863. [PMID: 31106069 PMCID: PMC6500376 DOI: 10.7717/peerj.6863] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 03/28/2019] [Indexed: 12/30/2022] Open
Abstract
The presence of many completely uncharacterized proteins, even in well-studied organisms such as humans, seriously hampers a full understanding of the functioning of living cells. One such example is the human protein C12ORF4, which belongs to the DUF2362 family, present in many eukaryotic lineages and conserved in metazoans. The only functional information available on C12ORF4 (Chromosome 12 Open Reading Frame 4) is its involvement in mast cell degranulation and its being a genetic cause of autosomal intellectual disability. Bioinformatics analysis of the DUF2362 family provides strong evidence that it is a novel member of the Macro clan/superfamily. Sequence similarity analysis versus other representatives of the Macro superfamily of ADP-ribose-binding proteins and mapping sequence conservation on predicted three-dimensional structure provides hypotheses regarding the molecular function for members of the DUF2362 family. For example, the available functional data suggest a possible role for C12ORF4 in ADP-ribosylation signaling in asthma and related inflammatory diseases. This novel family appears to be a likely novel ADP-ribosylation “reader” and “eraser,” a previously unnoticed putative new player in cell signaling by this emerging post-translational modification.
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Affiliation(s)
- Małgorzata Dudkiewicz
- Department of Experimental Design and Bioinformatics, Faculty of Agriculture and Biology, Warsaw University of Life Sciences, Warszawa, Poland
| | - Krzysztof Pawłowski
- Department of Experimental Design and Bioinformatics, Faculty of Agriculture and Biology, Warsaw University of Life Sciences, Warszawa, Poland.,Department of Translational Mecicine, Clinical Sciences, Lund University, Lund, Sweden
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37
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Zhou Q, Andersson R, Hu D, Bauden M, Kristl T, Sasor A, Pawłowski K, Pla I, Hilmersson KS, Zhou M, Lu F, Marko-Varga G, Ansari D. Quantitative proteomics identifies brain acid soluble protein 1 (BASP1) as a prognostic biomarker candidate in pancreatic cancer tissue. EBioMedicine 2019; 43:282-294. [PMID: 30982764 PMCID: PMC6557784 DOI: 10.1016/j.ebiom.2019.04.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 03/27/2019] [Accepted: 04/03/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Pancreatic cancer is a heterogenous disease with a poor prognosis. This study aimed to discover and validate prognostic tissue biomarkers in pancreatic cancer using a mass spectrometry (MS) based proteomics approach. METHODS Global protein sequencing of fresh frozen pancreatic cancer and healthy pancreas tissue samples was conducted by MS to discover potential protein biomarkers. Selected candidate proteins were further verified by targeted proteomics using parallel reaction monitoring (PRM). The expression of biomarker candidates was validated by immunohistochemistry in a large tissue microarray (TMA) cohort of 141 patients with resectable pancreatic cancer. Kaplan-Meier and Cox proportional hazard modelling was used to investigate the prognostic utility of candidate protein markers. FINDINGS In the initial MS-discovery phase, 165 proteins were identified as potential biomarkers. In the subsequent MS-verification phase, a panel of 45 candidate proteins was verified by the development of a PRM assay. Brain acid soluble protein 1 (BASP1) was identified as a new biomarker candidate for pancreatic cancer possessing largely unknown biological and clinical functions and was selected for further analysis. Importantly, bioinformatic analysis indicated that BASP1 interacts with Wilms tumour protein (WT1) in pancreatic cancer. TMA-based immunohistochemistry analysis showed that BASP1 was an independent predictor of prolonged survival (HR 0.468, 95% CI 0.257-0.852, p = .013) and predicted favourable response to adjuvant chemotherapy, whereas WT1 indicated a worsened survival (HR 1.636, 95% CI 1.083-2.473, p = .019) and resistance to chemotherapy. Interaction analysis showed that patients with negative BASP1 and high WT1 expression had the poorest outcome (HR 3.536, 95% CI 1.336-9.362, p = .011). INTERPRETATION We here describe an MS-based proteomics platform for developing biomarkers for pancreatic cancer. Bioinformatic analysis and clinical data from our study suggest that BASP1 and its putative interaction partner WT1 can be used as biomarkers for predicting outcomes in pancreatic cancer patients.
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Affiliation(s)
- Qimin Zhou
- Department of Surgery, Clinical Sciences Lund, Lund University and Skåne University Hospital, Lund, Sweden; The Eye Hospital, School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang, China; Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Roland Andersson
- Department of Surgery, Clinical Sciences Lund, Lund University and Skåne University Hospital, Lund, Sweden
| | - Dingyuan Hu
- Department of Surgery, Clinical Sciences Lund, Lund University and Skåne University Hospital, Lund, Sweden
| | - Monika Bauden
- Department of Surgery, Clinical Sciences Lund, Lund University and Skåne University Hospital, Lund, Sweden
| | - Theresa Kristl
- Department of Surgery, Clinical Sciences Lund, Lund University and Skåne University Hospital, Lund, Sweden
| | - Agata Sasor
- Department of Pathology, Skåne University Hospital, Lund, Sweden
| | - Krzysztof Pawłowski
- Department of Experimental Design and Bioinformatics, Warsaw University of Life Sciences, Warsaw, Poland; Department of Translational Medicine, Lund University, Malmö, Sweden
| | - Indira Pla
- Department of Biomedical Engineering, Clinical Protein Science and Imaging, Lund University, Lund, Sweden
| | - Katarzyna Said Hilmersson
- Department of Surgery, Clinical Sciences Lund, Lund University and Skåne University Hospital, Lund, Sweden
| | - Mengtao Zhou
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Fan Lu
- The Eye Hospital, School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - György Marko-Varga
- Department of Biomedical Engineering, Clinical Protein Science and Imaging, Lund University, Lund, Sweden
| | - Daniel Ansari
- Department of Surgery, Clinical Sciences Lund, Lund University and Skåne University Hospital, Lund, Sweden.
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Kristensen MA, Christensen MB, Gajdacz M, Iglicki M, Pawłowski K, Klempt C, Sherson JF, Rzążewski K, Hilliard AJ, Arlt JJ. Observation of Atom Number Fluctuations in a Bose-Einstein Condensate. Phys Rev Lett 2019; 122:163601. [PMID: 31075024 DOI: 10.1103/physrevlett.122.163601] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Indexed: 06/09/2023]
Abstract
Fluctuations are a key property of both classical and quantum systems. While the fluctuations are well understood for many quantum systems at zero temperature, the case of an interacting quantum system at finite temperature still poses numerous challenges. Despite intense theoretical investigations of atom number fluctuations in Bose-Einstein condensates, their amplitude in experimentally relevant interacting systems is still not fully understood. Moreover, technical limitations have prevented their experimental investigation to date. Here we report the observation of these fluctuations. Our experiments are based on a stabilization technique, which allows for the preparation of ultracold thermal clouds at the shot noise level, thereby eliminating numerous technical noise sources. Furthermore, we make use of the correlations established by the evaporative cooling process to precisely determine the fluctuations and the sample temperature. This allows us to observe a telltale signature: the sudden increase in fluctuations of the condensate atom number close to the critical temperature.
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Affiliation(s)
- M A Kristensen
- Institut for Fysik og Astronomi, Aarhus Universitet, Ny Munkegade 120, 8000 Aarhus C, Denmark
| | - M B Christensen
- Institut for Fysik og Astronomi, Aarhus Universitet, Ny Munkegade 120, 8000 Aarhus C, Denmark
| | - M Gajdacz
- Institut for Fysik og Astronomi, Aarhus Universitet, Ny Munkegade 120, 8000 Aarhus C, Denmark
| | - M Iglicki
- Center for Theoretical Physics, Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw, Poland
- Faculty of Physics, University of Warsaw, Pasteura 5, PL-02093 Warsaw, Poland
| | - K Pawłowski
- Center for Theoretical Physics, Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw, Poland
| | - C Klempt
- Institut für Quantenoptik, Leibniz Universität Hannover, Welfengarten 1, 30167 Hannover, Germany
| | - J F Sherson
- Institut for Fysik og Astronomi, Aarhus Universitet, Ny Munkegade 120, 8000 Aarhus C, Denmark
| | - K Rzążewski
- Center for Theoretical Physics, Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw, Poland
| | - A J Hilliard
- Institut for Fysik og Astronomi, Aarhus Universitet, Ny Munkegade 120, 8000 Aarhus C, Denmark
| | - J J Arlt
- Institut for Fysik og Astronomi, Aarhus Universitet, Ny Munkegade 120, 8000 Aarhus C, Denmark
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Betancourt LH, Pawłowski K, Eriksson J, Szasz AM, Mitra S, Pla I, Welinder C, Ekedahl H, Broberg P, Appelqvist R, Yakovleva M, Sugihara Y, Miharada K, Ingvar C, Lundgren L, Baldetorp B, Olsson H, Rezeli M, Wieslander E, Horvatovich P, Malm J, Jönsson G, Marko-Varga G. Improved survival prognostication of node-positive malignant melanoma patients utilizing shotgun proteomics guided by histopathological characterization and genomic data. Sci Rep 2019; 9:5154. [PMID: 30914758 PMCID: PMC6435712 DOI: 10.1038/s41598-019-41625-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 03/13/2019] [Indexed: 12/18/2022] Open
Abstract
Metastatic melanoma is one of the most common deadly cancers, and robust biomarkers are still needed, e.g. to predict survival and treatment efficiency. Here, protein expression analysis of one hundred eleven melanoma lymph node metastases using high resolution mass spectrometry is coupled with in-depth histopathology analysis, clinical data and genomics profiles. This broad view of protein expression allowed to identify novel candidate protein markers that improved prediction of survival in melanoma patients. Some of the prognostic proteins have not been reported in the context of melanoma before, and few of them exhibit unexpected relationship to survival, which likely reflects the limitations of current knowledge on melanoma and shows the potential of proteomics in clinical cancer research.
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Affiliation(s)
| | - Krzysztof Pawłowski
- Lund University, Lund, Sweden.
- Warsaw University of Life Sciences SGGW, Warszawa, Poland.
| | | | - A Marcell Szasz
- Lund University, Lund, Sweden
- National Koranyi Institute of Pulmonology, Budapest, Hungary
- Semmelweis University, Budapest, Hungary
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Peter Horvatovich
- Lund University, Lund, Sweden
- University of Groningen, Groningen, The Netherlands
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40
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Pawłowski K, Krajewska M. The thermal quality of housing elements and energy consumption of low-energy buildings - selected aspects. BoZPE 2019. [DOI: 10.17512/bozpe.2019.2.03] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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41
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Wróblewski T, Spiridon L, Martin EC, Petrescu AJ, Cavanaugh K, Truco MJ, Xu H, Gozdowski D, Pawłowski K, Michelmore RW, Takken FL. Genome-wide functional analyses of plant coiled-coil NLR-type pathogen receptors reveal essential roles of their N-terminal domain in oligomerization, networking, and immunity. PLoS Biol 2018; 16:e2005821. [PMID: 30540748 PMCID: PMC6312357 DOI: 10.1371/journal.pbio.2005821] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 12/31/2018] [Accepted: 11/16/2018] [Indexed: 12/22/2022] Open
Abstract
The ability to induce a defense response after pathogen attack is a critical feature of the immune system of any organism. Nucleotide-binding leucine-rich repeat receptors (NLRs) are key players in this process and perceive the occurrence of nonself-activities or foreign molecules. In plants, coevolution with a variety of pests and pathogens has resulted in repertoires of several hundred diverse NLRs in single individuals and many more in populations as a whole. However, the mechanism by which defense signaling is triggered by these NLRs in plants is poorly understood. Here, we show that upon pathogen perception, NLRs use their N-terminal domains to transactivate other receptors. Their N-terminal domains homo- and heterodimerize, suggesting that plant NLRs oligomerize upon activation, similar to the vertebrate NLRs; however, consistent with their large number in plants, the complexes are highly heterometric. Also, in contrast to metazoan NLRs, the N-terminus, rather than their centrally located nucleotide-binding (NB) domain, can mediate initial partner selection. The highly redundant network of NLR interactions in plants is proposed to provide resilience to perturbation by pathogens.
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Affiliation(s)
- Tadeusz Wróblewski
- The Genome Center, University of California–Davis, Davis, California, United States of America
| | - Laurentiu Spiridon
- Department of Bioinformatics and Structural Biochemistry, Institute of Biochemistry of the Romanian Academy, Bucharest, Romania
| | - Eliza Cristina Martin
- Department of Bioinformatics and Structural Biochemistry, Institute of Biochemistry of the Romanian Academy, Bucharest, Romania
| | - Andrei-Jose Petrescu
- Department of Bioinformatics and Structural Biochemistry, Institute of Biochemistry of the Romanian Academy, Bucharest, Romania
| | - Keri Cavanaugh
- The Genome Center, University of California–Davis, Davis, California, United States of America
| | - Maria José Truco
- The Genome Center, University of California–Davis, Davis, California, United States of America
| | - Huaqin Xu
- The Genome Center, University of California–Davis, Davis, California, United States of America
| | - Dariusz Gozdowski
- Department of Experimental Design and Bioinformatics, Faculty of Agriculture and Biology, Warsaw University of Life Sciences, Warsaw, Poland
| | - Krzysztof Pawłowski
- Department of Experimental Design and Bioinformatics, Faculty of Agriculture and Biology, Warsaw University of Life Sciences, Warsaw, Poland
| | - Richard W. Michelmore
- The Genome Center, University of California–Davis, Davis, California, United States of America
- Departments of Plant Sciences, Molecular & Cellular Biology, and Medical Microbiology & Immunology, University of California–Davis, Davis, California, United States of America
- Department of Medical Microbiology and Immunology, University of California–Davis, Davis, California, United States of America
| | - Frank L.W. Takken
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
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42
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Sreelatha A, Yee SS, Lopez VA, Park BC, Kinch LN, Pilch S, Servage KA, Zhang J, Jiou J, Karasiewicz-Urbańska M, Łobocka M, Grishin NV, Orth K, Kucharczyk R, Pawłowski K, Tomchick DR, Tagliabracci VS. Protein AMPylation by an Evolutionarily Conserved Pseudokinase. Cell 2018; 175:809-821.e19. [PMID: 30270044 DOI: 10.1016/j.cell.2018.08.046] [Citation(s) in RCA: 115] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 07/19/2018] [Accepted: 08/17/2018] [Indexed: 02/06/2023]
Abstract
Approximately 10% of human protein kinases are believed to be inactive and named pseudokinases because they lack residues required for catalysis. Here, we show that the highly conserved pseudokinase selenoprotein-O (SelO) transfers AMP from ATP to Ser, Thr, and Tyr residues on protein substrates (AMPylation), uncovering a previously unrecognized activity for a member of the protein kinase superfamily. The crystal structure of a SelO homolog reveals a protein kinase-like fold with ATP flipped in the active site, thus providing a structural basis for catalysis. SelO pseudokinases localize to the mitochondria and AMPylate proteins involved in redox homeostasis. Consequently, SelO activity is necessary for the proper cellular response to oxidative stress. Our results suggest that AMPylation may be a more widespread post-translational modification than previously appreciated and that pseudokinases should be analyzed for alternative transferase activities.
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Affiliation(s)
- Anju Sreelatha
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Samantha S Yee
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Victor A Lopez
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Brenden C Park
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Lisa N Kinch
- Howard Hughes Medical Institute, Dallas, TX 75390, USA
| | - Sylwia Pilch
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw 02-106, Poland
| | - Kelly A Servage
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Junmei Zhang
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jenny Jiou
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | | | - Małgorzata Łobocka
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw 02-106, Poland; Faculty of Agriculture and Biology, Warsaw University of Life Sciences, Warsaw 02-776, Poland
| | - Nick V Grishin
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Howard Hughes Medical Institute, Dallas, TX 75390, USA; Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Kim Orth
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Howard Hughes Medical Institute, Dallas, TX 75390, USA; Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Roza Kucharczyk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw 02-106, Poland
| | - Krzysztof Pawłowski
- Faculty of Agriculture and Biology, Warsaw University of Life Sciences, Warsaw 02-776, Poland
| | - Diana R Tomchick
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Vincent S Tagliabracci
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA; Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.
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43
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Hareza A, Bakun M, Świderska B, Dudkiewicz M, Koscielny A, Bajur A, Jaworski J, Dadlez M, Pawłowski K. Phosphoproteomic insights into processes influenced by the kinase-like protein DIA1/C3orf58. PeerJ 2018; 6:e4599. [PMID: 29666759 PMCID: PMC5896498 DOI: 10.7717/peerj.4599] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 03/21/2018] [Indexed: 12/27/2022] Open
Abstract
Many kinases are still ‘orphans,’ which means knowledge about their substrates, and often also about the processes they regulate, is lacking. Here, DIA1/C3orf58, a member of a novel predicted kinase-like family, is shown to be present in the endoplasmic reticulum and to influence trafficking via the secretory pathway. Subsequently, DIA1 is subjected to phosphoproteomics analysis to cast light on its signalling pathways. A liquid chromatography–tandem mass spectrometry proteomic approach with phosphopeptide enrichment is applied to membrane fractions of DIA1-overexpressing and control HEK293T cells, and phosphosites dependent on the presence of DIA1 are elucidated. Most of these phosphosites belonged to CK2- and proline-directed kinase types. In parallel, the proteomics of proteins immunoprecipitated with DIA1 reported its probable interactors. This pilot study provides the basis for deeper studies of DIA1 signalling.
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Affiliation(s)
- Agnieszka Hareza
- Department of Experimental Design and Bioinformatics, Faculty of Agriculture and Biology, Warsaw University of Life Sciences, Warszawa, Poland.,International Institute of Molecular and Cellular Biology, Warszawa, Poland
| | - Magda Bakun
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warszawa, Poland
| | - Bianka Świderska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warszawa, Poland
| | - Małgorzata Dudkiewicz
- Department of Experimental Design and Bioinformatics, Faculty of Agriculture and Biology, Warsaw University of Life Sciences, Warszawa, Poland
| | - Alicja Koscielny
- International Institute of Molecular and Cellular Biology, Warszawa, Poland
| | - Anna Bajur
- Department of Experimental Design and Bioinformatics, Faculty of Agriculture and Biology, Warsaw University of Life Sciences, Warszawa, Poland.,International Institute of Molecular and Cellular Biology, Warszawa, Poland.,Current affiliation: Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Jacek Jaworski
- International Institute of Molecular and Cellular Biology, Warszawa, Poland
| | - Michał Dadlez
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warszawa, Poland
| | - Krzysztof Pawłowski
- Department of Experimental Design and Bioinformatics, Faculty of Agriculture and Biology, Warsaw University of Life Sciences, Warszawa, Poland.,Department of Translational Medicine, Clinical Sciences, Lund University, Lund, Sweden
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44
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Hu D, Ansari D, Pawłowski K, Zhou Q, Sasor A, Welinder C, Kristl T, Bauden M, Rezeli M, Jiang Y, Marko-Varga G, Andersson R. Proteomic analyses identify prognostic biomarkers for pancreatic ductal adenocarcinoma. Oncotarget 2018. [PMID: 29515771 PMCID: PMC5839402 DOI: 10.18632/oncotarget.23929] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive malignancy. Here we show that shotgun and targeted protein sequencing can be used to identify potential prognostic biomarkers in formalin-fixed paraffin-embedded specimens from 9 patients with PDAC with “short” survival (<12 months) and 10 patients with “long” survival (>45 months) undergoing surgical resection. A total of 24 and 147 proteins were significantly upregulated [fold change ≥2 or ≤0.5 and P<0.05; or different detection frequencies (≥5 samples)] in patients with “short” survival (including GLUT1) and “long” survival (including C9orf64, FAM96A, CDH1 and CDH17), respectively. STRING analysis of these proteins indicated a tight protein-protein interaction network centered on TP53. Ingenuity pathway analysis linked proteins representing “activated stroma factors” and “basal tumor factors” to poor prognosis of PDAC. It also highlighted TCF1 and CTNNB1 as possible upstream regulators. Further parallel reaction monitoring verified that seven proteins were upregulated in patients with “short” survival (MMP9, CLIC3, MMP8, PRTN3, P4HA2, THBS1 and FN1), while 18 proteins were upregulated in patients with “long” survival, including EPCAM, LGALS4, VIL1, CLCA1 and TPPP3. Thus, we verified 25 protein biomarker candidates for PDAC prognosis at the tissue level. Furthermore, an activated stroma status and protein-protein interactions with TP53 might be linked to poor prognosis of PDAC.
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Affiliation(s)
- Dingyuan Hu
- Lund University, Faculty of Medicine, Department of Clinical Sciences Lund (Surgery), Lund, Sweden.,Department of Gastroenterology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Daniel Ansari
- Lund University, Skane University Hospital, Department of Clinical Sciences Lund (Surgery), Lund, Sweden
| | - Krzysztof Pawłowski
- Department of Experimental Design and Bioinformatics, Warsaw University of Life Sciences, Warsaw, Poland.,Department of Translational Medicine, Lund University, Malmö, Sweden
| | - Qimin Zhou
- Lund University, Faculty of Medicine, Department of Clinical Sciences Lund (Surgery), Lund, Sweden
| | - Agata Sasor
- Department of Pathology, Skåne University Hospital, Lund, Sweden
| | - Charlotte Welinder
- Lund University, Department of Clinical Sciences Lund, Division of Oncology and Pathology, Lund, Sweden
| | - Theresa Kristl
- Lund University, Department of Clinical Sciences Lund, Division of Oncology and Pathology, Lund, Sweden
| | - Monika Bauden
- Lund University, Faculty of Medicine, Department of Clinical Sciences Lund (Surgery), Lund, Sweden
| | - Melinda Rezeli
- Department of Biomedical Engineering, Clinical Protein Science and Imaging, Lund University, Lund, Sweden
| | - Yi Jiang
- Department of Gastroenterology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - György Marko-Varga
- Department of Biomedical Engineering, Clinical Protein Science and Imaging, Lund University, Lund, Sweden
| | - Roland Andersson
- Lund University, Skane University Hospital, Department of Clinical Sciences Lund (Surgery), Lund, Sweden
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46
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Gradowski M, Pawłowski K. The Legionella pneumophila effector Lpg1137 is a homologue of mitochondrial SLC25 carrier proteins, not of known serine proteases. PeerJ 2017; 5:e3849. [PMID: 28966893 PMCID: PMC5621508 DOI: 10.7717/peerj.3849] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 09/01/2017] [Indexed: 01/08/2023] Open
Abstract
Many bacterial effector proteins that are delivered to host cells during infection are enzymes targeting host cell signalling. Recently, Legionella pneumophila effector Lpg1137 was experimentally characterised as a serine protease that cleaves human syntaxin 17. We present strong bioinformatic evidence that Lpg1137 is a homologue of mitochondrial carrier proteins and is not related to known serine proteases. We also discuss how this finding can be reconciled with the apparently contradictory experimental results.
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Affiliation(s)
- Marcin Gradowski
- Department of Experimental Design and Bioinformatics, Faculty of Agriculture and Biology, Warsaw University of Life Sciences, Warszawa, Poland
| | - Krzysztof Pawłowski
- Department of Experimental Design and Bioinformatics, Faculty of Agriculture and Biology, Warsaw University of Life Sciences, Warszawa, Poland.,Department of Translational Medicine, Clinical Sciences, Lund University, Lund, Sweden
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47
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Welinder C, Pawłowski K, Szasz AM, Yakovleva M, Sugihara Y, Malm J, Jönsson G, Ingvar C, Lundgren L, Baldetorp B, Olsson H, Rezeli M, Laurell T, Wieslander E, Marko-Varga G. Correlation of histopathologic characteristics to protein expression and function in malignant melanoma. PLoS One 2017; 12:e0176167. [PMID: 28445515 PMCID: PMC5405986 DOI: 10.1371/journal.pone.0176167] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 04/06/2017] [Indexed: 12/11/2022] Open
Abstract
Background Metastatic melanoma is still one of the most prevalent skin cancers, which upon progression has neither a prognostic marker nor a specific and lasting treatment. Proteomic analysis is a versatile approach with high throughput data and results that can be used for characterizing tissue samples. However, such analysis is hampered by the complexity of the disease, heterogeneity of patients, tumors, and samples themselves. With the long term aim of quest for better diagnostics biomarkers, as well as predictive and prognostic markers, we focused on relating high resolution proteomics data to careful histopathological evaluation of the tumor samples and patient survival information. Patients and methods Regional lymph node metastases obtained from ten patients with metastatic melanoma (stage III) were analyzed by histopathology and proteomics using mass spectrometry. Out of the ten patients, six had clinical follow-up data. The protein deep mining mass spectrometry data was related to the histopathology tumor tissue sections adjacent to the area used for deep-mining. Clinical follow-up data provided information on disease progression which could be linked to protein expression aiming to identify tissue-based specific protein markers for metastatic melanoma and prognostic factors for prediction of progression of stage III disease. Results In this feasibility study, several proteins were identified that positively correlated to tumor tissue content including IF6, ARF4, MUC18, UBC12, CSPG4, PCNA, PMEL and MAGD2. The study also identified MYC, HNF4A and TGFB1 as top upstream regulators correlating to tumor tissue content. Other proteins were inversely correlated to tumor tissue content, the most significant being; TENX, EHD2, ZA2G, AOC3, FETUA and THRB. A number of proteins were significantly related to clinical outcome, among these, HEXB, PKM and GPNMB stood out, as hallmarks of processes involved in progression from stage III to stage IV disease and poor survival. Conclusion In this feasibility study, promising results show the feasibility of relating proteomics to histopathology and clinical outcome, and insight thus can be gained into the molecular processes driving the disease. The combined analysis of histological features including the sample cellular composition with protein expression of each metastasis enabled the identification of novel, differentially expressed proteins. Further studies are necessary to determine whether these putative biomarkers can be utilized in diagnostics and prognostic prediction of metastatic melanoma.
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Affiliation(s)
- Charlotte Welinder
- Division of Oncology and Pathology, Dept. of Clinical Sciences Lund, Lund University, Lund, Sweden
- Centre of Excellence in Biological and Medical Mass Spectrometry “CEBMMS”, Biomedical Centre D13, Lund University, Lund, Sweden
| | - Krzysztof Pawłowski
- Faculty of Agriculture and Biology, Dept. of Experimental Design and Bioinformatics, Warsaw University of Life Sciences, Warszawa, Poland
- Dept. of Translational Medicine, Lund University, Malmö, Sweden
| | - A. Marcell Szasz
- Division of Oncology and Pathology, Dept. of Clinical Sciences Lund, Lund University, Lund, Sweden
- Centre of Excellence in Biological and Medical Mass Spectrometry “CEBMMS”, Biomedical Centre D13, Lund University, Lund, Sweden
- 2nd Dept. of Pathology, Semmelweis University, Budapest, Hungary
| | - Maria Yakovleva
- Centre of Excellence in Biological and Medical Mass Spectrometry “CEBMMS”, Biomedical Centre D13, Lund University, Lund, Sweden
| | - Yutaka Sugihara
- Division of Oncology and Pathology, Dept. of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Johan Malm
- Centre of Excellence in Biological and Medical Mass Spectrometry “CEBMMS”, Biomedical Centre D13, Lund University, Lund, Sweden
- Dept. of Translational Medicine, Lund University, Malmö, Sweden
| | - Göran Jönsson
- Division of Oncology and Pathology, Dept. of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Christian Ingvar
- Dept. of Surgery, Dept. of Clinical Sciences Lund, Lund University, Skåne University Hospital, Lund, Sweden
| | - Lotta Lundgren
- Division of Oncology and Pathology, Dept. of Clinical Sciences Lund, Lund University, Lund, Sweden
- Dept. of Oncology, Skåne University Hospital, Lund, Sweden
| | - Bo Baldetorp
- Division of Oncology and Pathology, Dept. of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Håkan Olsson
- Division of Oncology and Pathology, Dept. of Clinical Sciences Lund, Lund University, Lund, Sweden
- Dept. of Oncology, Skåne University Hospital, Lund, Sweden
- Cancer Epidemiology, Dept. of Clinical Sciences, Lund University, Lund, Sweden
| | - Melinda Rezeli
- Clinical Protein Science & Imaging, Biomedical Centre, Dept. of Biomedical Engineering, Lund University, BMC D13, Lund, Sweden
| | - Thomas Laurell
- Centre of Excellence in Biological and Medical Mass Spectrometry “CEBMMS”, Biomedical Centre D13, Lund University, Lund, Sweden
- Clinical Protein Science & Imaging, Biomedical Centre, Dept. of Biomedical Engineering, Lund University, BMC D13, Lund, Sweden
| | - Elisabet Wieslander
- Division of Oncology and Pathology, Dept. of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - György Marko-Varga
- Centre of Excellence in Biological and Medical Mass Spectrometry “CEBMMS”, Biomedical Centre D13, Lund University, Lund, Sweden
- Clinical Protein Science & Imaging, Biomedical Centre, Dept. of Biomedical Engineering, Lund University, BMC D13, Lund, Sweden
- First Dept. of Surgery, Tokyo Medical University, Tokyo, Japan
- * E-mail:
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Kurach K, Pawłowski K. Predicting Dangerous Seismic Activity with Recurrent Neural Networks. Annals of Computer Science and Information Systems 2016. [DOI: 10.15439/2016f134] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Rezeli M, Gidlöf O, Evander M, Bryl-Górecka P, Sathanoori R, Gilje P, Pawłowski K, Horvatovich P, Erlinge D, Marko-Varga G, Laurell T. Comparative Proteomic Analysis of Extracellular Vesicles Isolated by Acoustic Trapping or Differential Centrifugation. Anal Chem 2016; 88:8577-86. [PMID: 27487081 DOI: 10.1021/acs.analchem.6b01694] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Extracellular vesicles (ECVs), including microparticles and exosomes, are submicrometer membrane vesicles released by diverse cell types upon activation or stress. Circulating ECVs are potential reservoirs of disease biomarkers, and the complexity of these vesicles is significantly lower compared to their source, blood plasma, which makes ECV-based biomarker studies more promising. Proteomic profiling of ECVs is important not only to discover new diagnostic or prognostic markers but also to understand their roles in biological function. In the current study, we investigated the protein composition of plasma-derived ECVs isolated by acoustic seed trapping. Additionally, the protein composition of ECVs isolated with acoustic trapping was compared to that isolated with a conventional differential centrifugation protocol. Finally, the proteome of ECVs originating from ST-elevation myocardial infarction patients was compared with that of healthy controls using label-free LC-MS quantification. The acoustic trapping platform allows rapid and automated preparation of ECVs from small sample volumes, which are therefore well-suited for biobank repositories. We found that the protein composition of trapped ECVs is very similar to that isolated by the conventional differential centrifugation method.
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Affiliation(s)
| | | | | | | | | | | | - Krzysztof Pawłowski
- Department of Experimental Design and Bioinformatics, Faculty of Agriculture and Biology, Warsaw University of Life Sciences , Warsaw, Poland
| | - Péter Horvatovich
- Analytical Biochemistry, Department of Pharmacy, University of Groningen , Groningen, The Netherlands
| | | | | | - Thomas Laurell
- Department of Biomedical Engineering, Dongguk University , Seoul, Korea
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Yakovleva ME, Welinder C, Sugihara Y, Pawłowski K, Rezeli M, Wieslander E, Malm J, Marko-Varga G. Workflow for large-scale analysis of melanoma tissue samples. EuPA Open Proteomics 2015. [DOI: 10.1016/j.euprot.2015.07.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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