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Wickramarachchi A, Hosking B, Jain Y, Grimes J, O'Brien MJ, Wright T, Burgess MA, Lin VSK, Reisinger F, Hofmann O, Lawley M, Wilson LOW, Twine NA, Bauer DC. Scalable genomic data exchange and analytics with sBeacon. Nat Biotechnol 2023; 41:1510-1512. [PMID: 37709914 DOI: 10.1038/s41587-023-01972-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/16/2023]
Affiliation(s)
- Anuradha Wickramarachchi
- Australian e-Health Research Centre, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Westmead, New South Wales, Australia
| | - Brendan Hosking
- Australian e-Health Research Centre, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Westmead, New South Wales, Australia
| | - Yatish Jain
- Australian e-Health Research Centre, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Westmead, New South Wales, Australia
- Applied BioSciences, Faculty of Science and Engineering, Macquarie University, Macquarie Park, New South Wales, Australia
| | - John Grimes
- Australian e-Health Research Centre, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Herston, Queensland, Australia
| | - Mitchell J O'Brien
- Australian e-Health Research Centre, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Westmead, New South Wales, Australia
| | - Tracey Wright
- Australian e-Health Research Centre, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Herston, Queensland, Australia
| | - Mark A Burgess
- Australian e-Health Research Centre, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Canberra, Australian Capital Territory, Australia
| | - Victor San Kho Lin
- Centre for Cancer Research, University of Melbourne, Victorian Comprehensive Cancer Centre, Melbourne, Victoria, Australia
| | - Florian Reisinger
- Centre for Cancer Research, University of Melbourne, Victorian Comprehensive Cancer Centre, Melbourne, Victoria, Australia
| | - Oliver Hofmann
- Centre for Cancer Research, University of Melbourne, Victorian Comprehensive Cancer Centre, Melbourne, Victoria, Australia
| | - Michael Lawley
- Australian e-Health Research Centre, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Herston, Queensland, Australia
| | - Laurence O W Wilson
- Australian e-Health Research Centre, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Westmead, New South Wales, Australia
- Applied BioSciences, Faculty of Science and Engineering, Macquarie University, Macquarie Park, New South Wales, Australia
| | - Natalie A Twine
- Australian e-Health Research Centre, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Westmead, New South Wales, Australia
- Applied BioSciences, Faculty of Science and Engineering, Macquarie University, Macquarie Park, New South Wales, Australia
| | - Denis C Bauer
- Applied BioSciences, Faculty of Science and Engineering, Macquarie University, Macquarie Park, New South Wales, Australia.
- Department of Biomedical Sciences, Macquarie University, Macquarie Park, New South Wales, Australia.
- Australian e-Health Research Centre, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Adelaide, South Australia, Australia.
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Faure-Dupuy S, Riedl T, Rolland M, Hizir Z, Reisinger F, Neuhaus K, Schuehle S, Remouchamps C, Gillet N, Schönung M, Stadler M, Wettengel J, Barnault R, Parent R, Schuster LC, Farhat R, Prokosch S, Leuchtenberger C, Öllinger R, Engleitner T, Rippe K, Rad R, Unger K, Tscharahganeh D, Lipka DB, Protzer U, Durantel D, Lucifora J, Dejardin E, Heikenwälder M. Control of APOBEC3B induction and cccDNA decay by NF-κB and miR-138-5p. JHEP Rep 2021; 3:100354. [PMID: 34704004 PMCID: PMC8523871 DOI: 10.1016/j.jhepr.2021.100354] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 07/28/2021] [Accepted: 08/17/2021] [Indexed: 12/13/2022] Open
Abstract
Background & Aims Immune-mediated induction of cytidine deaminase APOBEC3B (A3B) expression leads to HBV covalently closed circular DNA (cccDNA) decay. Here, we aimed to decipher the signalling pathway(s) and regulatory mechanism(s) involved in A3B induction and related HBV control. Methods Differentiated HepaRG cells (dHepaRG) knocked-down for NF-κB signalling components, transfected with siRNA or micro RNAs (miRNA), and primary human hepatocytes ± HBV or HBVΔX or HBV-RFP, were treated with lymphotoxin beta receptor (LTβR)-agonist (BS1). The biological outcomes were analysed by reverse transcriptase-qPCR, immunoblotting, luciferase activity, chromatin immune precipitation, electrophoretic mobility-shift assay, targeted-bisulfite-, miRNA-, RNA-, genome-sequencing, and mass-spectrometry. Results We found that canonical and non-canonical NF-κB signalling pathways are mandatory for A3B induction and anti-HBV effects. The degree of immune-mediated A3B production is independent of A3B promoter demethylation but is controlled post-transcriptionally by the miRNA 138-5p expression (hsa-miR-138-5p), promoting A3B mRNA decay. Hsa-miR-138-5p over-expression reduced A3B levels and its antiviral effects. Of note, established infection inhibited BS1-induced A3B expression through epigenetic modulation of A3B promoter. Twelve days of treatment with a LTβR-specific agonist BS1 is sufficient to reduce the cccDNA pool by 80% without inducing significant damages to a subset of cancer-related host genes. Interestingly, the A3B-mediated effect on HBV is independent of the transcriptional activity of cccDNA as well as on rcDNA synthesis. Conclusions Altogether, A3B represents the only described enzyme to target both transcriptionally active and inactive cccDNA. Thus, inhibiting hsa-miR-138-5p expression should be considered in the combinatorial design of new therapies against HBV, especially in the context of immune-mediated A3B induction. Lay summary Immune-mediated induction of cytidine deaminase APOBEC3B is transcriptionally regulated by NF-κB signalling and post-transcriptionally downregulated by hsa-miR-138-5p expression, leading to cccDNA decay. Timely controlled APOBEC3B-mediated cccDNA decay occurs independently of cccDNA transcriptional activity and without damage to a subset of cancer-related genes. Thus, APOBEC3B-mediated cccDNA decay could offer an efficient therapeutic alternative to target hepatitis B virus chronic infection. Impairment of NF-κB signalling prevents APOBEC3B induction and cccDNA decay. APOBEC3B is post-transcriptionally regulated by the hsa-miR-138-5p. Over-expression of the hsa-miR-138-5p inhibits APOBEC3B expression and cccDNA decay. A3B timely induces cccDNA decay without damage to cancer-related genes. APOBEC3B-mediated cccDNA decay is independent of cccDNA transcriptional activity.
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Key Words
- A20, tumour necrosis factor alpha-induced protein 3
- APOBEC3A/A3A, apolipoprotein B mRNA editing catalytic polypeptide-like A
- APOBEC3B
- APOBEC3B/A3B, apolipoprotein B mRNA editing catalytic polypeptide-like B
- APOBEC3G/A3G, apolipoprotein B mRNA editing catalytic polypeptide-like G
- BCA, bicinchoninic acid assay
- CHB, chronic hepatitis B
- CXCL10, C-X-C motif chemokine ligand 10
- ChIP, chromatin immune precipitation
- EMSA, electrophoretic mobility-shift assay
- H3K4Me3, histone 3 lysine 4 trimethylation
- HBx
- Hepatitis B virus
- IFNα/γ, interferon alpha/gamma
- IKKα/β, IκB kinase alpha/beta
- JMJD8, jumonji domain containing 8
- LPS, lipopolysaccharide
- LTβR, lymphotoxin beta receptor
- MAPK, mitogen-activated protein kinase
- NEMO, NF-κB essential modulator
- NF-κB
- NF-κB, nuclear factor kappa B
- NIK, NF-κB inducing kinase
- NT, non-treated
- RT-qPCR, reverse transcription-quantitative PCR
- RelA, NF-κB p65 subunit
- TNF, tumour necrosis factor
- UBE2V1, ubiquitin conjugating enzyme E2 V1
- UTR, untranslated region
- cccDNA
- cccDNA, covalently closed circular DNA
- d.p.i., days post infection
- miRNA
- miRNA, micro RNA
- siCTRL, siRNA control
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Affiliation(s)
- Suzanne Faure-Dupuy
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Tobias Riedl
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Maude Rolland
- Laboratory of Molecular Immunology and Signal Transduction, GIGA-Institute, University of Liège, Liège, Belgium
| | - Zoheir Hizir
- Laboratory of Molecular Immunology and Signal Transduction, GIGA-Institute, University of Liège, Liège, Belgium
| | - Florian Reisinger
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute of Virology, Helmholtz Zentrum München, Munich, Germany
| | - Katharina Neuhaus
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Svenja Schuehle
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Caroline Remouchamps
- Laboratory of Molecular Immunology and Signal Transduction, GIGA-Institute, University of Liège, Liège, Belgium
| | - Nicolas Gillet
- Integrated Veterinary Research Unit, Namur Research Institute for Life Sciences, Namur, Belgium
| | - Maximilian Schönung
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
- Section Translational Cancer Epigenomics, Division of Translational Medical Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Mira Stadler
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Jochen Wettengel
- Institute of Virology, Helmholtz Zentrum München, Munich, Germany
| | - Romain Barnault
- INSERM, U1052, Cancer Research Center of Lyon (CRCL), University of Lyon (UCBL1), CNRS UMR_5286, Centre Léon Bérard (CLB), Lyon, France
| | - Romain Parent
- INSERM, U1052, Cancer Research Center of Lyon (CRCL), University of Lyon (UCBL1), CNRS UMR_5286, Centre Léon Bérard (CLB), Lyon, France
| | - Linda Christina Schuster
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
| | - Rayan Farhat
- INSERM, U1052, Cancer Research Center of Lyon (CRCL), University of Lyon (UCBL1), CNRS UMR_5286, Centre Léon Bérard (CLB), Lyon, France
| | - Sandra Prokosch
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Corinna Leuchtenberger
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Rupert Öllinger
- Institute of Molecular Oncology and Functional Genomics, Rechts der Isar University Hospital, Munich, Germany
| | - Thomas Engleitner
- Institute of Molecular Oncology and Functional Genomics, Rechts der Isar University Hospital, Munich, Germany
| | - Karsten Rippe
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
| | - Roland Rad
- Institute of Molecular Oncology and Functional Genomics, Rechts der Isar University Hospital, Munich, Germany
| | - Kristian Unger
- Research Unit of Radiation Cytogenetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Darjus Tscharahganeh
- Helmholtz-University Group 'Cell Plasticity and Epigenetic Remodeling', German Cancer Research Center (DKFZ) and Institute of Pathology University Hospital, Heidelberg, Germany
| | - Daniel B. Lipka
- Section Translational Cancer Epigenomics, Division of Translational Medical Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
- Faculty of Medicine, Otto-von-Guericke-University, Magdeburg, Germany
| | - Ulrike Protzer
- Institute of Virology, Helmholtz Zentrum München, Munich, Germany
| | - David Durantel
- INSERM, U1052, Cancer Research Center of Lyon (CRCL), University of Lyon (UCBL1), CNRS UMR_5286, Centre Léon Bérard (CLB), Lyon, France
| | - Julie Lucifora
- INSERM, U1052, Cancer Research Center of Lyon (CRCL), University of Lyon (UCBL1), CNRS UMR_5286, Centre Léon Bérard (CLB), Lyon, France
| | - Emmanuel Dejardin
- Laboratory of Molecular Immunology and Signal Transduction, GIGA-Institute, University of Liège, Liège, Belgium
- Corresponding authors. Addresses: Laboratory of Molecular Immunology and Signal Transduction, University of Liège, GIGA-Institute, Avenue de l'Hôpital, 1, CHU, B34, 4000 Liege, Belgium. Tel.: +32 4 366 4472; fax: +32 4 366 4534
| | - Mathias Heikenwälder
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
- Division Chronic Inflammation and Cancer (F180), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 242, 69120 Heidelberg, Germany. Tel.: +49 6221 42 3891; Fax: +49 6221 42 3899
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Dahlberg J, Hermansson J, Sturlaugsson S, Lysenkova M, Smeds P, Ladenvall C, Guimera RV, Reisinger F, Hofmann O, Larsson P. Arteria: An automation system for a sequencing core facility. Gigascience 2019; 8:giz135. [PMID: 31825479 PMCID: PMC6905352 DOI: 10.1093/gigascience/giz135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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: 05/21/2019] [Revised: 09/19/2019] [Accepted: 10/22/2019] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND In recent years, nucleotide sequencing has become increasingly instrumental in both research and clinical settings. This has led to an explosive growth in sequencing data produced worldwide. As the amount of data increases, so does the need for automated solutions for data processing and analysis. The concept of workflows has gained favour in the bioinformatics community, but there is little in the scientific literature describing end-to-end automation systems. Arteria is an automation system that aims at providing a solution to the data-related operational challenges that face sequencing core facilities. FINDINGS Arteria is built on existing open source technologies, with a modular design allowing for a community-driven effort to create plug-and-play micro-services. In this article we describe the system, elaborate on the underlying conceptual framework, and present an example implementation. Arteria can be reduced to 3 conceptual levels: orchestration (using an event-based model of automation), process (the steps involved in processing sequencing data, modelled as workflows), and execution (using a series of RESTful micro-services). This creates a system that is both flexible and scalable. Arteria-based systems have been successfully deployed at 3 sequencing core facilities. The Arteria Project code, written largely in Python, is available as open source software, and more information can be found at https://arteria-project.github.io/ . CONCLUSIONS We describe the Arteria system and the underlying conceptual framework, demonstrating how this model can be used to automate data handling and analysis in the context of a sequencing core facility.
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Affiliation(s)
- Johan Dahlberg
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Box 1432, BMC 751 44, Uppsala, Sweden
| | - Johan Hermansson
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Box 1432, BMC 751 44, Uppsala, Sweden
| | - Steinar Sturlaugsson
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Box 1432, BMC 751 44, Uppsala, Sweden
| | - Mariya Lysenkova
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Box 1432, BMC 751 44, Uppsala, Sweden
| | - Patrik Smeds
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Rudbecklaboratoriet, 751 84, Uppsala, Sweden
| | - Claes Ladenvall
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Rudbecklaboratoriet, 751 84, Uppsala, Sweden
| | - Roman Valls Guimera
- University of Melbourne Center for Cancer Research, University of Melbourne, Victorian Comprehensive Cancer Centre, Level 10, UMCCR, 305 Grattan St, Melbourne VIC 3000, Australia
| | - Florian Reisinger
- University of Melbourne Center for Cancer Research, University of Melbourne, Victorian Comprehensive Cancer Centre, Level 10, UMCCR, 305 Grattan St, Melbourne VIC 3000, Australia
| | - Oliver Hofmann
- University of Melbourne Center for Cancer Research, University of Melbourne, Victorian Comprehensive Cancer Centre, Level 10, UMCCR, 305 Grattan St, Melbourne VIC 3000, Australia
| | - Pontus Larsson
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Box 1432, BMC 751 44, Uppsala, Sweden
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Yuan D, Huang S, Berger E, Liu L, Gross N, Heinzmann F, Ringelhan M, Connor TO, Stadler M, Meister M, Weber J, Öllinger R, Simonavicius N, Reisinger F, Hartmann D, Meyer R, Reich M, Seehawer M, Leone V, Höchst B, Wohlleber D, Jörs S, Prinz M, Spalding D, Protzer U, Luedde T, Terracciano L, Matter M, Longerich T, Knolle P, Ried T, Keitel V, Geisler F, Unger K, Cinnamon E, Pikarsky E, Hüser N, Davis RJ, Tschaharganeh DF, Rad R, Weber A, Zender L, Haller D, Heikenwalder M. Kupffer Cell-Derived Tnf Triggers Cholangiocellular Tumorigenesis through JNK due to Chronic Mitochondrial Dysfunction and ROS. Cancer Cell 2017; 31:771-789.e6. [PMID: 28609656 PMCID: PMC7909318 DOI: 10.1016/j.ccell.2017.05.006] [Citation(s) in RCA: 134] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 01/31/2017] [Accepted: 05/11/2017] [Indexed: 12/15/2022]
Abstract
Intrahepatic cholangiocarcinoma (ICC) is a highly malignant, heterogeneous cancer with poor treatment options. We found that mitochondrial dysfunction and oxidative stress trigger a niche favoring cholangiocellular overgrowth and tumorigenesis. Liver damage, reactive oxygen species (ROS) and paracrine tumor necrosis factor (Tnf) from Kupffer cells caused JNK-mediated cholangiocellular proliferation and oncogenic transformation. Anti-oxidant treatment, Kupffer cell depletion, Tnfr1 deletion, or JNK inhibition reduced cholangiocellular pre-neoplastic lesions. Liver-specific JNK1/2 deletion led to tumor reduction and enhanced survival in Akt/Notch- or p53/Kras-induced ICC models. In human ICC, high Tnf expression near ICC lesions, cholangiocellular JNK-phosphorylation, and ROS accumulation in surrounding hepatocytes are present. Thus, Kupffer cell-derived Tnf favors cholangiocellular proliferation/differentiation and carcinogenesis. Targeting the ROS/Tnf/JNK axis may provide opportunities for ICC therapy.
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Affiliation(s)
- Detian Yuan
- Institute of Virology, Technische Universität München and Helmholtz Zentrum München, 81675 Munich, Germany; Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Shan Huang
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Emanuel Berger
- Chair of Nutrition and Immunology, Technische Universität München, Gregor-Mendel-Straße 2, 85350 Freising-Weihenstephan, Germany
| | - Lei Liu
- Department of Surgery, Technische Universität München, 81675 Munich, Germany
| | - Nina Gross
- 2nd Department of Internal Medicine, Klinikum Rechts der Isar, Technische Universität München, 81675 Munich, Germany
| | - Florian Heinzmann
- Department of Internal Medicine VIII, University Hospital Tübingen, 72076 Tübingen, Germany; Department of Physiology I, Institute of Physiology, Eberhard Karls University Tübingen, 72076 Tübingen, Germany
| | - Marc Ringelhan
- Institute of Virology, Technische Universität München and Helmholtz Zentrum München, 81675 Munich, Germany; 2nd Department of Internal Medicine, Klinikum Rechts der Isar, Technische Universität München, 81675 Munich, Germany
| | - Tracy O Connor
- Institute of Virology, Technische Universität München and Helmholtz Zentrum München, 81675 Munich, Germany; Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Mira Stadler
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Michael Meister
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Julia Weber
- 2nd Department of Internal Medicine, Klinikum Rechts der Isar, Technische Universität München, 81675 Munich, Germany
| | - Rupert Öllinger
- 2nd Department of Internal Medicine, Klinikum Rechts der Isar, Technische Universität München, 81675 Munich, Germany
| | - Nicole Simonavicius
- Institute of Virology, Technische Universität München and Helmholtz Zentrum München, 81675 Munich, Germany
| | - Florian Reisinger
- Institute of Virology, Technische Universität München and Helmholtz Zentrum München, 81675 Munich, Germany
| | - Daniel Hartmann
- Department of Surgery, Technische Universität München, 81675 Munich, Germany
| | - Rüdiger Meyer
- Genome Technology Branch, National Human Genome Research Institute, U.S. National Institutes of Health, Bethesda, MD 20892, USA
| | - Maria Reich
- Clinic for Gastroenterology, Hepatology, and Infectious Diseases, Heinrich-Heine University, 40204 Düsseldorf, Germany
| | - Marco Seehawer
- Department of Internal Medicine VIII, University Hospital Tübingen, 72076 Tübingen, Germany; Department of Physiology I, Institute of Physiology, Eberhard Karls University Tübingen, 72076 Tübingen, Germany
| | - Valentina Leone
- Institute of Virology, Technische Universität München and Helmholtz Zentrum München, 81675 Munich, Germany
| | - Bastian Höchst
- Institute of Molecular Immunology, Klinikum rechts der Isar, Technische Universität München, 81675 Munich, Germany
| | - Dirk Wohlleber
- Institute of Molecular Immunology, Klinikum rechts der Isar, Technische Universität München, 81675 Munich, Germany
| | - Simone Jörs
- 2nd Department of Internal Medicine, Klinikum Rechts der Isar, Technische Universität München, 81675 Munich, Germany
| | - Marco Prinz
- Institute of Neuropathology, University of Freiburg, 79106 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79106 Freiburg, Germany
| | - Duncan Spalding
- Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, UK
| | - Ulrike Protzer
- Institute of Virology, Technische Universität München and Helmholtz Zentrum München, 81675 Munich, Germany
| | - Tom Luedde
- Division of Gastroenterology, Hepatology and Hepatobiliary Oncology, RWTH Aachen University, 52074 Aachen, Germany
| | - Luigi Terracciano
- Institute of Pathology, University Hospital of Basel, 4003 Basel, Switzerland
| | - Matthias Matter
- Institute of Pathology, University Hospital of Basel, 4003 Basel, Switzerland
| | - Thomas Longerich
- Institute of Pathology, University Hospital RWTH, 52074 Aachen, Germany
| | - Percy Knolle
- Institute of Molecular Immunology, Klinikum rechts der Isar, Technische Universität München, 81675 Munich, Germany
| | - Thomas Ried
- Genome Technology Branch, National Human Genome Research Institute, U.S. National Institutes of Health, Bethesda, MD 20892, USA
| | - Verena Keitel
- Clinic for Gastroenterology, Hepatology, and Infectious Diseases, Heinrich-Heine University, 40204 Düsseldorf, Germany
| | - Fabian Geisler
- 2nd Department of Internal Medicine, Klinikum Rechts der Isar, Technische Universität München, 81675 Munich, Germany
| | - Kristian Unger
- Research Unit of Radiation Cytogenetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Einat Cinnamon
- The Lautenberg Center for Immunology and Cancer Research, IMRIC, Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Eli Pikarsky
- The Lautenberg Center for Immunology and Cancer Research, IMRIC, Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel; Department of Pathology, Hadassah-Hebrew University Medical Center, Jerusalem 91120, Israel
| | - Norbert Hüser
- Department of Surgery, Technische Universität München, 81675 Munich, Germany
| | - Roger J Davis
- Howard Hughes Medical Institute and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Darjus F Tschaharganeh
- Helmholtz-University Group "Cell Plasticity and Epigenetic Remodeling", German Cancer Research Center (DKFZ) & Institute of Pathology University Hospital, 69120 Heidelberg, Germany
| | - Roland Rad
- 2nd Department of Internal Medicine, Klinikum Rechts der Isar, Technische Universität München, 81675 Munich, Germany
| | - Achim Weber
- Department of Pathology and Molecular Pathology, University Zurich and University Hospital Zurich, 8091 Zurich, Switzerland
| | - Lars Zender
- Department of Internal Medicine VIII, University Hospital Tübingen, 72076 Tübingen, Germany; Department of Physiology I, Institute of Physiology, Eberhard Karls University Tübingen, 72076 Tübingen, Germany; Translational Gastrointestinal Oncology Group within the German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Dirk Haller
- Chair of Nutrition and Immunology, Technische Universität München, Gregor-Mendel-Straße 2, 85350 Freising-Weihenstephan, Germany; ZIEL - Institute for Food & Health, Technische Universität München, 85350 Freising-Weihenstephan, Germany.
| | - Mathias Heikenwalder
- Institute of Virology, Technische Universität München and Helmholtz Zentrum München, 81675 Munich, Germany; Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.
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Vizcaíno JA, Csordas A, Del-Toro N, Dianes JA, Griss J, Lavidas I, Mayer G, Perez-Riverol Y, Reisinger F, Ternent T, Xu QW, Wang R, Hermjakob H. 2016 update of the PRIDE database and its related tools. Nucleic Acids Res 2016; 44:11033. [PMID: 27683222 PMCID: PMC5159556 DOI: 10.1093/nar/gkw880] [Citation(s) in RCA: 600] [Impact Index Per Article: 75.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Juan Antonio Vizcaíno
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Attila Csordas
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Noemi Del-Toro
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - José A Dianes
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Johannes Griss
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
- Division of Immunology, Allergy and Infectious Diseases, Department of Dermatology, Medical University of Vienna, Austria
| | - Ilias Lavidas
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Gerhard Mayer
- Medizinisches Proteom Center (MPC), Ruhr-Universität Bochum, D-44801 Bochum, Germany
| | - Yasset Perez-Riverol
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Florian Reisinger
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Tobias Ternent
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Qing-Wei Xu
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
- Department of Computer Science and Technology, Hubei University of Education, Wuhan, China
| | - Rui Wang
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Henning Hermjakob
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
- National Center for Protein Sciences, Beijing, China
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6
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Eggert T, Wolter K, Ji J, Ma C, Yevsa T, Klotz S, Medina-Echeverz J, Longerich T, Forgues M, Reisinger F, Heikenwalder M, Wang XW, Zender L, Greten TF. Distinct Functions of Senescence-Associated Immune Responses in Liver Tumor Surveillance and Tumor Progression. Cancer Cell 2016; 30:533-547. [PMID: 27728804 PMCID: PMC7789819 DOI: 10.1016/j.ccell.2016.09.003] [Citation(s) in RCA: 363] [Impact Index Per Article: 45.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 03/28/2016] [Accepted: 09/12/2016] [Indexed: 02/08/2023]
Abstract
Oncogene-induced senescence causes hepatocytes to secrete cytokines, which induce their immune-mediated clearance to prevent tumor initiation, a process termed "senescence surveillance." However, senescent hepatocytes give rise to hepatocellular carcinomas (HCCs), if the senescence program is bypassed or if senescent cells are not cleared. Here, we show context-specific roles for CCR2+ myeloid cells in liver cancer. Senescence surveillance requires the recruitment and maturation of CCR2+ myeloid cells, and CCR2 ablation caused outgrowth of HCC. In contrast, HCC cells block the maturation of recruited myeloid precursors, which, through NK cell inhibition, promote growth of murine HCC and worsen the prognosis and survival of human HCC patients. Thus, while senescent hepatocyte-secreted chemokines suppress liver cancer initiation, they may accelerate the growth of fully established HCC.
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Affiliation(s)
- Tobias Eggert
- Gastrointestinal Malignancy Section, Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Katharina Wolter
- Division of Gastrointestinal Oncology, Department of Internal Medicine I, University of Tübingen, 72076 Tübingen, Germany
| | - Juling Ji
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Chi Ma
- Gastrointestinal Malignancy Section, Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tetyana Yevsa
- Division of Gastrointestinal Oncology, Department of Internal Medicine I, University of Tübingen, 72076 Tübingen, Germany
| | - Sabrina Klotz
- Division of Gastrointestinal Oncology, Department of Internal Medicine I, University of Tübingen, 72076 Tübingen, Germany
| | - José Medina-Echeverz
- Gastrointestinal Malignancy Section, Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Thomas Longerich
- Institute of Pathology, University Hospital RWTH Aachen, 52074 Aachen, Germany
| | - Marshonna Forgues
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Florian Reisinger
- Institute of Virology, Technische Universität München and Helmholtz Zentrum München, 81675 Munich, Germany; Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Mathias Heikenwalder
- Institute of Virology, Technische Universität München and Helmholtz Zentrum München, 81675 Munich, Germany; Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Xin Wei Wang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lars Zender
- Division of Gastrointestinal Oncology, Department of Internal Medicine I, University of Tübingen, 72076 Tübingen, Germany; Translational Gastrointestinal Oncology Group within the German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.
| | - Tim F Greten
- Gastrointestinal Malignancy Section, Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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7
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Koppe C, Verheugd P, Gautheron J, Reisinger F, Kreggenwinkel K, Roderburg C, Quagliata L, Terracciano L, Gassler N, Tolba RH, Boege Y, Weber A, Karin M, Luedde M, Neumann UP, Weiskirchen R, Tacke F, Vucur M, Trautwein C, Lüscher B, Preisinger C, Heikenwalder M, Luedde T. IκB kinaseα/β control biliary homeostasis and hepatocarcinogenesis in mice by phosphorylating the cell-death mediator receptor-interacting protein kinase 1. Hepatology 2016; 64:1217-31. [PMID: 27396433 DOI: 10.1002/hep.28723] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 07/01/2016] [Indexed: 02/06/2023]
Abstract
UNLABELLED The IκB-Kinase (IKK) complex-consisting of the catalytic subunits, IKKα and IKKβ, as well as the regulatory subunit, NEMO-mediates activation of the nuclear factor κB (NF-κB) pathway, but previous studies suggested the existence of NF-κB-independent functions of IKK subunits with potential impact on liver physiology and disease. Programmed cell death is a crucial factor in the progression of liver diseases, and receptor-interacting kinases (RIPKs) exerts strategic control over multiple pathways involved in regulating novel programmed cell-death pathways and inflammation. We hypothesized that RIPKs might be unrecognized targets of the catalytic IKK-complex subunits, thereby regulating hepatocarcinogenesis and cholestasis. In this present study, mice with specific genetic inhibition of catalytic IKK activity in liver parenchymal cells (LPCs; IKKα/β(LPC-KO) ) were intercrossed with RIPK1(LPC-KO) or RIPK3(-/-) mice to examine whether RIPK1 or RIPK3 might be downstream targets of IKKs. Moreover, we performed in vivo phospho-proteome analyses and in vitro kinase assays, mass spectrometry, and mutagenesis experiments. These analyses revealed that IKKα and IKKβ-in addition to their known function in NF-κB activation-directly phosphorylate RIPK1 at distinct regions of the protein, thereby regulating cell viability. Loss of this IKKα/β-dependent RIPK1 phosphorylation in LPCs inhibits compensatory proliferation of hepatocytes and intrahepatic biliary cells, thus impeding HCC development, but promoting biliary cell paucity and lethal cholestasis. CONCLUSIONS IKK-complex subunits transmit a previously unrecognized signal through RIPK1, which is fundamental for the long-term consequences of chronic hepatic inflammation and might have potential implications for future pharmacological strategies against cholestatic liver disease and cancer. (Hepatology 2016;64:1217-1231).
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Affiliation(s)
- Christiane Koppe
- Department of Medicine III, Division of Gastroenterology, Hepatology and Hepatobiliary Oncology, University Hospital RWTH Aachen, Aachen, Germany
| | - Patricia Verheugd
- Institute of Biochemistry and Molecular Biology, University Hospital RWTH Aachen University, Aachen, Germany
| | - Jérémie Gautheron
- Department of Medicine III, Division of Gastroenterology, Hepatology and Hepatobiliary Oncology, University Hospital RWTH Aachen, Aachen, Germany
| | - Florian Reisinger
- Department of Virology, Technische Universität München/Helmholtz Zentrum München für Gesundheit und Umwelt (HMGU), Munich, Germany
| | - Karina Kreggenwinkel
- Department of Medicine III, Division of Gastroenterology, Hepatology and Hepatobiliary Oncology, University Hospital RWTH Aachen, Aachen, Germany
| | - Christoph Roderburg
- Department of Medicine III, Division of Gastroenterology, Hepatology and Hepatobiliary Oncology, University Hospital RWTH Aachen, Aachen, Germany
| | - Luca Quagliata
- Institute of Pathology, University Hospital of Basel, Basel, Switzerland
| | - Luigi Terracciano
- Institute of Pathology, University Hospital of Basel, Basel, Switzerland
| | - Nikolaus Gassler
- Institute of Pathology, Hospital of Braunschweig, Braunschweig, Germany
| | - René H Tolba
- Department of Laboratory Animal Research, University Hospital RWTH Aachen, Aachen, Germany
| | - Yannick Boege
- Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Achim Weber
- Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Michael Karin
- Department of Pharmacology and Pathology, School of Medicine, UCSD, La Jolla, CA
| | - Mark Luedde
- Department of Cardiology and Angiology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Ulf P Neumann
- Department of Visceral and Transplantation Surgery, University Hospital RWTH Aachen, Aachen, Germany
| | - Ralf Weiskirchen
- Institute of Molecular Pathobiochemistry, Experimental Gene Therapy and Clinical Chemistry, University Hospital RWTH Aachen, Aachen, Germany
| | - Frank Tacke
- Department of Medicine III, Division of Gastroenterology, Hepatology and Hepatobiliary Oncology, University Hospital RWTH Aachen, Aachen, Germany
| | - Mihael Vucur
- Department of Medicine III, Division of Gastroenterology, Hepatology and Hepatobiliary Oncology, University Hospital RWTH Aachen, Aachen, Germany
| | - Christian Trautwein
- Department of Medicine III, Division of Gastroenterology, Hepatology and Hepatobiliary Oncology, University Hospital RWTH Aachen, Aachen, Germany
| | - Bernhard Lüscher
- Institute of Biochemistry and Molecular Biology, University Hospital RWTH Aachen University, Aachen, Germany
| | - Christian Preisinger
- Proteomics Facility, Interdisciplinary Center for Clinical Research (IZKF) Aachen, University Hospital RWTH Aachen, Aachen, Germany
| | - Mathias Heikenwalder
- Department of Virology, Technische Universität München/Helmholtz Zentrum München für Gesundheit und Umwelt (HMGU), Munich, Germany.,Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Tom Luedde
- Department of Medicine III, Division of Gastroenterology, Hepatology and Hepatobiliary Oncology, University Hospital RWTH Aachen, Aachen, Germany.
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8
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Endig J, Buitrago-Molina LE, Marhenke S, Reisinger F, Saborowski A, Schütt J, Limbourg F, Könecke C, Schreder A, Michael A, Misslitz AC, Healy ME, Geffers R, Clavel T, Haller D, Unger K, Finegold M, Weber A, Manns MP, Longerich T, Heikenwälder M, Vogel A. Dual Role of the Adaptive Immune System in Liver Injury and Hepatocellular Carcinoma Development. Cancer Cell 2016; 30:308-323. [PMID: 27478039 DOI: 10.1016/j.ccell.2016.06.009] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Revised: 03/09/2016] [Accepted: 06/16/2016] [Indexed: 12/19/2022]
Abstract
Hepatocellular carcinoma (HCC) represents a classic example of inflammation-linked cancer. To characterize the role of the immune system in hepatic injury and tumor development, we comparatively studied the extent of liver disease and hepatocarcinogenesis in immunocompromised versus immunocompetent Fah-deficient mice. Strikingly, chronic liver injury and tumor development were markedly suppressed in alymphoid Fah(-/-) mice despite an overall increased mortality. Mechanistically, we show that CD8(+) T cells and lymphotoxin β are central mediators of HCC formation. Antibody-mediated depletion of CD8(+) T cells as well as pharmacological inhibition of the lymphotoxin-β receptor markedly delays tumor development in mice with chronic liver injury. Thus, our study unveils distinct functions of the immune system, which are required for liver regeneration, survival, and hepatocarcinogenesis.
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Affiliation(s)
- Jessica Endig
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, 30625 Hannover, Germany
| | - Laura Elisa Buitrago-Molina
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, 30625 Hannover, Germany
| | - Silke Marhenke
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, 30625 Hannover, Germany
| | - Florian Reisinger
- Institute of Virology, Technische Universität München, Helmholtz Zentrum Muenchen, 85764 Munich, Germany
| | - Anna Saborowski
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, 30625 Hannover, Germany
| | - Jutta Schütt
- Department of Cardiology, Philipps University Marburg, 35037 Marburg, Germany
| | - Florian Limbourg
- Department of Nephrology and Hypertension, Hannover Medical School, 30625 Hannover, Germany
| | - Christian Könecke
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, 30625 Hannover, Germany
| | - Alina Schreder
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, 30625 Hannover, Germany
| | - Alina Michael
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, 30625 Hannover, Germany
| | - Ana Clara Misslitz
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, 30625 Hannover, Germany
| | - Marc Eammonn Healy
- Institute of Surgical Pathology, University Hospital Zurich, 8091 Zürich, Switzerland
| | - Robert Geffers
- Department of Cell Biology, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Thomas Clavel
- ZIEL Institute for Food and Health, Technische Universität München, 85764 Munich, Germany
| | - Dirk Haller
- ZIEL Institute for Food and Health, Technische Universität München, 85764 Munich, Germany
| | - Kristian Unger
- Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, 85764 Munich, Germany
| | - Milton Finegold
- Department of Pathology, Texas Children's Hospital, Houston, TX 77030, USA
| | - Achim Weber
- Institute of Surgical Pathology, University Hospital Zurich, 8091 Zürich, Switzerland
| | - Michael P Manns
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, 30625 Hannover, Germany
| | - Thomas Longerich
- Institute of Pathology, Aachen University Hospital, 52074 Aachen, Germany
| | - Mathias Heikenwälder
- Department of Cardiology, Philipps University Marburg, 35037 Marburg, Germany; Division of Chronic Inflammation and Cancer, German Cancer Research Center Heidelberg, 69121 Heidelberg, Germany
| | - Arndt Vogel
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, 30625 Hannover, Germany.
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9
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Höckendorf U, Yabal M, Herold T, Munkhbaatar E, Rott S, Jilg S, Kauschinger J, Magnani G, Reisinger F, Heuser M, Kreipe H, Sotlar K, Engleitner T, Rad R, Weichert W, Peschel C, Ruland J, Heikenwalder M, Spiekermann K, Slotta-Huspenina J, Groß O, Jost PJ. RIPK3 Restricts Myeloid Leukemogenesis by Promoting Cell Death and Differentiation of Leukemia Initiating Cells. Cancer Cell 2016; 30:75-91. [PMID: 27411587 DOI: 10.1016/j.ccell.2016.06.002] [Citation(s) in RCA: 128] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 03/04/2016] [Accepted: 06/01/2016] [Indexed: 01/08/2023]
Abstract
Since acute myeloid leukemia (AML) is characterized by the blockade of hematopoietic differentiation and cell death, we interrogated RIPK3 signaling in AML development. Genetic loss of Ripk3 converted murine FLT3-ITD-driven myeloproliferation into an overt AML by enhancing the accumulation of leukemia-initiating cells (LIC). Failed inflammasome activation and cell death mediated by tumor necrosis factor receptor caused this accumulation of LIC exemplified by accelerated leukemia onset in Il1r1(-/-), Pycard(-/-), and Tnfr1/2(-/-) mice. RIPK3 signaling was partly mediated by mixed lineage kinase domain-like. This link between suppression of RIPK3, failed interleukin-1β release, and blocked cell death was supported by significantly reduced RIPK3 in primary AML patient cohorts. Our data identify RIPK3 and the inflammasome as key tumor suppressors in AML.
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MESH Headings
- Animals
- Apoptosis
- Cell Differentiation
- Down-Regulation
- Gene Expression Profiling/methods
- Gene Expression Regulation, Leukemic
- Humans
- Inflammasomes/metabolism
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/pathology
- Mice
- Neoplasms, Experimental
- Neoplastic Stem Cells/cytology
- Receptor-Interacting Protein Serine-Threonine Kinases/genetics
- Receptor-Interacting Protein Serine-Threonine Kinases/metabolism
- Receptors, Tumor Necrosis Factor/metabolism
- Tumor Cells, Cultured
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Affiliation(s)
- Ulrike Höckendorf
- III. Medical Department for Hematology and Oncology, Klinikum rechts der Isar, Technische Universität München, 81675 München, Germany
| | - Monica Yabal
- III. Medical Department for Hematology and Oncology, Klinikum rechts der Isar, Technische Universität München, 81675 München, Germany
| | - Tobias Herold
- Department of Internal Medicine 3, University Hospital Grosshadern, Ludwig-Maximilians-Universität (LMU), 81377 München, Germany
| | - Enkhtsetseg Munkhbaatar
- III. Medical Department for Hematology and Oncology, Klinikum rechts der Isar, Technische Universität München, 81675 München, Germany
| | - Stephanie Rott
- III. Medical Department for Hematology and Oncology, Klinikum rechts der Isar, Technische Universität München, 81675 München, Germany
| | - Stefanie Jilg
- III. Medical Department for Hematology and Oncology, Klinikum rechts der Isar, Technische Universität München, 81675 München, Germany
| | - Johanna Kauschinger
- III. Medical Department for Hematology and Oncology, Klinikum rechts der Isar, Technische Universität München, 81675 München, Germany
| | - Giovanni Magnani
- Institute of Clinical Chemistry and Pathobiochemistry, Klinikum rechts der Isar, Technische Universität München, 81675 München, Germany
| | - Florian Reisinger
- Institute of Virology, Helmholtz Zentrum München für Gesundheit und Umwelt (HMGU), 85764 Neuherberg, Germany
| | - Michael Heuser
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, 30625 Hannover, Germany
| | - Hans Kreipe
- Institute of Pathology, Hannover Medical School, 30625 Hannover, Germany
| | - Karl Sotlar
- Institute of Pathology, Ludwig-Maximilians-University (LMU), 80337 München, Germany
| | - Thomas Engleitner
- II. Medical Department for Gastroentreology, Klinikum rechts der Isar, Technische Universität München, 81675 München, Germany; German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Roland Rad
- II. Medical Department for Gastroentreology, Klinikum rechts der Isar, Technische Universität München, 81675 München, Germany; German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Wilko Weichert
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Institute of Pathology, Klinikum rechts der Isar, Technische Universität München, 81675 München, Germany
| | - Christian Peschel
- III. Medical Department for Hematology and Oncology, Klinikum rechts der Isar, Technische Universität München, 81675 München, Germany; German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Jürgen Ruland
- Institute of Clinical Chemistry and Pathobiochemistry, Klinikum rechts der Isar, Technische Universität München, 81675 München, Germany; German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Mathias Heikenwalder
- Institute of Virology, Helmholtz Zentrum München für Gesundheit und Umwelt (HMGU), 85764 Neuherberg, Germany; Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Karsten Spiekermann
- Department of Internal Medicine 3, University Hospital Grosshadern, Ludwig-Maximilians-Universität (LMU), 81377 München, Germany; German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Julia Slotta-Huspenina
- Institute of Pathology, Klinikum rechts der Isar, Technische Universität München, 81675 München, Germany
| | - Olaf Groß
- Institute of Clinical Chemistry and Pathobiochemistry, Klinikum rechts der Isar, Technische Universität München, 81675 München, Germany
| | - Philipp J Jost
- III. Medical Department for Hematology and Oncology, Klinikum rechts der Isar, Technische Universität München, 81675 München, Germany; German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.
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10
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Vizcaíno JA, Csordas A, del-Toro N, Dianes JA, Griss J, Lavidas I, Mayer G, Perez-Riverol Y, Reisinger F, Ternent T, Xu QW, Wang R, Hermjakob H. 2016 update of the PRIDE database and its related tools. Nucleic Acids Res 2016; 44:D447-56. [PMID: 26527722 PMCID: PMC4702828 DOI: 10.1093/nar/gkv1145] [Citation(s) in RCA: 2499] [Impact Index Per Article: 312.4] [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: 09/08/2015] [Revised: 10/14/2015] [Accepted: 10/16/2015] [Indexed: 11/18/2022] Open
Abstract
The PRoteomics IDEntifications (PRIDE) database is one of the world-leading data repositories of mass spectrometry (MS)-based proteomics data. Since the beginning of 2014, PRIDE Archive (http://www.ebi.ac.uk/pride/archive/) is the new PRIDE archival system, replacing the original PRIDE database. Here we summarize the developments in PRIDE resources and related tools since the previous update manuscript in the Database Issue in 2013. PRIDE Archive constitutes a complete redevelopment of the original PRIDE, comprising a new storage backend, data submission system and web interface, among other components. PRIDE Archive supports the most-widely used PSI (Proteomics Standards Initiative) data standard formats (mzML and mzIdentML) and implements the data requirements and guidelines of the ProteomeXchange Consortium. The wide adoption of ProteomeXchange within the community has triggered an unprecedented increase in the number of submitted data sets (around 150 data sets per month). We outline some statistics on the current PRIDE Archive data contents. We also report on the status of the PRIDE related stand-alone tools: PRIDE Inspector, PRIDE Converter 2 and the ProteomeXchange submission tool. Finally, we will give a brief update on the resources under development 'PRIDE Cluster' and 'PRIDE Proteomes', which provide a complementary view and quality-scored information of the peptide and protein identification data available in PRIDE Archive.
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Affiliation(s)
- Juan Antonio Vizcaíno
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Attila Csordas
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Noemi del-Toro
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - José A Dianes
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Johannes Griss
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK Division of Immunology, Allergy and Infectious Diseases, Department of Dermatology, Medical University of Vienna, Austria
| | - Ilias Lavidas
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Gerhard Mayer
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK Medizinisches Proteom Center (MPC), Ruhr-Universität Bochum, D-44801 Bochum, Germany
| | - Yasset Perez-Riverol
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Florian Reisinger
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Tobias Ternent
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Qing-Wei Xu
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK Department of Computer Science and Technology, Hubei University of Education, Wuhan, China
| | - Rui Wang
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Henning Hermjakob
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK National Center for Protein Sciences, Beijing, China
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11
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Xia Y, Stadler D, Lucifora J, Reisinger F, Webb D, Hösel M, Michler T, Wisskirchen K, Cheng X, Zhang K, Chou WM, Wettengel JM, Malo A, Bohne F, Hoffmann D, Eyer F, Thimme R, Falk CS, Thasler WE, Heikenwalder M, Protzer U. Interferon-γ and Tumor Necrosis Factor-α Produced by T Cells Reduce the HBV Persistence Form, cccDNA, Without Cytolysis. Gastroenterology 2016; 150:194-205. [PMID: 26416327 DOI: 10.1053/j.gastro.2015.09.026] [Citation(s) in RCA: 229] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2014] [Revised: 09/05/2015] [Accepted: 09/19/2015] [Indexed: 12/11/2022]
Abstract
BACKGROUND & AIMS Viral clearance involves immune cell cytolysis of infected cells. However, studies of hepatitis B virus (HBV) infection in chimpanzees have indicated that cytokines released by T cells also can promote viral clearance via noncytolytic processes. We investigated the noncytolytic mechanisms by which T cells eliminate HBV from infected hepatocytes. METHODS We performed a cytokine enzyme-linked immunosorbent assay of serum samples from patients with acute and chronic hepatitis B. Liver biopsy specimens were analyzed by in situ hybridization. HepG2-H1.3 cells, HBV-infected HepaRG cells, and primary human hepatocytes were incubated with interferon-γ (IFNγ) or tumor necrosis factor-α (TNF-α), or co-cultured with T cells. We measured markers of HBV replication, including the covalently closed circular DNA (cccDNA). RESULTS Levels of IFNγ and TNF-α were increased in serum samples from patients with acute vs chronic hepatitis B and controls. In human hepatocytes with stably replicating HBV, as well as in HBV-infected primary human hepatocytes or HepaRG cells, IFNγ and TNF-α each induced deamination of cccDNA and interfered with its stability; their effects were additive. HBV-specific T cells, through secretion of IFNγ and TNF-α, inhibited HBV replication and reduced cccDNA in infected cells without the direct contact required for cytolysis. Blocking IFNγ and TNF-α after T-cell stimulation prevented the loss of cccDNA. Deprivation of cccDNA required activation of nuclear APOBEC3 deaminases by the cytokines. In liver biopsy specimens from patients with acute hepatitis B, but not chronic hepatitis B or controls, hepatocytes expressed APOBEC3A and APOBEC3B. CONCLUSIONS IFNγ and TNF-α, produced by T cells, reduce levels of HBV cccDNA in hepatocytes by inducing deamination and subsequent cccDNA decay.
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Affiliation(s)
- Yuchen Xia
- Institute of Virology, Technische Universität München/Helmholtz Zentrum München, Munich, Germany
| | - Daniela Stadler
- Institute of Virology, Technische Universität München/Helmholtz Zentrum München, Munich, Germany
| | - Julie Lucifora
- Institute of Virology, Technische Universität München/Helmholtz Zentrum München, Munich, Germany; German Center for Infection Research, Munich and Hannover, Germany
| | - Florian Reisinger
- Institute of Virology, Technische Universität München/Helmholtz Zentrum München, Munich, Germany
| | - Dennis Webb
- Institute for Medical Microbiology, Immunology and Hygiene, University Hospital Cologne, Cologne, Germany
| | - Marianna Hösel
- Institute for Medical Microbiology, Immunology and Hygiene, University Hospital Cologne, Cologne, Germany; Center for Molecular Medicine Cologne, University Hospital Cologne, Cologne, Germany
| | - Thomas Michler
- Institute of Virology, Technische Universität München/Helmholtz Zentrum München, Munich, Germany
| | - Karin Wisskirchen
- Institute of Virology, Technische Universität München/Helmholtz Zentrum München, Munich, Germany; German Center for Infection Research, Munich and Hannover, Germany
| | - Xiaoming Cheng
- Institute of Virology, Technische Universität München/Helmholtz Zentrum München, Munich, Germany
| | - Ke Zhang
- Institute of Virology, Technische Universität München/Helmholtz Zentrum München, Munich, Germany
| | - Wen-Min Chou
- Institute of Virology, Technische Universität München/Helmholtz Zentrum München, Munich, Germany
| | - Jochen M Wettengel
- Institute of Virology, Technische Universität München/Helmholtz Zentrum München, Munich, Germany
| | - Antje Malo
- Institute of Virology, Technische Universität München/Helmholtz Zentrum München, Munich, Germany
| | - Felix Bohne
- Institute of Virology, Technische Universität München/Helmholtz Zentrum München, Munich, Germany
| | - Dieter Hoffmann
- Institute of Virology, Technische Universität München/Helmholtz Zentrum München, Munich, Germany
| | - Florian Eyer
- Medicine II, Department of Clinical Toxicology, University Hospital rechts der Isar of the Technical University of Munich, Munich, Germany
| | - Robert Thimme
- Department of Medicine II, University Hospital Freiburg, Freiburg, Germany
| | - Christine S Falk
- German Center for Infection Research, Munich and Hannover, Germany; Abt Transplantationsimmunologie, Medizinische Hochschule Hannover, Hannover, Germany
| | - Wolfgang E Thasler
- Department of General, Visceral, Transplantation, Vascular and Thoracic Surgery, Grosshadern Hospital, Ludwig Maximilians University, Munich, Germany
| | - Mathias Heikenwalder
- Institute of Virology, Technische Universität München/Helmholtz Zentrum München, Munich, Germany
| | - Ulrike Protzer
- Institute of Virology, Technische Universität München/Helmholtz Zentrum München, Munich, Germany; German Center for Infection Research, Munich and Hannover, Germany.
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12
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Boutaffala L, Bertrand MJM, Remouchamps C, Seleznik G, Reisinger F, Janas M, Bénézech C, Fernandes MT, Marchetti S, Mair F, Ganeff C, Hupalowska A, Ricci JE, Becher B, Piette J, Knolle P, Caamano J, Vandenabeele P, Heikenwalder M, Dejardin E. NIK promotes tissue destruction independently of the alternative NF-κB pathway through TNFR1/RIP1-induced apoptosis. Cell Death Differ 2015; 22:2020-33. [PMID: 26045047 PMCID: PMC4816116 DOI: 10.1038/cdd.2015.69] [Citation(s) in RCA: 30] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 04/27/2015] [Accepted: 04/28/2015] [Indexed: 12/21/2022] Open
Abstract
NF-κB-inducing kinase (NIK) is well-known for its role in promoting p100/NF-κB2 processing into p52, a process defined as the alternative, or non-canonical, NF-κB pathway. Here we reveal an unexpected new role of NIK in TNFR1-mediated RIP1-dependent apoptosis, a consequence of TNFR1 activation observed in c-IAP1/2-depleted conditions. We show that NIK stabilization, obtained by activation of the non-death TNFRs Fn14 or LTβR, is required for TNFα-mediated apoptosis. These apoptotic stimuli trigger the depletion of c-IAP1/2, the phosphorylation of RIP1 and the RIP1 kinase-dependent assembly of the RIP1/FADD/caspase-8 complex. In the absence of NIK, the phosphorylation of RIP1 and the formation of RIP1/FADD/caspase-8 complex are compromised while c-IAP1/2 depletion is unaffected. In vitro kinase assays revealed that recombinant RIP1 is a bona fide substrate of NIK. In vivo, we demonstrated the requirement of NIK pro-death function, but not the processing of its substrate p100 into p52, in a mouse model of TNFR1/LTβR-induced thymus involution. In addition, we also highlight a role for NIK in hepatocyte apoptosis in a mouse model of virus-induced TNFR1/RIP1-dependent liver damage. We conclude that NIK not only contributes to lymphoid organogenesis, inflammation and cell survival but also to TNFR1/RIP1-dependent cell death independently of the alternative NF-κB pathway.
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Affiliation(s)
- L Boutaffala
- Laboratory of Molecular Immunology and Signal Transduction, GIGA-Research, University of Liège, Liège, Belgium
| | - M J M Bertrand
- The Inflammation Research Center IRC, VIB, DMBR, Ghent University, Ghent, Belgium
| | - C Remouchamps
- Laboratory of Molecular Immunology and Signal Transduction, GIGA-Research, University of Liège, Liège, Belgium
| | - G Seleznik
- Institute of Neuropathology, University Hospital Zürich, Zürich, Switzerland
| | | | - M Janas
- Institute of Molecular Immunology and Technische Universität München (TUM)/Helmholtz Zentrum München (HMGU), Munich, Germany
| | - C Bénézech
- School of Immunity and Infection, IBR-MRC, Centre for Immune Regulation, University of Birmingham, Birmingham, UK
| | - M T Fernandes
- Laboratory of Molecular Immunology and Signal Transduction, GIGA-Research, University of Liège, Liège, Belgium
| | - S Marchetti
- INSERM U1065, Centre Méditéranéen de Médecine Moléculaire, Nice, France
| | - F Mair
- Institute of Experimental Immunology, University of Zurich, Zürich, Switzerland
| | - C Ganeff
- Laboratory of Molecular Immunology and Signal Transduction, GIGA-Research, University of Liège, Liège, Belgium
| | - A Hupalowska
- Laboratory of Molecular Immunology and Signal Transduction, GIGA-Research, University of Liège, Liège, Belgium
| | - J-E Ricci
- INSERM U1065, Centre Méditéranéen de Médecine Moléculaire, Nice, France
| | - B Becher
- Institute of Experimental Immunology, University of Zurich, Zürich, Switzerland
| | - J Piette
- Laboratory of Virology, GIGA-Research, University of Liège, Liège, Belgium
| | - P Knolle
- Institute of Molecular Immunology and Technische Universität München (TUM)/Helmholtz Zentrum München (HMGU), Munich, Germany
| | - J Caamano
- School of Immunity and Infection, IBR-MRC, Centre for Immune Regulation, University of Birmingham, Birmingham, UK
| | - P Vandenabeele
- The Inflammation Research Center IRC, VIB, DMBR, Ghent University, Ghent, Belgium
| | - M Heikenwalder
- Institute of Virology, Munich, Germany
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - E Dejardin
- Laboratory of Molecular Immunology and Signal Transduction, GIGA-Research, University of Liège, Liège, Belgium
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13
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Perez-Riverol Y, Xu QW, Wang R, Uszkoreit J, Griss J, Sanchez A, Reisinger F, Csordas A, Ternent T, Del-Toro N, Dianes JA, Eisenacher M, Hermjakob H, Vizcaíno JA. PRIDE Inspector Toolsuite: Moving Toward a Universal Visualization Tool for Proteomics Data Standard Formats and Quality Assessment of ProteomeXchange Datasets. Mol Cell Proteomics 2015; 15:305-17. [PMID: 26545397 PMCID: PMC4762524 DOI: 10.1074/mcp.o115.050229] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Indexed: 12/25/2022] Open
Abstract
The original PRIDE Inspector tool was developed as an open source standalone tool to enable the visualization and validation of mass-spectrometry (MS)-based proteomics data before data submission or already publicly available in the Proteomics Identifications (PRIDE) database. The initial implementation of the tool focused on visualizing PRIDE data by supporting the PRIDE XML format and a direct access to private (password protected) and public experiments in PRIDE. The ProteomeXchange (PX) Consortium has been set up to enable a better integration of existing public proteomics repositories, maximizing its benefit to the scientific community through the implementation of standard submission and dissemination pipelines. Within the Consortium, PRIDE is focused on supporting submissions of tandem MS data. The increasing use and popularity of the new Proteomics Standards Initiative (PSI) data standards such as mzIdentML and mzTab, and the diversity of workflows supported by the PX resources, prompted us to design and implement a new suite of algorithms and libraries that would build upon the success of the original PRIDE Inspector and would enable users to visualize and validate PX “complete” submissions. The PRIDE Inspector Toolsuite supports the handling and visualization of different experimental output files, ranging from spectra (mzML, mzXML, and the most popular peak lists formats) and peptide and protein identification results (mzIdentML, PRIDE XML, mzTab) to quantification data (mzTab, PRIDE XML), using a modular and extensible set of open-source, cross-platform libraries. We believe that the PRIDE Inspector Toolsuite represents a milestone in the visualization and quality assessment of proteomics data. It is freely available at http://github.com/PRIDE-Toolsuite/.
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Affiliation(s)
- Yasset Perez-Riverol
- From the ‡European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Qing-Wei Xu
- From the ‡European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Rui Wang
- From the ‡European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Julian Uszkoreit
- §Ruhr-Universität Bochum, Medizinisches Proteom-Zenter, Medical Bioinformatics, ZKF, E.142, Universitätsstr. 150, D-44801 Bochum, Germany
| | - Johannes Griss
- From the ‡European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK; ¶Division of Immunology, Allergy and Infectious Diseases, Department of Dermatology, Medical University of Vienna, Austria
| | - Aniel Sanchez
- ‖Department of Proteomics, Center for Genetic Engineering and Biotechnology, Ciudad de la Habana, Cuba
| | - Florian Reisinger
- From the ‡European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Attila Csordas
- From the ‡European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Tobias Ternent
- From the ‡European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Noemi Del-Toro
- From the ‡European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Jose A Dianes
- From the ‡European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Martin Eisenacher
- §Ruhr-Universität Bochum, Medizinisches Proteom-Zenter, Medical Bioinformatics, ZKF, E.142, Universitätsstr. 150, D-44801 Bochum, Germany
| | - Henning Hermjakob
- From the ‡European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Juan Antonio Vizcaíno
- From the ‡European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK;
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14
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Herranz N, Gallage S, Mellone M, Wuestefeld T, Klotz S, Hanley CJ, Raguz S, Acosta JC, Innes AJ, Banito A, Georgilis A, Montoya A, Wolter K, Dharmalingam G, Faull P, Carroll T, Martínez-Barbera JP, Cutillas P, Reisinger F, Heikenwalder M, Miller RA, Withers D, Zender L, Thomas GJ, Gil J. Erratum: mTOR regulates MAPKAPK2 translation to control the senescence-associated secretory phenotype. Nat Cell Biol 2015; 17:1370. [DOI: 10.1038/ncb3243] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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15
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Herranz N, Gallage S, Mellone M, Wuestefeld T, Klotz S, Hanley CJ, Raguz S, Acosta JC, Innes AJ, Banito A, Georgilis A, Montoya A, Wolter K, Dharmalingam G, Faull P, Carroll T, Martínez-Barbera JP, Cutillas P, Reisinger F, Heikenwalder M, Miller RA, Withers D, Zender L, Thomas GJ, Gil J. mTOR regulates MAPKAPK2 translation to control the senescence-associated secretory phenotype. Nat Cell Biol 2015; 17:1205-17. [PMID: 26280535 PMCID: PMC4589897 DOI: 10.1038/ncb3225] [Citation(s) in RCA: 474] [Impact Index Per Article: 52.7] [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: 05/27/2015] [Accepted: 07/20/2015] [Indexed: 12/15/2022]
Abstract
Senescent cells secrete a combination of factors collectively known as the senescence-associated secretory phenotype (SASP). The SASP reinforces senescence and activates an immune surveillance response, but it can also show pro-tumorigenic properties and contribute to age-related pathologies. In a drug screen to find new SASP regulators, we uncovered the mTOR inhibitor rapamycin as a potent SASP suppressor. Here we report a mechanism by which mTOR controls the SASP by differentially regulating the translation of the MK2 (also known as MAPKAPK2) kinase through 4EBP1. In turn, MAPKAPK2 phosphorylates the RNA-binding protein ZFP36L1 during senescence, inhibiting its ability to degrade the transcripts of numerous SASP components. Consequently, mTOR inhibition or constitutive activation of ZFP36L1 impairs the non-cell-autonomous effects of senescent cells in both tumour-suppressive and tumour-promoting contexts. Altogether, our results place regulation of the SASP as a key mechanism by which mTOR could influence cancer, age-related diseases and immune responses.
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Affiliation(s)
- Nicolás Herranz
- Cell Proliferation Group, MRC Clinical Sciences Centre, Imperial College London, Hammersmith Campus, London W12 0NN, UK
- Epigenetics Section, MRC Clinical Sciences Centre, Imperial College London, Hammersmith Campus, London W12 0NN, UK
| | - Suchira Gallage
- Cell Proliferation Group, MRC Clinical Sciences Centre, Imperial College London, Hammersmith Campus, London W12 0NN, UK
- Epigenetics Section, MRC Clinical Sciences Centre, Imperial College London, Hammersmith Campus, London W12 0NN, UK
- Metabolic Signalling Group, MRC Clinical Sciences Centre, Imperial College London, Hammersmith Campus, London W12 0NN, UK
| | - Massimiliano Mellone
- Cancer Sciences Unit, Cancer Research UK Centre, Somers Building, University of Southampton, Southampton SO16 6YD, UK
| | - Torsten Wuestefeld
- Division of Molecular Oncology of Solid Tumors, Dept. of Internal Medicine I, Eberhard Karls University Tübingen, 72076 Tübingen, Germany
| | - Sabrina Klotz
- Division of Molecular Oncology of Solid Tumors, Dept. of Internal Medicine I, Eberhard Karls University Tübingen, 72076 Tübingen, Germany
| | - Christopher J. Hanley
- Cancer Sciences Unit, Cancer Research UK Centre, Somers Building, University of Southampton, Southampton SO16 6YD, UK
| | - Selina Raguz
- Cell Proliferation Group, MRC Clinical Sciences Centre, Imperial College London, Hammersmith Campus, London W12 0NN, UK
- Epigenetics Section, MRC Clinical Sciences Centre, Imperial College London, Hammersmith Campus, London W12 0NN, UK
| | - Juan Carlos Acosta
- Cell Proliferation Group, MRC Clinical Sciences Centre, Imperial College London, Hammersmith Campus, London W12 0NN, UK
- Epigenetics Section, MRC Clinical Sciences Centre, Imperial College London, Hammersmith Campus, London W12 0NN, UK
| | - Andrew J Innes
- Cell Proliferation Group, MRC Clinical Sciences Centre, Imperial College London, Hammersmith Campus, London W12 0NN, UK
- Epigenetics Section, MRC Clinical Sciences Centre, Imperial College London, Hammersmith Campus, London W12 0NN, UK
| | - Ana Banito
- Cell Proliferation Group, MRC Clinical Sciences Centre, Imperial College London, Hammersmith Campus, London W12 0NN, UK
- Epigenetics Section, MRC Clinical Sciences Centre, Imperial College London, Hammersmith Campus, London W12 0NN, UK
| | - Athena Georgilis
- Cell Proliferation Group, MRC Clinical Sciences Centre, Imperial College London, Hammersmith Campus, London W12 0NN, UK
- Epigenetics Section, MRC Clinical Sciences Centre, Imperial College London, Hammersmith Campus, London W12 0NN, UK
| | - Alex Montoya
- Proteomics Facility; MRC Clinical Sciences Centre, Imperial College London, Hammersmith Campus, London W12 0NN, UK
| | - Katharina Wolter
- Division of Molecular Oncology of Solid Tumors, Dept. of Internal Medicine I, Eberhard Karls University Tübingen, 72076 Tübingen, Germany
| | - Gopuraja Dharmalingam
- Epigenetics Section, MRC Clinical Sciences Centre, Imperial College London, Hammersmith Campus, London W12 0NN, UK
| | - Peter Faull
- Proteomics Facility; MRC Clinical Sciences Centre, Imperial College London, Hammersmith Campus, London W12 0NN, UK
| | - Thomas Carroll
- Epigenetics Section, MRC Clinical Sciences Centre, Imperial College London, Hammersmith Campus, London W12 0NN, UK
| | | | - Pedro Cutillas
- Proteomics Facility; MRC Clinical Sciences Centre, Imperial College London, Hammersmith Campus, London W12 0NN, UK
| | - Florian Reisinger
- Institute for Virology, Technische Universität München/Helmholtz Zentrum München, Munich, Germany
| | - Mathias Heikenwalder
- Institute for Virology, Technische Universität München/Helmholtz Zentrum München, Munich, Germany
- Division of Chronic Inflammation and Cancer, German Cancer Research (DKFZ), Heidelberg, Germany
| | - Richard A. Miller
- Department of Pathology and Geriatrics Center, University of Michigan, Ann Arbor, MI 48109-2200, USA
| | - Dominic Withers
- Metabolic Signalling Group, MRC Clinical Sciences Centre, Imperial College London, Hammersmith Campus, London W12 0NN, UK
| | - Lars Zender
- Division of Molecular Oncology of Solid Tumors, Dept. of Internal Medicine I, Eberhard Karls University Tübingen, 72076 Tübingen, Germany
| | - Gareth J. Thomas
- Cancer Sciences Unit, Cancer Research UK Centre, Somers Building, University of Southampton, Southampton SO16 6YD, UK
| | - Jesús Gil
- Cell Proliferation Group, MRC Clinical Sciences Centre, Imperial College London, Hammersmith Campus, London W12 0NN, UK
- Epigenetics Section, MRC Clinical Sciences Centre, Imperial College London, Hammersmith Campus, London W12 0NN, UK
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16
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Reisinger F, del-Toro N, Ternent T, Hermjakob H, Vizcaíno JA. Introducing the PRIDE Archive RESTful web services. Nucleic Acids Res 2015; 43:W599-604. [PMID: 25904633 PMCID: PMC4489246 DOI: 10.1093/nar/gkv382] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [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: 01/31/2015] [Accepted: 04/11/2015] [Indexed: 12/02/2022] Open
Abstract
The PRIDE (PRoteomics IDEntifications) database is one of the world-leading public repositories of mass spectrometry (MS)-based proteomics data and it is a founding member of the ProteomeXchange Consortium of proteomics resources. In the original PRIDE database system, users could access data programmatically by accessing the web services provided by the PRIDE BioMart interface. New REST (REpresentational State Transfer) web services have been developed to serve the most popular functionality provided by BioMart (now discontinued due to data scalability issues) and address the data access requirements of the newly developed PRIDE Archive. Using the API (Application Programming Interface) it is now possible to programmatically query for and retrieve peptide and protein identifications, project and assay metadata and the originally submitted files. Searching and filtering is also possible by metadata information, such as sample details (e.g. species and tissues), instrumentation (mass spectrometer), keywords and other provided annotations. The PRIDE Archive web services were first made available in April 2014. The API has already been adopted by a few applications and standalone tools such as PeptideShaker, PRIDE Inspector, the Unipept web application and the Python-based BioServices package. This application is free and open to all users with no login requirement and can be accessed at http://www.ebi.ac.uk/pride/ws/archive/.
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Affiliation(s)
- Florian Reisinger
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Noemi del-Toro
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Tobias Ternent
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Henning Hermjakob
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Juan Antonio Vizcaíno
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
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17
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Gautheron J, Vucur M, Reisinger F, Cardenas DV, Roderburg C, Koppe C, Kreggenwinkel K, Schneider AT, Bartneck M, Neumann UP, Canbay A, Reeves HL, Luedde M, Tacke F, Trautwein C, Heikenwalder M, Luedde T. A positive feedback loop between RIP3 and JNK controls non-alcoholic steatohepatitis. EMBO Mol Med 2015; 6:1062-74. [PMID: 24963148 PMCID: PMC4154133 DOI: 10.15252/emmm.201403856] [Citation(s) in RCA: 317] [Impact Index Per Article: 35.2] [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: 12/01/2022] Open
Abstract
Non-alcoholic fatty liver disease (NAFLD) represents the most common liver disease in Western countries and often progresses to non-alcoholic steatohepatitis (NASH) leading ultimately to liver fibrosis and liver cancer. The occurrence of hepatocyte cell death—so far characterized as hepatocyte apoptosis—represents a fundamental step from benign steatosis toward progressive steatohepatitis. In contrast, the function of RIP3-dependent “necroptosis” in NASH and NASH-induced fibrosis is currently unknown. We show that RIP3 is upregulated in human NASH and in a dietary mouse model of steatohepatitis. RIP3 mediates liver injury, inflammation, induction of hepatic progenitor cells/activated cholangiocytes, and liver fibrosis through a pathway suppressed by Caspase-8. This function of RIP3 is mediated by a positive feedback loop involving activation of Jun-(N)-terminal Kinase (JNK). Furthermore, RIP3-dependent JNK activation promotes the release of pro-inflammatory mediators like MCP-1, thereby attracting macrophages to the injured liver and further augmenting RIP3-dependent signaling, cell death, and liver fibrosis. Thus, RIP3-dependent necroptosis controls NASH-induced liver fibrosis. This pathway might represent a novel and specific target for pharmacological strategies in patients with NASH. Subject Categories Digestive System; Metabolism
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Affiliation(s)
- Jérémie Gautheron
- Department of Gastroenterology, Digestive Diseases and Intensive Care Medicine (Department of Medicine III), University Hospital RWTH Aachen, Aachen, Germany Interdisciplinary Centre for Clinical Research Aachen, University Hospital RWTH Aachen, Aachen, Germany
| | - Mihael Vucur
- Department of Gastroenterology, Digestive Diseases and Intensive Care Medicine (Department of Medicine III), University Hospital RWTH Aachen, Aachen, Germany
| | - Florian Reisinger
- Institute of Virology, Technische Universität München and Helmholtz Zentrum München für Gesundheit und Umwelt (HMGU), Munich, Germany
| | - David Vargas Cardenas
- Department of Gastroenterology, Digestive Diseases and Intensive Care Medicine (Department of Medicine III), University Hospital RWTH Aachen, Aachen, Germany
| | - Christoph Roderburg
- Department of Gastroenterology, Digestive Diseases and Intensive Care Medicine (Department of Medicine III), University Hospital RWTH Aachen, Aachen, Germany
| | - Christiane Koppe
- Department of Gastroenterology, Digestive Diseases and Intensive Care Medicine (Department of Medicine III), University Hospital RWTH Aachen, Aachen, Germany
| | - Karina Kreggenwinkel
- Department of Gastroenterology, Digestive Diseases and Intensive Care Medicine (Department of Medicine III), University Hospital RWTH Aachen, Aachen, Germany
| | - Anne Theres Schneider
- Department of Gastroenterology, Digestive Diseases and Intensive Care Medicine (Department of Medicine III), University Hospital RWTH Aachen, Aachen, Germany
| | - Matthias Bartneck
- Department of Gastroenterology, Digestive Diseases and Intensive Care Medicine (Department of Medicine III), University Hospital RWTH Aachen, Aachen, Germany
| | - Ulf Peter Neumann
- Department of Visceral and Transplantation Surgery, University Hospital RWTH Aachen, Aachen, Germany
| | - Ali Canbay
- Department of Gastroenterology and Hepatology, University Hospital University Duisburg-Essen, Essen, Germany
| | - Helen Louise Reeves
- The Liver Group, Department of Medicine, Freeman Hospital Newcastle-upon-Tyne Hospitals NHS Foundation Trust, Newcastle-upon-Tyne, UK
| | - Mark Luedde
- Department of Cardiology and Angiology, University Hospital Kiel, Kiel, Germany
| | - Frank Tacke
- Department of Gastroenterology, Digestive Diseases and Intensive Care Medicine (Department of Medicine III), University Hospital RWTH Aachen, Aachen, Germany
| | - Christian Trautwein
- Department of Gastroenterology, Digestive Diseases and Intensive Care Medicine (Department of Medicine III), University Hospital RWTH Aachen, Aachen, Germany
| | - Mathias Heikenwalder
- Institute of Virology, Technische Universität München and Helmholtz Zentrum München für Gesundheit und Umwelt (HMGU), Munich, Germany
| | - Tom Luedde
- Department of Gastroenterology, Digestive Diseases and Intensive Care Medicine (Department of Medicine III), University Hospital RWTH Aachen, Aachen, Germany
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Vizcaíno JA, Deutsch EW, Wang R, Csordas A, Reisinger F, Ríos D, Dianes JA, Sun Z, Farrah T, Bandeira N, Binz PA, Xenarios I, Eisenacher M, Mayer G, Gatto L, Campos A, Chalkley RJ, Kraus HJ, Albar JP, Martinez-Bartolomé S, Apweiler R, Omenn GS, Martens L, Jones AR, Hermjakob H. ProteomeXchange provides globally coordinated proteomics data submission and dissemination. Nat Biotechnol 2015; 32:223-6. [PMID: 24727771 PMCID: PMC3986813 DOI: 10.1038/nbt.2839] [Citation(s) in RCA: 2143] [Impact Index Per Article: 238.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Juan A Vizcaíno
- 1] European Molecular Biology Laboratory, European Bioinformatics Institute (EMBLEBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK. [2]
| | - Eric W Deutsch
- 1] Institute for Systems Biology, Seattle, Washington, USA. [2]
| | - Rui Wang
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBLEBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Attila Csordas
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBLEBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Florian Reisinger
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBLEBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Daniel Ríos
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBLEBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - José A Dianes
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBLEBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Zhi Sun
- Institute for Systems Biology, Seattle, Washington, USA
| | - Terry Farrah
- Institute for Systems Biology, Seattle, Washington, USA
| | - Nuno Bandeira
- Center for Computational Mass Spectrometry, University of California, San Diego, La Jolla, California, USA
| | - Pierre-Alain Binz
- Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Ioannis Xenarios
- 1] Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland. [2] University of Lausanne, Lausanne, Switzerland, and Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland. [3] Vital-IT Group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Martin Eisenacher
- Medizinisches Proteom-Center, Ruhr-Universität Bochum, Bochum, Germany
| | - Gerhard Mayer
- Medizinisches Proteom-Center, Ruhr-Universität Bochum, Bochum, Germany
| | - Laurent Gatto
- Computational Proteomics Unit and Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Alex Campos
- Integromics SL, Santiago Grisolia, Madrid, Spain
| | - Robert J Chalkley
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, USA
| | | | - Juan Pablo Albar
- ProteoRed-ISCIII, National Center for Biotechnology-CSIC, Madrid, Spain
| | | | - Rolf Apweiler
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBLEBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Gilbert S Omenn
- 1] Institute for Systems Biology, Seattle, Washington, USA. [2] Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Lennart Martens
- 1] Department of Medical Protein Research, VIB, Ghent, Belgium. [2] Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Andrew R Jones
- Institute of Integrative Biology, University of Liverpool, UK
| | - Henning Hermjakob
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBLEBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
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19
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Ringelhan M, Reisinger F, Yuan D, Weber A, Heikenwalder M. Modeling human liver cancer heterogeneity: virally induced transgenic models and mouse genetic models of chronic liver inflammation. Curr Protoc Pharmacol 2014; 67:14.31.1-14.31.17. [PMID: 25446288 DOI: 10.1002/0471141755.ph1431s67] [Citation(s) in RCA: 3] [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] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
In addition to being the most common primary liver cancer, hepatocellular carcinoma (HCC) is the second most common cause of cancer-related death in humans. Treatment options are limited for this chemoresistant cancer, with liver transplantation and surgical intervention in early stages being the most successful treatments. Drug development over the past 15 years has focused on generating mouse models that mimic the human pathology for HCC. This has enabled the laboratory testing of potentially new human therapeutics. Described in this unit are the classification of HCC and an overview of hepatitis virus-related transgenic and genetically engineered mouse models (GEMMs) that are employed for elucidating the mechanism(s) responsible for the development of HCC, with particular emphasis on genetic, dietary, and environmental factors.
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Affiliation(s)
- Marc Ringelhan
- Institute of Virology, München, Germany.,2nd Medical Department, Klinikum rechts der Isar, Technische Universität München, München, Germany.,German Center for Infection Research (DZIF), München, Germany
| | | | | | - Achim Weber
- Institute of Surgical Pathology, Zürich, Switzerland
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20
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Lucifora J, Xia Y, Reisinger F, Stadler D, Heikenwälder M, Protzer U. [Specific degradation of nuclear hepatitis B virus covalently closed circular DNA]. Med Sci (Paris) 2014; 30:724-6. [PMID: 25174742 DOI: 10.1051/medsci/20143008003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Affiliation(s)
- Julie Lucifora
- Institute of Virology, Technische Universität München/Helmholtz Zentrum München, Munich, Allemagne - German Center for Infection Research (DZIF), Allemagne - affiliation actuelle : Inserm U1052, CNRS UMR 5286, centre de recherche en cancérologie de Lyon (CRCL), Université de Lyon (UCBL), Lyon, France
| | - Yuchen Xia
- Institute of Virology, Technische Universität München/Helmholtz Zentrum München, Munich, Allemagne
| | - Florian Reisinger
- Institute of Virology, Technische Universität München/Helmholtz Zentrum München, Munich, Allemagne
| | - Daniela Stadler
- Institute of Virology, Technische Universität München/Helmholtz Zentrum München, Munich, Allemagne
| | - Mathias Heikenwälder
- Institute of Virology, Technische Universität München/Helmholtz Zentrum München, Munich, Allemagne
| | - Ulrike Protzer
- Institute of Virology, Technische Universität München/Helmholtz Zentrum München, Munich, Allemagne - German Center for Infection Research (DZIF), Allemagne
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21
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Luedde M, Lutz M, Carter N, Sosna J, Jacoby C, Vucur M, Gautheron J, Roderburg C, Borg N, Reisinger F, Hippe HJ, Linkermann A, Wolf MJ, Rose-John S, Lüllmann-Rauch R, Adam D, Flögel U, Heikenwalder M, Luedde T, Frey N. RIP3, a kinase promoting necroptotic cell death, mediates adverse remodelling after myocardial infarction. Cardiovasc Res 2014; 103:206-16. [PMID: 24920296 DOI: 10.1093/cvr/cvu146] [Citation(s) in RCA: 229] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
AIMS Programmed necrosis (necroptosis) represents a newly identified mechanism of cell death combining features of both apoptosis and necrosis. Like apoptosis, necroptosis is tightly regulated by distinct signalling pathways. A key regulatory role in programmed necrosis has been attributed to interactions of the receptor-interacting protein kinases, RIP1 and RIP3. However, the specific functional role of RIP3-dependent signalling and necroptosis in the heart is unknown. The aims of this study were thus to assess the significance of necroptosis and RIP3 in the context of myocardial ischaemia. METHODS AND RESULTS Immunoblots revealed strong expression of RIP3 in murine hearts, indicating potential functional significance of this protein in the myocardium. Consistent with a role in promoting necroptosis, adenoviral overexpression of RIP3 in neonatal rat cardiomyocytes and stimulation with TNF-α induced the formation of a complex of RIP1 and RIP3. Moreover, RIP3 overexpression was sufficient to induce necroptosis of cardiomyocytes. In vivo, cardiac expression of RIP3 was up-regulated upon myocardial infarction (MI). Conversely, mice deficient for RIP3 (RIP3(-/-)) showed a significantly better ejection fraction (45 ± 3.6 vs. 32 ± 4.4%, P < 0.05) and less hypertrophy in magnetic resonance imaging studies 30 days after experimental infarction due to left anterior descending coronary artery ligation. This was accompanied by a diminished inflammatory response of infarcted hearts and decreased generation of reactive oxygen species. CONCLUSION Here, we show that RIP3-dependent necroptosis modulates post-ischaemic adverse remodelling in a mouse model of MI. This novel signalling pathway may thus be an attractive target for future therapies that aim to limit the adverse consequences of myocardial ischaemia.
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Affiliation(s)
- Mark Luedde
- Department of Internal Medicine III: Cardiology and Angiology, University of Kiel, Arnold-Heller-Straße 3, Haus 6, 24105 Kiel, Germany
| | - Matthias Lutz
- Department of Internal Medicine III: Cardiology and Angiology, University of Kiel, Arnold-Heller-Straße 3, Haus 6, 24105 Kiel, Germany
| | - Natalie Carter
- Department of Internal Medicine III: Cardiology and Angiology, University of Kiel, Arnold-Heller-Straße 3, Haus 6, 24105 Kiel, Germany
| | - Justyna Sosna
- Institute of Immunology, University of Kiel, Kiel, Germany
| | - Christoph Jacoby
- Department of Molecular Cardiology, University of Duesseldorf, Duesseldorf, Germany
| | - Mihael Vucur
- Department of Internal Medicine III, University Hospital, Aachen, Germany
| | - Jérémie Gautheron
- Department of Internal Medicine III, University Hospital, Aachen, Germany
| | | | - Nadine Borg
- Department of Molecular Cardiology, University of Duesseldorf, Duesseldorf, Germany
| | - Florian Reisinger
- Institute of Virology, Technical University of Munich, Munich, Germany
| | - Hans-Joerg Hippe
- Department of Internal Medicine III: Cardiology and Angiology, University of Kiel, Arnold-Heller-Straße 3, Haus 6, 24105 Kiel, Germany
| | | | - Monika J Wolf
- Institute of Physiology, University of Zurich and Zurich Center for Integrative Human Physiology, Zurich, Switzerland
| | | | | | - Dieter Adam
- Institute of Immunology, University of Kiel, Kiel, Germany
| | - Ulrich Flögel
- Department of Molecular Cardiology, University of Duesseldorf, Duesseldorf, Germany
| | | | - Tom Luedde
- Department of Internal Medicine III, University Hospital, Aachen, Germany
| | - Norbert Frey
- Department of Internal Medicine III: Cardiology and Angiology, University of Kiel, Arnold-Heller-Straße 3, Haus 6, 24105 Kiel, Germany DZHK (German Centre for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, Kiel, Germany
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22
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Griss J, Jones AR, Sachsenberg T, Walzer M, Gatto L, Hartler J, Thallinger GG, Salek RM, Steinbeck C, Neuhauser N, Cox J, Neumann S, Fan J, Reisinger F, Xu QW, Del Toro N, Pérez-Riverol Y, Ghali F, Bandeira N, Xenarios I, Kohlbacher O, Vizcaíno JA, Hermjakob H. The mzTab data exchange format: communicating mass-spectrometry-based proteomics and metabolomics experimental results to a wider audience. Mol Cell Proteomics 2014; 13:2765-75. [PMID: 24980485 PMCID: PMC4189001 DOI: 10.1074/mcp.o113.036681] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [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] [Indexed: 11/06/2022] Open
Abstract
The HUPO Proteomics Standards Initiative has developed several standardized data formats to facilitate data sharing in mass spectrometry (MS)-based proteomics. These allow researchers to report their complete results in a unified way. However, at present, there is no format to describe the final qualitative and quantitative results for proteomics and metabolomics experiments in a simple tabular format. Many downstream analysis use cases are only concerned with the final results of an experiment and require an easily accessible format, compatible with tools such as Microsoft Excel or R. We developed the mzTab file format for MS-based proteomics and metabolomics results to meet this need. mzTab is intended as a lightweight supplement to the existing standard XML-based file formats (mzML, mzIdentML, mzQuantML), providing a comprehensive summary, similar in concept to the supplemental material of a scientific publication. mzTab files can contain protein, peptide, and small molecule identifications together with experimental metadata and basic quantitative information. The format is not intended to store the complete experimental evidence but provides mechanisms to report results at different levels of detail. These range from a simple summary of the final results to a representation of the results including the experimental design. This format is ideally suited to make MS-based proteomics and metabolomics results available to a wider biological community outside the field of MS. Several software tools for proteomics and metabolomics have already adapted the format as an output format. The comprehensive mzTab specification document and extensive additional documentation can be found online.
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Affiliation(s)
- Johannes Griss
- From the ‡European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, CB10 1SD, Hinxton, Cambridge, UK; §Division of Immunology, Allergy and Infectious Diseases, Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Andrew R Jones
- ‖Institute of Integrative Biology, University of Liverpool, L69 7ZB, Liverpool, UK
| | - Timo Sachsenberg
- **Center for Bioinformatics and Department of Computer Science, University of Tübingen, D-72076 Tübingen, Germany
| | - Mathias Walzer
- **Center for Bioinformatics and Department of Computer Science, University of Tübingen, D-72076 Tübingen, Germany
| | - Laurent Gatto
- ‡‡Computational Proteomics Unit and Cambridge Centre for Proteomics, Cambridge Systems Biology Centre, Department of Biochemistry, University of Cambridge, CB2 1QR, Cambridge, UK
| | - Jürgen Hartler
- §§Institute for Genomics and Bioinformatics, Graz University of Technology, Petersgasse 14/V, 8010 Graz, Austria; ¶¶Core Facility Bioinformatics, Austrian Centre of Industrial Biotechnology (ACIB GmbH), Petersgasse 14/V, 8010 Graz, Austria
| | - Gerhard G Thallinger
- §§Institute for Genomics and Bioinformatics, Graz University of Technology, Petersgasse 14/V, 8010 Graz, Austria; ¶¶Core Facility Bioinformatics, Austrian Centre of Industrial Biotechnology (ACIB GmbH), Petersgasse 14/V, 8010 Graz, Austria
| | - Reza M Salek
- From the ‡European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, CB10 1SD, Hinxton, Cambridge, UK
| | - Christoph Steinbeck
- From the ‡European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, CB10 1SD, Hinxton, Cambridge, UK
| | - Nadin Neuhauser
- ‖‖Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Jürgen Cox
- ‖‖Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Steffen Neumann
- Department of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany
| | - Jun Fan
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Florian Reisinger
- From the ‡European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, CB10 1SD, Hinxton, Cambridge, UK
| | - Qing-Wei Xu
- From the ‡European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, CB10 1SD, Hinxton, Cambridge, UK; College of Computer, Hubei University of Education, Wuhan, China
| | - Noemi Del Toro
- From the ‡European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, CB10 1SD, Hinxton, Cambridge, UK
| | - Yasset Pérez-Riverol
- From the ‡European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, CB10 1SD, Hinxton, Cambridge, UK
| | - Fawaz Ghali
- ‖Institute of Integrative Biology, University of Liverpool, L69 7ZB, Liverpool, UK
| | - Nuno Bandeira
- Center for Computational Mass Spectrometry, University of California, San Diego, La Jolla, CA
| | - Ioannis Xenarios
- Swiss-Prot group, SIB Swiss Institute of Bioinformatics, 1 Rue Michel Servet, 1211 Geneva, Switzerland; Vital-IT group, SIB Swiss Institute of Bioinformatics, Quartier Sorge, Genopode 1015 Lausanne; Center of Integrative Genomics, University of Lausanne, Quartier Sorge Genopode, 1015 Lausanne
| | - Oliver Kohlbacher
- **Center for Bioinformatics and Department of Computer Science, University of Tübingen, D-72076 Tübingen, Germany; Quantitative Biology Center, University of Tübingen, D-72076 Tübingen, Germany
| | - Juan Antonio Vizcaíno
- From the ‡European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, CB10 1SD, Hinxton, Cambridge, UK;
| | - Henning Hermjakob
- From the ‡European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, CB10 1SD, Hinxton, Cambridge, UK
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Xia Y, Lucifora J, Reisinger F, Heikenwalder M, Protzer U. Virology. Response to Comment on "Specific and nonhepatotoxic degradation of nuclear hepatitis B virus cccDNA". Science 2014; 344:1237. [PMID: 24926011 DOI: 10.1126/science.1254083] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Chisari et al. challenge our central conclusion that the hepatitis B virus (HBV) persistent form, the covalently closed circular DNA (cccDNA), is degraded in a noncytotoxic and specific fashion in the nucleus of infected hepatocytes. Specificity of the assays used, exclusion of cell division or death, and activity of APOBEC3 deaminases in the nucleus, however, were addressed in the paper.
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Affiliation(s)
- Yuchen Xia
- Institute of Virology, Technische Universität München, Helmholtz Zentrum München, Munich, Germany
| | - Julie Lucifora
- Institute of Virology, Technische Universität München, Helmholtz Zentrum München, Munich, Germany
| | - Florian Reisinger
- Institute of Virology, Technische Universität München, Helmholtz Zentrum München, Munich, Germany
| | - Mathias Heikenwalder
- Institute of Virology, Technische Universität München, Helmholtz Zentrum München, Munich, Germany
| | - Ulrike Protzer
- Institute of Virology, Technische Universität München, Helmholtz Zentrum München, Munich, Germany.
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24
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Lucifora J, Xia Y, Reisinger F, Zhang K, Stadler D, Cheng X, Sprinzl MF, Koppensteiner H, Makowska Z, Volz T, Remouchamps C, Chou WM, Thasler WE, Hüser N, Durantel D, Liang TJ, Münk C, Heim MH, Browning JL, Dejardin E, Dandri M, Schindler M, Heikenwalder M, Protzer U. Specific and nonhepatotoxic degradation of nuclear hepatitis B virus cccDNA. Science 2014; 343:1221-8. [PMID: 24557838 DOI: 10.1126/science.1243462] [Citation(s) in RCA: 694] [Impact Index Per Article: 69.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Current antiviral agents can control but not eliminate hepatitis B virus (HBV), because HBV establishes a stable nuclear covalently closed circular DNA (cccDNA). Interferon-α treatment can clear HBV but is limited by systemic side effects. We describe how interferon-α can induce specific degradation of the nuclear viral DNA without hepatotoxicity and propose lymphotoxin-β receptor activation as a therapeutic alternative. Interferon-α and lymphotoxin-β receptor activation up-regulated APOBEC3A and APOBEC3B cytidine deaminases, respectively, in HBV-infected cells, primary hepatocytes, and human liver needle biopsies. HBV core protein mediated the interaction with nuclear cccDNA, resulting in cytidine deamination, apurinic/apyrimidinic site formation, and finally cccDNA degradation that prevented HBV reactivation. Genomic DNA was not affected. Thus, inducing nuclear deaminases-for example, by lymphotoxin-β receptor activation-allows the development of new therapeutics that, in combination with existing antivirals, may cure hepatitis B.
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Affiliation(s)
- Julie Lucifora
- Institute of Virology, Technische Universität München-Helmholtz Zentrum München, 81675 Munich, Germany
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25
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Vucur M, Reisinger F, Gautheron J, Janssen J, Roderburg C, Cardenas D, Kreggenwinkel K, Koppe C, Hammerich L, Hakem R, Unger K, Weber A, Gassler N, Luedde M, Frey N, Neumann U, Tacke F, Trautwein C, Heikenwalder M, Luedde T. RIP3 Inhibits Inflammatory Hepatocarcinogenesis but Promotes Cholestasis by Controlling Caspase-8- and JNK-Dependent Compensatory Cell Proliferation. Cell Rep 2013; 4:776-90. [PMID: 23972991 DOI: 10.1016/j.celrep.2013.07.035] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Revised: 06/18/2013] [Accepted: 07/26/2013] [Indexed: 02/03/2023] Open
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Ghali F, Krishna R, Lukasse P, Martínez-Bartolomé S, Reisinger F, Hermjakob H, Vizcaíno JA, Jones AR. Tools (Viewer, Library and Validator) that facilitate use of the peptide and protein identification standard format, termed mzIdentML. Mol Cell Proteomics 2013; 12:3026-35. [PMID: 23813117 PMCID: PMC3820921 DOI: 10.1074/mcp.o113.029777] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [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] [Indexed: 11/30/2022] Open
Abstract
The Proteomics Standards Initiative has recently released the mzIdentML data standard for representing peptide and protein identification results, for example, created by a search engine. When a new standard format is produced, it is important that software tools are available that make it straightforward for laboratory scientists to use it routinely and for bioinformaticians to embed support in their own tools. Here we report the release of several open-source Java-based software packages based on mzIdentML: ProteoIDViewer, mzidLibrary, and mzidValidator. The ProteoIDViewer is a desktop application allowing users to visualize mzIdentML-formatted results originating from any appropriate identification software; it supports visualization of all the features of the mzIdentML format. The mzidLibrary is a software library containing routines for importing data from external search engines, post-processing identification data (such as false discovery rate calculations), combining results from multiple search engines, performing protein inference, setting identification thresholds, and exporting results from mzIdentML to plain text files. The mzidValidator is able to process files and report warnings or errors if files are not correctly formatted or contain some semantic error. We anticipate that these developments will simplify adoption of the new standard in proteomics laboratories and the integration of mzIdentML into other software tools. All three tools are freely available in the public domain.
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Affiliation(s)
- Fawaz Ghali
- Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, United Kingdom
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27
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Sprinzl MF, Reisinger F, Puschnik A, Ringelhan M, Ackermann K, Hartmann D, Schiemann M, Weinmann A, Galle PR, Schuchmann M, Friess H, Otto G, Heikenwalder M, Protzer U. Sorafenib perpetuates cellular anticancer effector functions by modulating the crosstalk between macrophages and natural killer cells. Hepatology 2013; 57:2358-68. [PMID: 23424039 DOI: 10.1002/hep.26328] [Citation(s) in RCA: 126] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/22/2012] [Accepted: 01/10/2013] [Indexed: 12/07/2022]
Abstract
UNLABELLED Alternatively polarized macrophages (Mϕ) shape the microenvironment of hepatocellular carcinoma (HCC) and temper anticancer immune responses. We investigated if sorafenib alters the HCC microenvironment by restoring classical macrophage polarization and triggering tumor-directed natural killer (NK) cell responses. In vivo experiments were conducted with sorafenib (25 mg/kg)-treated C57BL/6 wildtype as well as hepatitis B virus (HBV) and lymphotoxin transgenic mice with and without HCC. Monocyte-derived Mϕ or tumor-associated macrophages (TAM) isolated from HCC tissue were treated with sorafenib (0.07-5.0 μg/mL) and cocultured with autologous NK cells. Mϕ and NK cell activation was analyzed by flow cytometry and killing assays, respectively. Cytokine and growth factor release was measured by enzyme-linked immunosorbent assay. Short-term administration of sorafenib triggered activation of hepatic NK cells in wildtype and tumor-bearing mice. In vitro, sorafenib sensitized Mϕ to lipopolysaccharide, reverted alternative Mϕ polarization and enhanced IL12 secretion (P = 0.0133). NK cells activated by sorafenib-treated Mϕ showed increased degranulation (15.3 ± 0.2% versus 32.0 ± 0.9%, P < 0.0001) and interferon-gamma (IFN-γ) secretion (2.1 ± 0.2% versus 8.0 ± 0.2%, P < 0.0001) upon target cell contact. Sorafenib-triggered NK cell activation was verified by coculture experiments using TAM. Sorafenib-treated Mϕ increased cytolytic NK cell function against K562, Raji, and HepG2 target cells in a dose-dependent manner. Neutralization of interleukin (IL)12 or IL18 as well as inhibition of the nuclear factor kappa B (NF-κB) pathway reversed NK cell activation in Mϕ/NK cocultures. CONCLUSION Sorafenib triggers proinflammatory activity of TAM and subsequently induces antitumor NK cell responses in a cytokine- and NF-κB-dependent fashion. This observation is relevant for HCC therapy, as sorafenib is a compound in clinical use that reverts alternative polarization of TAM in HCC. (HEPATOLOGY 2013;57:2358-2368).
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Affiliation(s)
- Martin Franz Sprinzl
- Institute of Virology, Technische Universität München/Helmholtz Zentrum München, München, Germany
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Csordas A, Wang R, Ríos D, Reisinger F, Foster JM, Slotta DJ, Vizcaíno JA, Hermjakob H. From Peptidome to PRIDE: public proteomics data migration at a large scale. Proteomics 2013; 13:1692-5. [PMID: 23533138 PMCID: PMC3717177 DOI: 10.1002/pmic.201200514] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [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: 11/09/2012] [Revised: 02/14/2013] [Accepted: 02/28/2013] [Indexed: 11/07/2022]
Abstract
The PRIDE database, developed and maintained at the European Bioinformatics Institute (EBI), is one of the most prominent data repositories dedicated to high throughput MS-based proteomics data. Peptidome, developed by the National Center for Biotechnology Information (NCBI) as a sibling resource to PRIDE, was discontinued due to funding constraints in April 2011. A joint effort between the two teams was started soon after the Peptidome closure to ensure that data were not “lost” to the wider proteomics community by exporting it to PRIDE. As a result, data in the low terabyte range have been migrated from Peptidome to PRIDE and made publicly available under experiment accessions 17 900–18 271, representing 54 projects, ∼53 million mass spectra, ∼10 million peptide identifications, ∼650 000 protein identifications, ∼1.1 million biologically relevant protein modifications, and 28 species, from more than 30 different labs.
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Affiliation(s)
- Attila Csordas
- EMBL Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
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29
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Walzer M, Qi D, Mayer G, Uszkoreit J, Eisenacher M, Sachsenberg T, Gonzalez-Galarza FF, Fan J, Bessant C, Deutsch EW, Reisinger F, Vizcaíno JA, Medina-Aunon JA, Albar JP, Kohlbacher O, Jones AR. The mzQuantML data standard for mass spectrometry-based quantitative studies in proteomics. Mol Cell Proteomics 2013; 12:2332-40. [PMID: 23599424 PMCID: PMC3734589 DOI: 10.1074/mcp.o113.028506] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [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] [Indexed: 11/28/2022] Open
Abstract
The range of heterogeneous approaches available for quantifying protein abundance via mass spectrometry (MS)1 leads to considerable challenges in modeling, archiving, exchanging, or submitting experimental data sets as supplemental material to journals. To date, there has been no widely accepted format for capturing the evidence trail of how quantitative analysis has been performed by software, for transferring data between software packages, or for submitting to public databases. In the context of the Proteomics Standards Initiative, we have developed the mzQuantML data standard. The standard can represent quantitative data about regions in two-dimensional retention time versus mass/charge space (called features), peptides, and proteins and protein groups (where there is ambiguity regarding peptide-to-protein inference), and it offers limited support for small molecule (metabolomic) data. The format has structures for representing replicate MS runs, grouping of replicates (for example, as study variables), and capturing the parameters used by software packages to arrive at these values. The format has the capability to reference other standards such as mzML and mzIdentML, and thus the evidence trail for the MS workflow as a whole can now be described. Several software implementations are available, and we encourage other bioinformatics groups to use mzQuantML as an input, internal, or output format for quantitative software and for structuring local repositories. All project resources are available in the public domain from the HUPO Proteomics Standards Initiative http://www.psidev.info/mzquantml.
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Affiliation(s)
- Mathias Walzer
- Quantitative Biology Center and Department of Computer Science, Center for Bioinformatics, University of Tübingen, Sand 14, 72076 Tübingen, Germany
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Hulstaert N, Reisinger F, Rameseder J, Barsnes H, Vizcaíno JA, Martens L. Pride-asap: automatic fragment ion annotation of identified PRIDE spectra. J Proteomics 2013; 95:89-92. [PMID: 23603108 PMCID: PMC4085470 DOI: 10.1016/j.jprot.2013.04.011] [Citation(s) in RCA: 9] [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: 10/09/2012] [Revised: 03/27/2013] [Accepted: 04/09/2013] [Indexed: 11/13/2022]
Abstract
We present an open source software application and library written in Java that provides a uniform annotation of identified spectra stored in the PRIDE database. Pride-asap can be ran in a command line mode for automated processing of multiple PRIDE experiments, but also has a graphical user interface that allows end users to annotate the spectra in PRIDE experiments and to inspect the results in detail. Pride-asap binaries, source code and additional information can be downloaded from http://pride-asa-pipeline.googlecode.com.This article is part of a Special Issue entitled: Standardization and Quality Control in Proteomics. We have built an automatic spectrum annotation pipeline for PRIDE. The tool provides both a GUI and a command-line. The provided annotations are robust and consistent. The tool can be applied easily to thousands of PRIDE experiments. Results are available in the GUI, and as text files for downstream analysis.
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Affiliation(s)
- Niels Hulstaert
- Department of Medical Protein Research, VIB, Ghent, Belgium; Department of Biochemistry, Ghent University, Ghent, Belgium
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31
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Huang LR, Wohlleber D, Reisinger F, Jenne CN, Cheng RL, Abdullah Z, Schildberg FA, Odenthal M, Dienes HP, van Rooijen N, Schmitt E, Garbi N, Croft M, Kurts C, Kubes P, Protzer U, Heikenwalder M, Knolle PA. Intrahepatic myeloid-cell aggregates enable local proliferation of CD8+ T cells and successful immunotherapy against chronic viral liver infection. Nat Immunol 2013; 14:574-83. [DOI: 10.1038/ni.2573] [Citation(s) in RCA: 173] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Accepted: 02/20/2013] [Indexed: 12/13/2022]
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32
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Vizcaíno JA, Côté RG, Csordas A, Dianes JA, Fabregat A, Foster JM, Griss J, Alpi E, Birim M, Contell J, O'Kelly G, Schoenegger A, Ovelleiro D, Pérez-Riverol Y, Reisinger F, Ríos D, Wang R, Hermjakob H. The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013. Nucleic Acids Res 2012. [PMID: 23203882 PMCID: PMC3531176 DOI: 10.1093/nar/gks1262] [Citation(s) in RCA: 1579] [Impact Index Per Article: 131.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The PRoteomics IDEntifications (PRIDE, http://www.ebi.ac.uk/pride) database at the European Bioinformatics Institute is one of the most prominent data repositories of mass spectrometry (MS)-based proteomics data. Here, we summarize recent developments in the PRIDE database and related tools. First, we provide up-to-date statistics in data content, splitting the figures by groups of organisms and species, including peptide and protein identifications, and post-translational modifications. We then describe the tools that are part of the PRIDE submission pipeline, especially the recently developed PRIDE Converter 2 (new submission tool) and PRIDE Inspector (visualization and analysis tool). We also give an update about the integration of PRIDE with other MS proteomics resources in the context of the ProteomeXchange consortium. Finally, we briefly review the quality control efforts that are ongoing at present and outline our future plans.
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Affiliation(s)
- Juan Antonio Vizcaíno
- EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
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33
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Abstract
Cytokines have been implicated in a variety of physiological processes involving lymphoid tissue development, lymphocyte activation, and control of regenerative processes such as wound healing. The first characterization of a cytokine implicated in abolishing or killing tumor cells - the tumor necrosis factor (TNF) - fostered and boosted a completely new field of research that in addition to cancer research started to generate an overwhelming amount of knowledge in immunology, various pathological processes, and other fields of research. Due to the complex networks and versatile functions of cytokines, it soon became clear that cytokines can possess diametric functions in various biological processes. As for tumor research it was shown that some cytokines - depending on the type of organ, the time of action, gender, and the cellular environment - can have either pro- or anticarcinogenic action. For those cytokines reported to be procarcinogenic, this could be accomplished by directly acting as oncogenes or generating an inflammatory environment that is procarcinogenic. Here we review a novel role for TNF family members - in particular lymphotoxin (LT) α and β - in physiology and in driving tumorigenesis, with special focus on the liver. We believe that recent findings on this particular cytokine might have strong implications for the therapy of liver cancer or other inflammation-induced cancer types.
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Affiliation(s)
- Judith Bauer
- Institute for Virology, Helmholtz-Zentrum München, Munich, Germany
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34
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Côté RG, Griss J, Dianes JA, Wang R, Wright JC, van den Toorn HWP, van Breukelen B, Heck AJR, Hulstaert N, Martens L, Reisinger F, Csordas A, Ovelleiro D, Perez-Rivevol Y, Barsnes H, Hermjakob H, Vizcaíno JA. The PRoteomics IDEntification (PRIDE) Converter 2 framework: an improved suite of tools to facilitate data submission to the PRIDE database and the ProteomeXchange consortium. Mol Cell Proteomics 2012; 11:1682-9. [PMID: 22949509 PMCID: PMC3518121 DOI: 10.1074/mcp.o112.021543] [Citation(s) in RCA: 100] [Impact Index Per Article: 8.3] [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] [Indexed: 11/30/2022] Open
Abstract
The original PRIDE Converter tool greatly simplified the process of submitting mass spectrometry (MS)-based proteomics data to the PRIDE database. However, after much user feedback, it was noted that the tool had some limitations and could not handle several user requirements that were now becoming commonplace. This prompted us to design and implement a whole new suite of tools that would build on the successes of the original PRIDE Converter and allow users to generate submission-ready, well-annotated PRIDE XML files. The PRIDE Converter 2 tool suite allows users to convert search result files into PRIDE XML (the format needed for performing submissions to the PRIDE database), generate mzTab skeleton files that can be used as a basis to submit quantitative and gel-based MS data, and post-process PRIDE XML files by filtering out contaminants and empty spectra, or by merging several PRIDE XML files together. All the tools have both a graphical user interface that provides a dialog-based, user-friendly way to convert and prepare files for submission, as well as a command-line interface that can be used to integrate the tools into existing or novel pipelines, for batch processing and power users. The PRIDE Converter 2 tool suite will thus become a cornerstone in the submission process to PRIDE and, by extension, to the ProteomeXchange consortium of MS-proteomics data repositories.
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Affiliation(s)
- Richard G Côté
- Proteomics Services Team, EMBL Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
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35
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Griss J, Reisinger F, Hermjakob H, Vizcaíno JA. jmzReader: A Java parser library to process and visualize multiple text and XML-based mass spectrometry data formats. Proteomics 2012; 12:795-8. [PMID: 22539430 PMCID: PMC3472022 DOI: 10.1002/pmic.201100578] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [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] [Indexed: 12/12/2022]
Abstract
We here present the jmzReader library: a collection of Java application programming interfaces (APIs) to parse the most commonly used peak list and XML-based mass spectrometry (MS) data formats: DTA, MS2, MGF, PKL, mzXML, mzData, and mzML (based on the already existing API jmzML). The library is optimized to be used in conjunction with mzIdentML, the recently released standard data format for reporting protein and peptide identifications, developed by the HUPO proteomics standards initiative (PSI). mzIdentML files do not contain spectra data but contain references to different kinds of external MS data files. As a key functionality, all parsers implement a common interface that supports the various methods used by mzIdentML to reference external spectra. Thus, when developing software for mzIdentML, programmers no longer have to support multiple MS data file formats but only this one interface. The library (which includes a viewer) is open source and, together with detailed documentation, can be downloaded from http://code.google.com/p/jmzreader/.
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Affiliation(s)
- Johannes Griss
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
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36
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Jones AR, Eisenacher M, Mayer G, Kohlbacher O, Siepen J, Hubbard SJ, Selley JN, Searle BC, Shofstahl J, Seymour SL, Julian R, Binz PA, Deutsch EW, Hermjakob H, Reisinger F, Griss J, Vizcaíno JA, Chambers M, Pizarro A, Creasy D. The mzIdentML data standard for mass spectrometry-based proteomics results. Mol Cell Proteomics 2012. [PMID: 22375074 DOI: 10.1074/mcp.m111.014381 [epub ahead of print]] [Citation(s) in RCA: 0] [Impact Index Per Article: 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] [Indexed: 05/08/2023] Open
Abstract
We report the release of mzIdentML, an exchange standard for peptide and protein identification data, designed by the Proteomics Standards Initiative. The format was developed by the Proteomics Standards Initiative in collaboration with instrument and software vendors, and the developers of the major open-source projects in proteomics. Software implementations have been developed to enable conversion from most popular proprietary and open-source formats, and mzIdentML will soon be supported by the major public repositories. These developments enable proteomics scientists to start working with the standard for exchanging and publishing data sets in support of publications and they provide a stable platform for bioinformatics groups and commercial software vendors to work with a single file format for identification data.
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Affiliation(s)
- Andrew R Jones
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZJ, UK.
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37
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Jones AR, Eisenacher M, Mayer G, Kohlbacher O, Siepen J, Hubbard SJ, Selley JN, Searle BC, Shofstahl J, Seymour SL, Julian R, Binz PA, Deutsch EW, Hermjakob H, Reisinger F, Griss J, Vizcaíno JA, Chambers M, Pizarro A, Creasy D. The mzIdentML data standard for mass spectrometry-based proteomics results. Mol Cell Proteomics 2012; 11:M111.014381. [PMID: 22375074 PMCID: PMC3394945 DOI: 10.1074/mcp.m111.014381] [Citation(s) in RCA: 148] [Impact Index Per Article: 12.3] [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: 09/15/2011] [Revised: 12/20/2011] [Indexed: 11/06/2022] Open
Abstract
We report the release of mzIdentML, an exchange standard for peptide and protein identification data, designed by the Proteomics Standards Initiative. The format was developed by the Proteomics Standards Initiative in collaboration with instrument and software vendors, and the developers of the major open-source projects in proteomics. Software implementations have been developed to enable conversion from most popular proprietary and open-source formats, and mzIdentML will soon be supported by the major public repositories. These developments enable proteomics scientists to start working with the standard for exchanging and publishing data sets in support of publications and they provide a stable platform for bioinformatics groups and commercial software vendors to work with a single file format for identification data.
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Affiliation(s)
- Andrew R Jones
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZJ, UK.
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38
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Abstract
The Protein Identifier Cross-Reference (PICR) service is a tool that allows users to map protein identifiers, protein sequences and gene identifiers across over 100 different source databases. PICR takes input through an interactive website as well as Representational State Transfer (REST) and Simple Object Access Protocol (SOAP) services. It returns the results as HTML pages, XLS and CSV files. It has been in production since 2007 and has been recently enhanced to add new functionality and increase the number of databases it covers. Protein subsequences can be Basic Local Alignment Search Tool (BLAST) against the UniProt Knowledgebase (UniProtKB) to provide an entry point to the standard PICR mapping algorithm. In addition, gene identifiers from UniProtKB and Ensembl can now be submitted as input or mapped to as output from PICR. We have also implemented a 'best-guess' mapping algorithm for UniProt. In this article, we describe the usefulness of PICR, how these changes have been implemented, and the corresponding additions to the web services. Finally, we explain that the number of source databases covered by PICR has increased from the initial 73 to the current 102. New resources include several new species-specific Ensembl databases as well as the Ensembl Genome ones. PICR can be accessed at http://www.ebi.ac.uk/Tools/picr/.
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Affiliation(s)
- Samuel P Wein
- EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
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39
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Reisinger F, Krishna R, Ghali F, Ríos1 D, Hermjakob H, Vizcaíno JA, Jones AR. jmzIdentML API: A Java interface to the mzIdentML standard for peptide and protein identification data. Proteomics 2012; 12:790-4. [PMID: 22539429 PMCID: PMC3933944 DOI: 10.1002/pmic.201100577] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [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: 11/04/2011] [Accepted: 12/15/2011] [Indexed: 12/03/2022]
Abstract
We present a Java application programming interface (API), jmzIdentML, for the Human Proteome Organisation (HUPO) Proteomics Standards Initiative (PSI) mzIdentML standard for peptide and protein identification data. The API combines the power of Java Architecture of XML Binding (JAXB) and an XPath-based random-access indexer to allow a fast and efficient mapping of extensible markup language (XML) elements to Java objects. The internal references in the mzIdentML files are resolved in an on-demand manner, where the whole file is accessed as a random-access swap file, and only the relevant piece of XMLis selected for mapping to its corresponding Java object. The APIis highly efficient in its memory usage and can handle files of arbitrary sizes. The APIfollows the official release of the mzIdentML (version 1.1) specifications and is available in the public domain under a permissive licence at http://www.code.google.com/p/jmzidentml/.
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Affiliation(s)
- Florian Reisinger
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, HinxtonCambridge, CB10 1SD, UK
| | - Ritesh Krishna
- Institute of Integrative Biology, University of LiverpoolLiverpool, UK
| | - Fawaz Ghali
- Institute of Integrative Biology, University of LiverpoolLiverpool, UK
| | - Daniel Ríos1
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, HinxtonCambridge, CB10 1SD, UK
| | - Henning Hermjakob
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, HinxtonCambridge, CB10 1SD, UK
| | - Juan Antonio Vizcaíno
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, HinxtonCambridge, CB10 1SD, UK
| | - Andrew R Jones
- Institute of Integrative Biology, University of LiverpoolLiverpool, UK
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40
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Wang R, Fabregat A, Ríos D, Ovelleiro D, Foster JM, Côté RG, Griss J, Csordas A, Perez-Riverol Y, Reisinger F, Hermjakob H, Martens L, Vizcaíno JA. PRIDE Inspector: a tool to visualize and validate MS proteomics data. Nat Biotechnol 2012; 30:135-7. [PMID: 22318026 PMCID: PMC3277942 DOI: 10.1038/nbt.2112] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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41
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Abstract
Inflammatory responses in the liver--a central constituent of hepatic wound healing--can be self-limited or persistent depending on the aetiology, liver health state, concentration of toxins or pathogens, and the time frame of exposure to toxins or infection. In case the immune system eradicates a pathogen or in case toxin-exposure is transient, acute hepatitis resolves and the affected liver tissue regenerates ad integrum. However, in many cases liver damage remains chronic. Irrespective of the aetiology, chronic liver damage drives chronic hepatitis and hepatocyte death as well as compensatory proliferation, reflecting liver regeneration. Over time this potentially promotes further hepatic damage, fibrosis, cirrhosis and liver cancer. Here, we review the current knowledge on how chronic liver injury and inflammation is triggered and maintained, and how inflammation is linked to liver cancer. We also discuss the most frequently used animal models for damage or inflammation induced liver cancer and their suitability for conducting clinically relevant research.
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Affiliation(s)
- Achim Weber
- Institute of Virology, Technische Universität München, Helmholtz Zentrum München, Schneckenburgerstrasse 8, Munich, Germany.
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42
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Abstract
With the continuously growing amount of proteomics data being produced, it has become increasingly important to make these data publicly available so that they can be audited, reanalyzed, and reused. More and more journals are also starting to request the deposition of MS data in publicly available repositories for submitted proteomics manuscripts. In this chapter we focus on one of the most commonly used proteomics data repositories, PRIDE (the PRoteomics IDEntifications database, http://www.ebi.ac.uk/pride), and demonstrate how a new graphical user interface tool called PRIDE Converter (http://pride-converter.googlecode.com) greatly simplifies the submission of data to PRIDE.
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Affiliation(s)
- Harald Barsnes
- Department of Informatics, University of Bergen, Bergen, Norway
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43
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Abstract
The Proteomics Identifications Database (PRIDE, http://www.ebi.ac.uk/pride ) provides users with the ability to explore and compare mass spectrometry-based proteomics experiments that reveal details of the protein expression found in a broad range of taxonomic groups, tissues, and disease states. A PRIDE experiment typically includes identifications of proteins, peptides, and protein modifications. Additionally, many of the submitted experiments also include the mass spectra that provide the evidence for these identifications. Finally, one of the strongest advantages of PRIDE in comparison with other proteomics repositories is the amount of metadata it contains, a key point to put the above-mentioned data in biological and/or technical context. Several informatics tools have been developed in support of the PRIDE database. The most recent one is called "Database on Demand" (DoD), which allows custom sequence databases to be built in order to optimize the results from search engines. We describe the use of DoD in this chapter. Additionally, in order to show the potential of PRIDE as a source for data mining, we also explore complex queries using federated BioMart queries to integrate PRIDE data with other resources, such as Ensembl, Reactome, or UniProt.
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Affiliation(s)
- Juan Antonio Vizcaíno
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
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44
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Katayama T, Arakawa K, Nakao M, Ono K, Aoki-Kinoshita KF, Yamamoto Y, Yamaguchi A, Kawashima S, Chun HW, Aerts J, Aranda B, Barboza LH, Bonnal RJ, Bruskiewich R, Bryne JC, Fernández JM, Funahashi A, Gordon PM, Goto N, Groscurth A, Gutteridge A, Holland R, Kano Y, Kawas EA, Kerhornou A, Kibukawa E, Kinjo AR, Kuhn M, Lapp H, Lehvaslaiho H, Nakamura H, Nakamura Y, Nishizawa T, Nobata C, Noguchi T, Oinn TM, Okamoto S, Owen S, Pafilis E, Pocock M, Prins P, Ranzinger R, Reisinger F, Salwinski L, Schreiber M, Senger M, Shigemoto Y, Standley DM, Sugawara H, Tashiro T, Trelles O, Vos RA, Wilkinson MD, York W, Zmasek CM, Asai K, Takagi T. The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium*. J Biomed Semantics 2010; 1:8. [PMID: 20727200 PMCID: PMC2939597 DOI: 10.1186/2041-1480-1-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2009] [Accepted: 08/21/2010] [Indexed: 11/30/2022] Open
Abstract
Web services have become a key technology for bioinformatics, since life science databases are globally decentralized and the exponential increase in the amount of available data demands for efficient systems without the need to transfer entire databases for every step of an analysis. However, various incompatibilities among database resources and analysis services make it difficult to connect and integrate these into interoperable workflows. To resolve this situation, we invited domain specialists from web service providers, client software developers, Open Bio* projects, the BioMoby project and researchers of emerging areas where a standard exchange data format is not well established, for an intensive collaboration entitled the BioHackathon 2008. The meeting was hosted by the Database Center for Life Science (DBCLS) and Computational Biology Research Center (CBRC) and was held in Tokyo from February 11th to 15th, 2008. In this report we highlight the work accomplished and the common issues arisen from this event, including the standardization of data exchange formats and services in the emerging fields of glycoinformatics, biological interaction networks, text mining, and phyloinformatics. In addition, common shared object development based on BioSQL, as well as technical challenges in large data management, asynchronous services, and security are discussed. Consequently, we improved interoperability of web services in several fields, however, further cooperation among major database centers and continued collaborative efforts between service providers and software developers are still necessary for an effective advance in bioinformatics web service technologies.
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Affiliation(s)
- Toshiaki Katayama
- Database Center for Life Science, Research Organization of Information and Systems, 2-11-16 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan.
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45
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Martens L, Chambers M, Sturm M, Kessner D, Levander F, Shofstahl J, Tang WH, Römpp A, Neumann S, Pizarro AD, Montecchi-Palazzi L, Tasman N, Coleman M, Reisinger F, Souda P, Hermjakob H, Binz PA, Deutsch EW. mzML--a community standard for mass spectrometry data. Mol Cell Proteomics 2010; 10:R110.000133. [PMID: 20716697 PMCID: PMC3013463 DOI: 10.1074/mcp.r110.000133] [Citation(s) in RCA: 441] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Mass spectrometry is a fundamental tool for discovery and analysis in the life sciences. With the rapid advances in mass spectrometry technology and methods, it has become imperative to provide a standard output format for mass spectrometry data that will facilitate data sharing and analysis. Initially, the efforts to develop a standard format for mass spectrometry data resulted in multiple formats, each designed with a different underlying philosophy. To resolve the issues associated with having multiple formats, vendors, researchers, and software developers convened under the banner of the HUPO PSI to develop a single standard. The new data format incorporated many of the desirable technical attributes from the previous data formats, while adding a number of improvements, including features such as a controlled vocabulary with validation tools to ensure consistent usage of the format, improved support for selected reaction monitoring data, and immediately available implementations to facilitate rapid adoption by the community. The resulting standard data format, mzML, is a well tested open-source format for mass spectrometer output files that can be readily utilized by the community and easily adapted for incremental advances in mass spectrometry technology.
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Affiliation(s)
- Lennart Martens
- Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium
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Abstract
We here present jmzML, a Java API for the Proteomics Standards Initiative mzML data standard. Based on the Java Architecture for XML Binding and XPath-based XML indexer random-access XML parser, jmzML can handle arbitrarily large files in minimal memory, allowing easy and efficient processing of mzML files using the Java programming language. jmzML also automatically resolves internal XML references on-the-fly. The library (which includes a viewer) can be downloaded from http://jmzml.googlecode.com.
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Affiliation(s)
- Richard G Côté
- EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK
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47
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Smedley D, Schofield P, Chen CK, Aidinis V, Ainali C, Bard J, Balling R, Birney E, Blake A, Bongcam-Rudloff E, Brookes AJ, Cesareni G, Chandras C, Eppig J, Flicek P, Gkoutos G, Greenaway S, Gruenberger M, Hériché JK, Lyall A, Mallon AM, Muddyman D, Reisinger F, Ringwald M, Rosenthal N, Schughart K, Swertz M, Thorisson GA, Zouberakis M, Hancock JM. Finding and sharing: new approaches to registries of databases and services for the biomedical sciences. Database (Oxford) 2010; 2010:baq014. [PMID: 20627863 PMCID: PMC2911849 DOI: 10.1093/database/baq014] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [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: 04/26/2010] [Accepted: 06/20/2010] [Indexed: 11/14/2022]
Abstract
The recent explosion of biological data and the concomitant proliferation of distributed databases make it challenging for biologists and bioinformaticians to discover the best data resources for their needs, and the most efficient way to access and use them. Despite a rapid acceleration in uptake of syntactic and semantic standards for interoperability, it is still difficult for users to find which databases support the standards and interfaces that they need. To solve these problems, several groups are developing registries of databases that capture key metadata describing the biological scope, utility, accessibility, ease-of-use and existence of web services allowing interoperability between resources. Here, we describe some of these initiatives including a novel formalism, the Database Description Framework, for describing database operations and functionality and encouraging good database practise. We expect such approaches will result in improved discovery, uptake and utilization of data resources. Database URL: http://www.casimir.org.uk/casimir_ddf.
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Affiliation(s)
- Damian Smedley
- European Bioinformatics Institute, Genome Campus, Hinxton, Cambridgeshire, CB10 1SA.
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48
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Abstract
The Proteomics Identifications database (PRIDE, http://www.ebi.ac.uk/pride) is one of the main repositories designed to store, disseminate, and analyze mass spectrometry-based proteomics datasets. In this unit, an overview of the PRIDE system is given, including its key satellite tools: the Ontology Lookup Service (OLS), the Protein Identifier Cross-Referencing Service (PICR), and Database on Demand (DoD). Also described in detail are procedures for submitting data to PRIDE, and accessing data stored in PRIDE using the BioMart interface. Finally, to demonstrate the potential of PRIDE as a source for data mining, an example protocol is provided to showcase the powerful cross-domain query capabilities available through a combination of BioMarts.
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Affiliation(s)
- Juan Antonio Vizcaíno
- European Molecular Biology Laboratory-European Bioinformatics Institute, Hinxton, Cambridge, United Kingdom
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49
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Abstract
The Ontology Lookup Service (OLS; http://www.ebi.ac.uk/ols) has been providing several means to query, browse and navigate biomedical ontologies and controlled vocabularies since it first went into production 4 years ago, and usage statistics indicate that it has become a heavily accessed service with millions of hits monthly. The volume of data available for querying has increased 7-fold since its inception. OLS functionality has been integrated into several high-usage databases and data entry tools. Improvements in the data model and loaders, as well as interface enhancements have made the OLS easier to use and capture more annotations from the source data. In addition, newly released software packages now provide easy means to fully integrate OLS functionality in external applications.
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Affiliation(s)
- Richard Côté
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SD, UK.
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Montecchi-Palazzi L, Kerrien S, Reisinger F, Aranda B, Jones AR, Martens L, Hermjakob H. The PSI semantic validator: a framework to check MIAPE compliance of proteomics data. Proteomics 2010; 9:5112-9. [PMID: 19834897 DOI: 10.1002/pmic.200900189] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The Human Proteome Organization's Proteomics Standards Initiative (PSI) promotes the development of exchange standards to improve data integration and interoperability. PSI specifies the suitable level of detail required when reporting a proteomics experiment (via the Minimum Information About a Proteomics Experiment), and provides extensible markup language (XML) exchange formats and dedicated controlled vocabularies (CVs) that must be combined to generate a standard compliant document. The framework presented here tackles the issue of checking that experimental data reported using a specific format, CVs and public bio-ontologies (e.g. Gene Ontology, NCBI taxonomy) are compliant with the Minimum Information About a Proteomics Experiment recommendations. The semantic validator not only checks the XML syntax but it also enforces rules regarding the use of an ontology class or CV terms by checking that the terms exist in the resource and that they are used in the correct location of a document. Moreover, this framework is extremely fast, even on sizable data files, and flexible, as it can be adapted to any standard by customizing the parameters it requires: an XML Schema Definition, one or more CVs or ontologies, and a mapping file describing in a formal way how the semantic resources and the format are interrelated. As such, the validator provides a general solution to the common problem in data exchange: how to validate the correct usage of a data standard beyond simple XML Schema Definition validation. The framework source code and its various applications can be found at http://psidev.info/validator.
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Affiliation(s)
- Luisa Montecchi-Palazzi
- European Molecular Biology Laboratory-European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK.
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