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Varnai P, Davé A, Farla K, Nooijen A, Petrosova L. The Evidence REVEAL Study: Exploring the Use of Real-World Evidence and Complex Clinical Trial Design by the European Pharmaceutical Industry. Clin Pharmacol Ther 2020; 110:1180-1189. [PMID: 33216976 PMCID: PMC8596609 DOI: 10.1002/cpt.2103] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 10/15/2020] [Indexed: 11/22/2022]
Abstract
The rapid evolution of science and technology allows innovative approaches to generate new types of evidence about the effectiveness of medical product development so as to speed up patients’ access to better diagnostics and treatment. Our study explored how two emerging approaches, the use of real‐world evidence (RWE) and complex clinical trial (CCT) design, are currently being used by the pharmaceutical industry to support premarketing authorization of medical product development and reviewed the international landscape for regulatory acceptance of such novel approaches. Combining evidence from a literature review, company survey, and interviews with international regulators and experts, we found that 80% of Europe‐based pharmaceutical companies have used RWE and 50% have used CCTs, in some capacity. Further, we present case examples of how companies are using these approaches and how international regulators are preparing for such developments. To conclude, we provide a set of recommendations for European industry and regulators to consider so that these novel approaches achieve their full potential within the EU regulatory system.
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Ulengin-Talkish I, Bond R, St-Denis N, Gingras AC, Shih A, Conibear E, Balla T, Varnai P, Cyert MS. Uncovering The Unique Functions And Regulation Of The Palmitoylated Calcineurin Isoform, CNβ1. FASEB J 2020. [DOI: 10.1096/fasebj.2020.34.s1.07593] [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: 11/11/2022]
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3
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Matuska R, Zelena D, Könczöl K, Papp RS, Durst M, Guba D, Török B, Varnai P, Tóth ZE. Colocalized neurotransmitters in the hindbrain cooperate in adaptation to chronic hypernatremia. Brain Struct Funct 2020; 225:969-984. [PMID: 32200401 PMCID: PMC7166202 DOI: 10.1007/s00429-020-02049-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 02/13/2020] [Indexed: 11/29/2022]
Abstract
Chronic hypernatremia activates the central osmoregulatory mechanisms and inhibits the function of the hypothalamic-pituitary-adrenal (HPA) axis. Noradrenaline (NE) release into the periventricular anteroventral third ventricle region (AV3V), the supraoptic (SON) and hypothalamic paraventricular nuclei (PVN) from efferents of the caudal ventrolateral (cVLM) and dorsomedial (cDMM) medulla has been shown to be essential for the hypernatremia-evoked responses and for the HPA response to acute restraint. Notably, the medullary NE cell groups highly coexpress prolactin-releasing peptide (PrRP) and nesfatin-1/NUCB2 (nesfatin), therefore, we assumed they contributed to the reactions to chronic hypernatremia. To investigate this, we compared two models: homozygous Brattleboro rats with hereditary diabetes insipidus (DI) and Wistar rats subjected to chronic high salt solution (HS) intake. HS rats had higher plasma osmolality than DI rats. PrRP and nesfatin mRNA levels were higher in both models, in both medullary regions compared to controls. Elevated basal tyrosine hydroxylase (TH) expression and impaired restraint-induced TH, PrRP and nesfatin expression elevations in the cVLM were, however, detected only in HS, but not in DI rats. Simultaneously, only HS rats exhibited classical signs of chronic stress and severely blunted hormonal reactions to acute restraint. Data suggest that HPA axis responsiveness to restraint depends on the type of hypernatremia, and on NE capacity in the cVLM. Additionally, NE and PrRP signalization primarily of medullary origin is increased in the SON, PVN and AV3V in HS rats. This suggests a cooperative action in the adaptation responses and designates the AV3V as a new site for PrRP's action in hypernatremia.
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Affiliation(s)
- Rita Matuska
- Department of Physiology, Semmelweis University, Budapest, Hungary
| | - Dóra Zelena
- Behavioral Neurobiology, Institute of Experimental Medicine, Budapest, Hungary
- Centre for Neuroscience, Szentágothai Research Centre, Institute of Physiology, Medical School, University of Pécs, Pécs, Hungary
| | - Katalin Könczöl
- Department of Anatomy, Histology and Embryology, Semmelweis University, Budapest, Hungary
| | - Rege Sugárka Papp
- Human Brain Tissue Bank and Microdissection Laboratory, Semmelweis University, Budapest, Hungary
| | - Máté Durst
- Department of Anatomy, Histology and Embryology, Semmelweis University, Budapest, Hungary
| | - Dorina Guba
- Department of Anatomy, Histology and Embryology, Semmelweis University, Budapest, Hungary
| | - Bibiana Török
- Behavioral Neurobiology, Institute of Experimental Medicine, Budapest, Hungary
- Janos Szentagothai School of Neurosciences, Semmelweis University, Budapest, Hungary
| | - Peter Varnai
- Department of Physiology, Semmelweis University, Budapest, Hungary
| | - Zsuzsanna E Tóth
- Department of Anatomy, Histology and Embryology, Semmelweis University, Budapest, Hungary.
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4
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Huang KT, Paillard M, Varnai P, Hajnoczky G. The Function of MICU2 in Mitochondrial Calcium Uniport. Biophys J 2018. [DOI: 10.1016/j.bpj.2017.11.683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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5
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Auffray C, Balling R, Barroso I, Bencze L, Benson M, Bergeron J, Bernal-Delgado E, Blomberg N, Bock C, Conesa A, Del Signore S, Delogne C, Devilee P, Di Meglio A, Eijkemans M, Flicek P, Graf N, Grimm V, Guchelaar HJ, Guo YK, Gut IG, Hanbury A, Hanif S, Hilgers RD, Honrado Á, Hose DR, Houwing-Duistermaat J, Hubbard T, Janacek SH, Karanikas H, Kievits T, Kohler M, Kremer A, Lanfear J, Lengauer T, Maes E, Meert T, Müller W, Nickel D, Oledzki P, Pedersen B, Petkovic M, Pliakos K, Rattray M, I Màs JR, Schneider R, Sengstag T, Serra-Picamal X, Spek W, Vaas LAI, van Batenburg O, Vandelaer M, Varnai P, Villoslada P, Vizcaíno JA, Wubbe JPM, Zanetti G. Erratum to: Making sense of big data in health research: towards an EU action plan. Genome Med 2016; 8:118. [PMID: 27821178 PMCID: PMC5100330 DOI: 10.1186/s13073-016-0376-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 10/26/2016] [Indexed: 11/10/2022] Open
Affiliation(s)
- Charles Auffray
- European Institute for Systems Biology and Medicine, 1 avenue Claude Vellefaux, 75010, Paris, France. .,CIRI-UMR5308, CNRS-ENS-INSERM-UCBL, Université de Lyon, 50 avenue Tony Garnier, 69007, Lyon, France.
| | - Rudi Balling
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 Avenue des Hauts Fourneaux, 4362, Esch-sur-Alzette, Luxembourg.
| | - Inês Barroso
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - László Bencze
- Health Services Management Training Centre, Faculty of Health and Public Services, Semmelweis University, Kútvölgyi út 2, 1125, Budapest, Hungary
| | - Mikael Benson
- Centre for Personalised Medicine, Linköping University, 581 85, Linköping, Sweden
| | - Jay Bergeron
- Translational & Bioinformatics, Pfizer Inc., 300 Technology Square, Cambridge, MA, 02139, USA
| | - Enrique Bernal-Delgado
- Institute for Health Sciences, IACS - IIS Aragon, San Juan Bosco 13, 50009, Zaragoza, Spain
| | - Niklas Blomberg
- ELIXIR, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT25.2, 1090, Vienna, Austria.,Department of Laboratory Medicine, Medical University of Vienna, Lazarettgasse 14, AKH BT25.2, 1090, Vienna, Austria.,Max Planck Institute for Informatics, Campus E1 4, 66123, Saarbrücken, Germany
| | - Ana Conesa
- Príncipe Felipe Research Center, C/Eduardo Primo Yúfera 3, 46012, Valencia, Spain.,University of Florida, Institute of Food and Agricultural Sciences (IFAS), 2033 Mowry Road, Gainesville, FL, 32610, USA
| | | | - Christophe Delogne
- Technology, Data & Analytics, KPMG Luxembourg, Société Coopérative, 39 Avenue John F. Kennedy, 1855, Luxembourg, Luxembourg
| | - Peter Devilee
- Department of Human Genetics, Department of Pathology, Leiden University Medical Centre, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - Alberto Di Meglio
- Information Technology Department, European Organization for Nuclear Research (CERN), 385 Route de Meyrin, 1211, Geneva 23, Switzerland
| | - Marinus Eijkemans
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Heidelberglaan 100, 3508 GA, Utrecht, The Netherlands
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Norbert Graf
- Department of Pediatric Oncology/Hematology, Saarland University, Campus Homburg, Building 9, 66421, Homburg, Germany
| | - Vera Grimm
- Project Management Jülich, Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Straße, 52428, Jülich, Germany
| | - Henk-Jan Guchelaar
- Department of Clinical Pharmacy & Toxicology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Yi-Ke Guo
- Data Science Institute, Imperial College London, South Kensington, London, SW7 2AZ, UK
| | - Ivo Glynne Gut
- CNAG-CRG, Center for Genomic Regulation, Barcelona Institute for Science and Technology (BIST), C/Baldiri Reixac 4, 08029, Barcelona, Spain
| | - Allan Hanbury
- Institute of Software Technology and Interactive Systems, TU Wien, Favoritenstrasse 9-11/188, 1040, Vienna, Austria
| | - Shahid Hanif
- The Association of the British Pharmaceutical Industry, 7th Floor, Southside, 105 Victoria Street, London, SW1E 6QT, UK
| | - Ralf-Dieter Hilgers
- Department of Medical Statistics, RWTH-Aachen University, Universitätsklinikum Aachen, Pauwelsstraße 30, 52074, Aachen, Germany
| | - Ángel Honrado
- SYNAPSE Research Management Partners, Diputació 237, Àtic 3ª, 08007, Barcelona, Spain
| | - D Rod Hose
- Department of Infection, Immunity and Cardiovascular Disease and Insigneo Institute for In-Silico Medicine, Medical School, University of Sheffield, Beech Hill Road, Sheffield, S10 2RX, UK
| | | | - Tim Hubbard
- Department of Medical & Molecular Genetics, King's College London, London, SE1 9RT, UK.,Genomics England, London, EC1M 6BQ, UK
| | - Sophie Helen Janacek
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Haralampos Karanikas
- National and Kapodistrian University of Athens, Medical School, Xristou Lada 6, 10561, Athens, Greece
| | - Tim Kievits
- Vitromics Healthcare Holding B.V., Onderwijsboulevard 225, 5223 DE, 's-Hertogenbosch, The Netherlands
| | - Manfred Kohler
- Fraunhofer Institute for Molecular Biology and Applied Ecology ScreeningPort, Schnackenburgallee 114, 22525, Hamburg, Germany
| | - Andreas Kremer
- ITTM S.A., 9 avenue des Hauts Fourneaux, 4362, Esch-sur-Alzette, Luxembourg
| | - Jerry Lanfear
- Research Business Technology, Pfizer Ltd, GP4 Building, Granta Park, Cambridge, CB21 6GP, UK
| | - Thomas Lengauer
- Max Planck Institute for Informatics, Campus E1 4, 66123, Saarbrücken, Germany
| | - Edith Maes
- Health Economics & Outcomes Research, Deloitte Belgium, Berkenlaan 8A, 1831, Diegem, Belgium
| | - Theo Meert
- Janssen Pharmaceutica N.V., R&D G3O, Turnhoutseweg 30, 2340, Beerse, Belgium
| | - Werner Müller
- Faculty of Life Sciences, University of Manchester, AV Hill Building, Oxford Road, Manchester, M13 9PT, UK
| | - Dörthe Nickel
- UMR3664 IC/CNRS, Institut Curie, Section Recherche, Pavillon Pasteur, 26 rue d'Ulm, 75248, Paris cedex 05, France
| | - Peter Oledzki
- Linguamatics Ltd, 324 Cambridge Science Park Milton Rd, Cambridge, CB4 0WG, UK
| | - Bertrand Pedersen
- PwC Luxembourg, 2 rue Gerhard Mercator, 2182, Luxembourg, Luxembourg
| | - Milan Petkovic
- Philips, HighTechCampus 36, 5656AE, Eindhoven, The Netherlands
| | - Konstantinos Pliakos
- Department of Public Health and Primary Care, KU Leuven Kulak, Etienne Sabbelaan 53, 8500, Kortrijk, Belgium
| | - Magnus Rattray
- Faculty of Life Sciences, University of Manchester, AV Hill Building, Oxford Road, Manchester, M13 9PT, UK
| | - Josep Redón I Màs
- INCLIVA Health Research Institute, University of Valencia, CIBERobn ISCIII, Avenida Menéndez Pelayo 4 accesorio, 46010, Valencia, Spain
| | - Reinhard Schneider
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 Avenue des Hauts Fourneaux, 4362, Esch-sur-Alzette, Luxembourg
| | - Thierry Sengstag
- Swiss Institute of Bioinformatics (SIB) and University of Basel, Klingelbergstrasse 50/ 70, 4056, Basel, Switzerland
| | - Xavier Serra-Picamal
- Agency for Health Quality and Assessment of Catalonia (AQuAS), Carrer de Roc Boronat 81-95, 08005, Barcelona, Spain
| | - Wouter Spek
- EuroBioForum Foundation, Chrysantstraat 10, 3135 HG, Vlaardingen, The Netherlands
| | - Lea A I Vaas
- Fraunhofer Institute for Molecular Biology and Applied Ecology ScreeningPort, Schnackenburgallee 114, 22525, Hamburg, Germany
| | - Okker van Batenburg
- EuroBioForum Foundation, Chrysantstraat 10, 3135 HG, Vlaardingen, The Netherlands
| | - Marc Vandelaer
- Integrated BioBank of Luxembourg, 6 rue Nicolas-Ernest Barblé, 1210, Luxembourg, Luxembourg
| | - Peter Varnai
- Technopolis Group, 3 Pavilion Buildings, Brighton, BN1 1EE, UK
| | - Pablo Villoslada
- Hospital Clinic of Barcelona, Institute d'Investigacions Biomediques August Pi Sunyer (IDIBAPS), Rosello 149, 08036, Barcelona, Spain
| | - Juan Antonio Vizcaíno
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - John Peter Mary Wubbe
- European Platform for Patients' Organisations, Science and Industry (Epposi), De Meeûs Square 38-40, 1000, Brussels, Belgium
| | - Gianluigi Zanetti
- CRS4, Ed.1 POLARIS, 09129, Pula, Italy.,BBMRI-ERIC, Neue Stiftingtalstrasse 2/B/6, 8010, Graz, Austria
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6
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Auffray C, Balling R, Barroso I, Bencze L, Benson M, Bergeron J, Bernal-Delgado E, Blomberg N, Bock C, Conesa A, Del Signore S, Delogne C, Devilee P, Di Meglio A, Eijkemans M, Flicek P, Graf N, Grimm V, Guchelaar HJ, Guo YK, Gut IG, Hanbury A, Hanif S, Hilgers RD, Honrado Á, Hose DR, Houwing-Duistermaat J, Hubbard T, Janacek SH, Karanikas H, Kievits T, Kohler M, Kremer A, Lanfear J, Lengauer T, Maes E, Meert T, Müller W, Nickel D, Oledzki P, Pedersen B, Petkovic M, Pliakos K, Rattray M, I Màs JR, Schneider R, Sengstag T, Serra-Picamal X, Spek W, Vaas LAI, van Batenburg O, Vandelaer M, Varnai P, Villoslada P, Vizcaíno JA, Wubbe JPM, Zanetti G. Making sense of big data in health research: Towards an EU action plan. Genome Med 2016; 8:71. [PMID: 27338147 PMCID: PMC4919856 DOI: 10.1186/s13073-016-0323-y] [Citation(s) in RCA: 124] [Impact Index Per Article: 15.5] [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] [Indexed: 01/09/2023] Open
Abstract
Medicine and healthcare are undergoing profound changes. Whole-genome sequencing and high-resolution imaging technologies are key drivers of this rapid and crucial transformation. Technological innovation combined with automation and miniaturization has triggered an explosion in data production that will soon reach exabyte proportions. How are we going to deal with this exponential increase in data production? The potential of "big data" for improving health is enormous but, at the same time, we face a wide range of challenges to overcome urgently. Europe is very proud of its cultural diversity; however, exploitation of the data made available through advances in genomic medicine, imaging, and a wide range of mobile health applications or connected devices is hampered by numerous historical, technical, legal, and political barriers. European health systems and databases are diverse and fragmented. There is a lack of harmonization of data formats, processing, analysis, and data transfer, which leads to incompatibilities and lost opportunities. Legal frameworks for data sharing are evolving. Clinicians, researchers, and citizens need improved methods, tools, and training to generate, analyze, and query data effectively. Addressing these barriers will contribute to creating the European Single Market for health, which will improve health and healthcare for all Europeans.
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Affiliation(s)
- Charles Auffray
- European Institute for Systems Biology and Medicine, 1 avenue Claude Vellefaux, 75010, Paris, France.
- CIRI-UMR5308, CNRS-ENS-INSERM-UCBL, Université de Lyon, 50 avenue Tony Garnier, 69007, Lyon, France.
| | - Rudi Balling
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 Avenue des Hauts Fourneaux, 4362, Esch-sur-Alzette, Luxembourg.
| | - Inês Barroso
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - László Bencze
- Health Services Management Training Centre, Faculty of Health and Public Services, Semmelweis University, Kútvölgyi út 2, 1125, Budapest, Hungary
| | - Mikael Benson
- Centre for Personalised Medicine, Linköping University, 581 85, Linköping, Sweden
| | - Jay Bergeron
- Translational & Bioinformatics, Pfizer Inc., 300 Technology Square, Cambridge, MA, 02139, USA
| | - Enrique Bernal-Delgado
- Institute for Health Sciences, IACS - IIS Aragon, San Juan Bosco 13, 50009, Zaragoza, Spain
| | - Niklas Blomberg
- ELIXIR, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT25.2, 1090, Vienna, Austria
- Department of Laboratory Medicine, Medical University of Vienna, Lazarettgasse 14, AKH BT25.2, 1090, Vienna, Austria
- Max Planck Institute for Informatics, Campus E1 4, 66123, Saarbrücken, Germany
| | - Ana Conesa
- Príncipe Felipe Research Center, C/ Eduardo Primo Yúfera 3, 46012, Valencia, Spain
- University of Florida, Institute of Food and Agricultural Sciences (IFAS), 2033 Mowry Road, Gainesville, FL, 32610, USA
| | | | - Christophe Delogne
- Technology, Data & Analytics, KPMG Luxembourg, Société Coopérative, 39 Avenue John F. Kennedy, 1855, Luxembourg, Luxembourg
| | - Peter Devilee
- Department of Human Genetics, Department of Pathology, Leiden University Medical Centre, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - Alberto Di Meglio
- Information Technology Department, European Organization for Nuclear Research (CERN), 385 Route de Meyrin, 1211, Geneva 23, Switzerland
| | - Marinus Eijkemans
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Heidelberglaan 100, 3508 GA, Utrecht, The Netherlands
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Norbert Graf
- Department of Pediatric Oncology/Hematology, Saarland University, Campus Homburg, Building 9, 66421, Homburg, Germany
| | - Vera Grimm
- Project Management Jülich, Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Straße, 52428, Jülich, Germany
| | - Henk-Jan Guchelaar
- Department of Clinical Pharmacy & Toxicology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Yi-Ke Guo
- Data Science Institute, Imperial College London, South Kensington, London, SW7 2AZ, UK
| | - Ivo Glynne Gut
- CNAG-CRG, Center for Genomic Regulation, Barcelona Institute for Science and Technology (BIST), C/Baldiri Reixac 4, 08029, Barcelona, Spain
| | - Allan Hanbury
- Institute of Software Technology and Interactive Systems, TU Wien, Favoritenstrasse 9-11/188, 1040, Vienna, Austria
| | - Shahid Hanif
- The Association of the British Pharmaceutical Industry, 7th Floor, Southside, 105 Victoria Street, London, SW1E 6QT, UK
| | - Ralf-Dieter Hilgers
- Department of Medical Statistics, RWTH-Aachen University, Universitätsklinikum Aachen, Pauwelsstraße 30, 52074, Aachen, Germany
| | - Ángel Honrado
- SYNAPSE Research Management Partners, Diputació 237, Àtic 3ª, 08007, Barcelona, Spain
| | - D Rod Hose
- Department of Infection, Immunity and Cardiovascular Disease and Insigneo Institute for In-Silico Medicine, Medical School, University of Sheffield, Beech Hill Road, Sheffield, S10 2RX, UK
| | | | - Tim Hubbard
- Department of Medical & Molecular Genetics, King's College London, London, SE1 9RT, UK
- Genomics England, London, EC1M 6BQ, UK
| | - Sophie Helen Janacek
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Haralampos Karanikas
- National and Kapodistrian University of Athens, Medical School, Xristou Lada 6, 10561, Athens, Greece
| | - Tim Kievits
- Vitromics Healthcare Holding B.V., Onderwijsboulevard 225, 5223 DE, 's-Hertogenbosch, The Netherlands
| | - Manfred Kohler
- Fraunhofer Institute for Molecular Biology and Applied Ecology ScreeningPort, Schnackenburgallee 114, 22525, Hamburg, Germany
| | - Andreas Kremer
- ITTM S.A., 9 avenue des Hauts Fourneaux, 4362, Esch-sur-Alzette, Luxembourg
| | - Jerry Lanfear
- Research Business Technology, Pfizer Ltd, GP4 Building, Granta Park, Cambridge, CB21 6GP, UK
| | - Thomas Lengauer
- Max Planck Institute for Informatics, Campus E1 4, 66123, Saarbrücken, Germany
| | - Edith Maes
- Health Economics & Outcomes Research, Deloitte Belgium, Berkenlaan 8A, 1831, Diegem, Belgium
| | - Theo Meert
- Janssen Pharmaceutica N.V., R&D G3O, Turnhoutseweg 30, 2340, Beerse, Belgium
| | - Werner Müller
- Faculty of Life Sciences, University of Manchester, AV Hill Building, Oxford Road, Manchester, M13 9PT, UK
| | - Dörthe Nickel
- UMR3664 IC/CNRS, Institut Curie, Section Recherche, Pavillon Pasteur, 26 rue d'Ulm, 75248, Paris cedex 05, France
| | - Peter Oledzki
- Linguamatics Ltd, 324 Cambridge Science Park Milton Rd, Cambridge, CB4 0WG, UK
| | - Bertrand Pedersen
- PwC Luxembourg, 2 rue Gerhard Mercator, 2182, Luxembourg, Luxembourg
| | - Milan Petkovic
- Philips, HighTechCampus 36, 5656AE, Eindhoven, The Netherlands
| | - Konstantinos Pliakos
- Department of Public Health and Primary Care, KU Leuven Kulak, Etienne Sabbelaan 53, 8500, Kortrijk, Belgium
| | - Magnus Rattray
- Faculty of Life Sciences, University of Manchester, AV Hill Building, Oxford Road, Manchester, M13 9PT, UK
| | - Josep Redón I Màs
- INCLIVA Health Research Institute, University of Valencia, CIBERobn ISCIII, Avenida Menéndez Pelayo 4 accesorio, 46010, Valencia, Spain
| | - Reinhard Schneider
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 Avenue des Hauts Fourneaux, 4362, Esch-sur-Alzette, Luxembourg
| | - Thierry Sengstag
- Swiss Institute of Bioinformatics (SIB) and University of Basel, Klingelbergstrasse 50/70, 4056, Basel, Switzerland
| | - Xavier Serra-Picamal
- Agency for Health Quality and Assessment of Catalonia (AQuAS), Carrer de Roc Boronat 81-95, 08005, Barcelona, Spain
| | - Wouter Spek
- EuroBioForum Foundation, Chrysantstraat 10, 3135 HG, Vlaardingen, The Netherlands
| | - Lea A I Vaas
- Fraunhofer Institute for Molecular Biology and Applied Ecology ScreeningPort, Schnackenburgallee 114, 22525, Hamburg, Germany
| | - Okker van Batenburg
- EuroBioForum Foundation, Chrysantstraat 10, 3135 HG, Vlaardingen, The Netherlands
| | - Marc Vandelaer
- Integrated BioBank of Luxembourg, 6 rue Nicolas-Ernest Barblé, 1210, Luxembourg, Luxembourg
| | - Peter Varnai
- Technopolis Group, 3 Pavilion Buildings, Brighton, BN1 1EE, UK
| | - Pablo Villoslada
- Hospital Clinic of Barcelona, Institute d'Investigacions Biomediques August Pi Sunyer (IDIBAPS), Rosello 149, 08036, Barcelona, Spain
| | - Juan Antonio Vizcaíno
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - John Peter Mary Wubbe
- European Platform for Patients' Organisations, Science and Industry (Epposi), De Meeûs Square 38-40, 1000, Brussels, Belgium
| | - Gianluigi Zanetti
- CRS4, Ed.1 POLARIS, 09129, Pula, Italy
- BBMRI-ERIC, Neue Stiftingtalstrasse 2/B/6, 8010, Graz, Austria
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7
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Seifert E, Gal A, Acoba MG, Claypool SM, Anderson-Pullinger L, Varnai P, Moffat C, Weaver D, Sondheimer N, Hajnoczky G. Novel Mutations in SLC25A3 Encoding the Mitochondrial Phosphate Carrier. Biophys J 2016. [DOI: 10.1016/j.bpj.2015.11.2536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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8
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Toth J, Gulyas G, Toth D, Hunyady L, Balla T, Varnai P. Monitoring the Dynamic Change of Inositol Lipid Pools upon EGFR and M
3
R Activation in Live Cells. FASEB J 2015. [DOI: 10.1096/fasebj.29.1_supplement.715.1] [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: 11/11/2022]
Affiliation(s)
- Jozsef Toth
- HAS‐SE Laboratory of Molecular Physiology HASBudapestHungary
| | - Gergo Gulyas
- Department of PhysiologySemmelweis UniversityBudapestHungary
| | - Daniel Toth
- Department of PhysiologySemmelweis UniversityBudapestHungary
| | - Laszlo Hunyady
- HAS‐SE Laboratory of Molecular Physiology HASBudapestHungary
| | | | - Peter Varnai
- Department of PhysiologySemmelweis UniversityBudapestHungary
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9
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Abstract
BACKGROUND Arabinogalactan proteins (AGPs) are ubiquitous in green plants. AGPs comprise a widely varied group of hydroxyproline (Hyp)-rich cell surface glycoproteins (HRGPs). However, the more narrowly defined classical AGPs massively predominate and cover the plasma membrane. Extensive glycosylation by pendant polysaccharides O-linked to numerous Hyp residues like beads of a necklace creates a unique ionic compartment essential to a wide range of physiological processes including germination, cell extension and fertilization. The vital clue to a precise molecular function remained elusive until the recent isolation of small Hyp-arabinogalactan polysaccharide subunits; their structural elucidation by nuclear magentic resonance imaging, molecular simulations and direct experiment identified a 15-residue consensus subunit as a β-1,3-linked galactose trisaccharide with two short branched sidechains each with a single glucuronic acid residue that binds Ca(2+) when paired with its adjacent sidechain. SCOPE AGPs bind Ca(2+) (Kd ∼ 6 μm) at the plasma membrane (PM) at pH ∼5·5 but release it when auxin-dependent PM H(+)-ATPase generates a low periplasmic pH that dissociates AGP-Ca(2+) carboxylates (pka ∼3); the consequential large increase in free Ca(2+) drives entry into the cytosol via Ca(2+) channels that may be voltage gated. AGPs are thus arguably the primary source of cytosolic oscillatory Ca(2+) waves. This differs markedly from animals, in which cytosolic Ca(2+) originates mostly from internal stores such as the sarcoplasmic reticulum. In contrast, we propose that external dynamic Ca(2+) storage by a periplasmic AGP capacitor co-ordinates plant growth, typically involving exocytosis of AGPs and recycled Ca(2+), hence an AGP-Ca(2+) oscillator. CONCLUSIONS The novel concept of dynamic Ca(2+) recycling by an AGP-Ca(2+) oscillator solves the long-standing problem of a molecular-level function for classical AGPs and thus integrates three fields: AGPs, Ca(2+) signalling and auxin. This accounts for the involvement of AGPs in plant morphogenesis, including tropic and nastic movements.
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Affiliation(s)
- Derek T A Lamport
- School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QG, UK
| | - Peter Varnai
- School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QG, UK
| | - Charlotte E Seal
- Seed Conservation Department, Royal Botanic Gardens, Kew, Wakehurst Place, Ardingly, West Sussex RH17 6TN, UK
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10
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Weaver D, Liu X, Eisner V, Varnai P, Hunyady L, Hajnoczky G. Outer Mitochondrial Membrane Protein Distribution and Function Depend on Mitochondrial Fusion. Biophys J 2013. [DOI: 10.1016/j.bpj.2012.11.3622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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11
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Naghdi S, Varnai P, Roy SS, Hunyady L, Hajnoczky G. Which Domain of VDAC2 is Necessary for Bak Insertion to the Outer Mitochondrial Membrane and tBid - Induced Cytochrome C Release? Biophys J 2013. [DOI: 10.1016/j.bpj.2012.11.3621] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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12
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Weaver D, Eisner V, Varnai P, Hajnoczky G. Shuttling of Membrane-Bound Cytochrome B5 between Mitochondria and ER. Biophys J 2012. [DOI: 10.1016/j.bpj.2011.11.887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022] Open
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13
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Abstract
DNA self-assembly has crucial implications in reading out the genetic information in the cell and in nanotechnological applications. In a recent paper, self-assembled DNA crystals displaying spectacular triangular motifs have been described (Zheng et al., 2009). The authors claimed that their data demonstrate the possibility to rationally design well-ordered macromolecular 3D DNA lattice with precise spatial control using sticky ends. However, the authors did not recognize the fundamental features that control DNA self-assembly in the lateral direction. By analysing available crystallographic data and simulating a DNA triangle, we show that the double helix geometry, sequence-specific cytosine–phosphate interactions and divalent cations are in fact responsible for the precise spatial assembly of DNA.
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Affiliation(s)
- Youri Timsit
- Information Génomique et Structurale, CNRS-UPR2589, Institut de Microbiologie de la Méditerranée, Parc Scientifique de Luminy, Marseille, 13288, France.
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14
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Korzeniowski MK, Manjarrés IM, Varnai P, Balla T. Activation of STIM1‐Orai1 involves an intramolecular switching mechanism. FASEB J 2011. [DOI: 10.1096/fasebj.25.1_supplement.956.1] [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: 11/11/2022]
Affiliation(s)
| | | | - Peter Varnai
- Department of PhysiologySemmelweis UniversityBudapestHungary
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15
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Weaver D, Eisner V, Liu X, Varnai P, Hunyady L, Hajnoczky G. Signaling Complexes Transferred by Outer Mitochondrial Membrane Mixing. Biophys J 2011. [DOI: 10.1016/j.bpj.2010.12.436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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16
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Abstract
Stromal interaction molecule 1 (STIM1) stimulates calcium ion (Ca(2+)) entry through plasma membrane Orai1 channels in response to decreased Ca(2+) concentrations in the endoplasmic reticulum lumen. We identified an acidic motif within the STIM1 coiled-coil region that keeps its Ca(2+) activation domain [Ca(2+) release-activated Ca(2+) (CRAC) activation domain/STIM1-Orai activating region (CAD/SOAR)]-a cytoplasmic region required for its activation of Orai1-inactive. The sequence of the STIM1 acidic motif shows substantial similarity to that of the carboxyl-terminal coiled-coil segment of Orai1, which is the postulated site of interaction with STIM1. Mutations within this acidic region rendered STIM1 constitutively active, whereas mutations within a short basic segment of CAD/SOAR prevented Orai1 activation. We propose that the CAD/SOAR domain is released from an intramolecular clamp during STIM1 activation, allowing the basic segment to activate Orai1 channels. This evolutionarily conserved mechanism of STIM1 activation resembles the regulation of protein kinases by intramolecular silencing through pseudosubstrate binding.
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Affiliation(s)
- Marek K Korzeniowski
- Section on Molecular Signal Transduction, Program for Developmental Neuroscience, National Institute of Child Health and Human Development, Bethesda, MD 20892, USA
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17
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Cserzo M, Turu G, Varnai P, Hunyady L. Relating underrepresented genomic DNA patterns and tiRNAs: the rule behind the observation and beyond. Biol Direct 2010; 5:56. [PMID: 20860791 PMCID: PMC3583238 DOI: 10.1186/1745-6150-5-56] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2010] [Accepted: 09/22/2010] [Indexed: 11/10/2022] Open
Abstract
Background One of the central problems of post-genomic biology is the understanding of regulatory network of genes. Traditionally the problem is approached from the protein-DNA interaction perspective. In recent years various types of noncoding RNAs appeared on the scene as new potent players of the game. The exact role of these molecules in gene expression control is mostly unknown at present, while their importance is generally recognized. Results The Human and Mouse genomes have been screened with a statistical model for sequence patterns underrepresented in these genomes, and a subset of motifs, named spanions, has been identified. The common portion of the motif lists of the two species is 75% indicating evolutionary conservation of this feature. These motifs are arranged in clusters at close proximity of distinct genetic landmarks: 5' ends of genes, exon side of the exon/intron junctions and 5' ends of 3' UTRs. The length of the clusters is typically in the 20 to 25 bases range. The findings are in agreement with the known C/G bias of promoter regions while access much more sequential information than the simple composition based model. In the Human genome the recently reported transcription initiation RNAs (tiRNAs) are typically transcribed from these spanion clusters according to the presented results. The spanion clusters account for 70% of the published tiRNAs. Apparently, the model access the common statistical feature of this new and mostly uncharacterized non-coding RNA class and, in this way, supports the experimental observations with theoretical background. Conclusions The presented results seem to support the emerging model of the RNA-driven eukaryotic gene expression control. Beyond that, the model detects spanion clusters at genetic positions where no tiRNA counterpart was considered and reported. The GO-term analysis of genes with high concentration of spanion clusters in their promoter proximal region indicates involvement in gene regulatory processes. The results of the analysis suggest that the gene regulatory potential of the small non-coding RNAs is grossly underestimated at present. Reviewers This article was reviewed by Frank Eisenhaber, Sandor Pongor and Rotem Sorek (nominated by Doron Lancet).
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Affiliation(s)
- Miklos Cserzo
- Department of Physiology, Semmelweis University, Budapest, Tuzolto Street, 37-47, 1094, Hungary, EU.
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18
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Tan L, Varnai P, Lamport DTA, Yuan C, Xu J, Qiu F, Kieliszewski MJ. Plant O-hydroxyproline arabinogalactans are composed of repeating trigalactosyl subunits with short bifurcated side chains. J Biol Chem 2010; 285:24575-83. [PMID: 20489210 PMCID: PMC2915693 DOI: 10.1074/jbc.m109.100149] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2010] [Revised: 04/14/2010] [Indexed: 11/06/2022] Open
Abstract
Classical arabinogalactan proteins partially defined by type II O-Hyp-linked arabinogalactans (Hyp-AGs) are structural components of the plant extracellular matrix. Recently we described the structure of a small Hyp-AG putatively based on repetitive trigalactosyl subunits and suggested that AGs are less complex and varied than generally supposed. Here we describe three additional AGs with similar subunits. The Hyp-AGs were isolated from two different arabinogalactan protein fusion glycoproteins expressed in tobacco cells; that is, a 22-residue Hyp-AG and a 20-residue Hyp-AG, both isolated from interferon alpha2b-(Ser-Hyp)(20), and a 14-residue Hyp-AG isolated from (Ala-Hyp)(51)-green fluorescent protein. We used NMR spectroscopy to establish the molecular structure of these Hyp-AGs, which share common features: (i) a galactan main chain composed of two 1-->3 beta-linked trigalactosyl blocks linked by a beta-1-->6 bond; (ii) bifurcated side chains with Ara, Rha, GlcUA, and a Gal 6-linked to Gal-1 and Gal-2 of the main-chain trigalactosyl repeats; (iii) a common side chain structure composed of up to six residues, the largest consisting of an alpha-L-Araf-(1-->5)-alpha-L-Araf-(1-->3)-alpha-L-Araf-(1-->3- unit and an alpha-L-Rhap-(1-->4)-beta-D-GlcUAp-(1-->6)-unit, both linked to Gal. The conformational ensemble obtained by using nuclear Overhauser effect data in structure calculations revealed a galactan main chain with a reverse turn involving the beta-1-->6 link between the trigalactosyl blocks, yielding a moderately compact structure stabilized by H-bonds.
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Affiliation(s)
- Li Tan
- From the Department of Chemistry and Biochemistry, Biochemistry Research Facility, Ohio University, Athens, Ohio 45701
| | - Peter Varnai
- the Department of Chemistry and Biochemistry and
| | - Derek T. A. Lamport
- the School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QG, United Kingdom
| | - Chunhua Yuan
- the Campus Chemical Instrument Center, Ohio State University, Columbus, Ohio 43210, and
| | - Jianfeng Xu
- From the Department of Chemistry and Biochemistry, Biochemistry Research Facility, Ohio University, Athens, Ohio 45701
| | - Feng Qiu
- the Department of Chemistry, Temple University, Philadelphia, Pennsylvaina 19122
| | - Marcia J. Kieliszewski
- From the Department of Chemistry and Biochemistry, Biochemistry Research Facility, Ohio University, Athens, Ohio 45701
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19
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Allison JR, Varnai P, Dobson CM, Vendruscolo M. Determination of the free energy landscape of alpha-synuclein using spin label nuclear magnetic resonance measurements. J Am Chem Soc 2010; 131:18314-26. [PMID: 20028147 DOI: 10.1021/ja904716h] [Citation(s) in RCA: 156] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Natively unfolded proteins present a challenge for structure determination because they populate highly heterogeneous ensembles of conformations. A useful source of structural information about these states is provided by paramagnetic relaxation enhancement measurements by nuclear magnetic resonance spectroscopy, from which long-range interatomic distances can be estimated. Here we describe a method for using such distances as restraints in molecular dynamics simulations to obtain a mapping of the free energy landscapes of natively unfolded proteins. We demonstrate the method in the case of alpha-synuclein and validate the results by a comparison with electron transfer measurements. Our findings indicate that our procedure provides an accurate estimate of the relative statistical weights of the different conformations populated by alpha-synuclein in its natively unfolded state.
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Affiliation(s)
- Jane R Allison
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
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20
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Hsu STD, Varnai P, Bugaut A, Reszka AP, Neidle S, Balasubramanian S. A G-rich sequence within the c-kit oncogene promoter forms a parallel G-quadruplex having asymmetric G-tetrad dynamics. J Am Chem Soc 2009; 131:13399-409. [PMID: 19705869 PMCID: PMC3055164 DOI: 10.1021/ja904007p] [Citation(s) in RCA: 174] [Impact Index Per Article: 11.6] [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: 12/22/2022]
Abstract
Guanine-rich DNA sequences with the ability to form quadruplex structures are enriched in the promoter regions of protein-coding genes, particularly those of proto-oncogenes. G-quadruplexes are structurally polymorphic and their folding topologies can depend on the sample conditions. We report here on a structural study using solution state NMR spectroscopy of a second G-quadruplex-forming motif (c-kit2) that has been recently identified in the promoter region of the c-kit oncogene. In the presence of potassium ions, c-kit2 exists as an ensemble of structures that share the same parallel-stranded propeller-type conformations. Subtle differences in structural dynamics have been identified using hydrogen-deuterium exchange experiments by NMR spectroscopy, suggesting the coexistence of at least two structurally similar but dynamically distinct substates, which undergo slow interconversion on the NMR timescale.
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Affiliation(s)
- Shang-Te Danny Hsu
- University Chemical Laboratory, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United Kingdom
| | - Peter Varnai
- Department of Chemistry and Biochemistry, University of Sussex, Falmer Brighton BN1 9QJ, United Kingdom
| | - Anthony Bugaut
- University Chemical Laboratory, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United Kingdom
| | - Anthony P. Reszka
- The Cancer Research UK, Biomolecular Structure Group, The School of Pharmacy, University of London, 29-39 Brunswick Square, London WC1N 1AX, United Kingdom
| | - Stephen Neidle
- The Cancer Research UK, Biomolecular Structure Group, The School of Pharmacy, University of London, 29-39 Brunswick Square, London WC1N 1AX, United Kingdom
| | - Shankar Balasubramanian
- University Chemical Laboratory, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United Kingdom
- School of Clinical Medicine, University of Cambridge, Cambridge CB2 0SP, United Kingdom
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21
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Korzeniowski MK, Popovic MA, Szentpetery Z, Varnai P, Stojilkovic SS, Balla T. Dependence of STIM1/Orai1-mediated calcium entry on plasma membrane phosphoinositides. J Biol Chem 2009; 284:21027-35. [PMID: 19483082 DOI: 10.1074/jbc.m109.012252] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Recent studies identified two main components of store-operated calcium entry (SOCE): the endoplasmic reticulum-localized Ca2+ sensor protein, STIM1, and the plasma membrane (PM)-localized Ca2+ channel, Orai1/CRACM1. In the present study, we investigated the phosphoinositide dependence of Orai1 channel activation in the PM and of STIM1 movements from the tubular to PM-adjacent endoplasmic reticulum regions during Ca2+ store depletion. Phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P2) levels were changed either with agonist stimulation or by chemically induced recruitment of a phosphoinositide 5-phosphatase domain to the PM, whereas PtdIns4P levels were decreased by inhibition or down-regulation of phosphatidylinositol 4-kinases (PI4Ks). Agonist-induced phospholipase C activation and PI4K inhibition, but not isolated PtdIns(4,5)P(2) depletion, substantially reduced endogenous or STIM1/Orai1-mediated SOCE without preventing STIM1 movements toward the PM upon Ca2+ store depletion. Patch clamp analysis of cells overexpressing STIM1 and Orai1 proteins confirmed that phospholipase C activation or PI4K inhibition greatly reduced I(CRAC) currents. These results suggest an inositide requirement of Orai1 activation but not STIM1 movements and indicate that PtdIns4P rather than PtdIns(4,5)P2 is a likely determinant of Orai1 channel activity.
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Affiliation(s)
- Marek K Korzeniowski
- Sections on molecular signal transduction, National Institutes of Health, Bethesda, Maryland 20892, USA
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22
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Csordas G, Das S, Varnai P, Balla T, Hajnoczky G. Mitochondrial localization and function relationship. Biophys J 2009. [DOI: 10.1016/j.bpj.2008.12.2750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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23
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Balla A, Kim YJ, Varnai P, Szentpetery Z, Knight Z, Shokat KM, Balla T. Maintenance of hormone-sensitive phosphoinositide pools in the plasma membrane requires phosphatidylinositol 4-kinase IIIalpha. Mol Biol Cell 2007; 19:711-21. [PMID: 18077555 DOI: 10.1091/mbc.e07-07-0713] [Citation(s) in RCA: 153] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Type III phosphatidylinositol (PtdIns) 4-kinases (PI4Ks) have been previously shown to support plasma membrane phosphoinositide synthesis during phospholipase C activation and Ca(2+) signaling. Here, we use biochemical and imaging tools to monitor phosphoinositide changes in the plasma membrane in combination with pharmacological and genetic approaches to determine which of the type III PI4Ks (alpha or beta) is responsible for supplying phosphoinositides during agonist-induced Ca(2+) signaling. Using inhibitors that discriminate between the alpha- and beta-isoforms of type III PI4Ks, PI4KIIIalpha was found indispensable for the production of phosphatidylinositol 4-phosphate (PtdIns4P), phosphatidylinositol 4,5-bisphosphate [PtdIns(4,5)P(2)], and Ca(2+) signaling in angiotensin II (AngII)-stimulated cells. Down-regulation of either the type II or type III PI4K enzymes by small interfering RNA (siRNA) had small but significant effects on basal PtdIns4P and PtdIns(4,5)P(2) levels in (32)P-labeled cells, but only PI4KIIIalpha down-regulation caused a slight impairment of PtdIns4P and PtdIns(4,5)P(2) resynthesis in AngII-stimulated cells. None of the PI4K siRNA treatments had a measurable effect on AngII-induced Ca(2+) signaling. These results indicate that a small fraction of the cellular PI4K activity is sufficient to maintain plasma membrane phosphoinositide pools, and they demonstrate the value of the pharmacological approach in revealing the pivotal role of PI4KIIIalpha enzyme in maintaining plasma membrane phosphoinositides.
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Affiliation(s)
- Andras Balla
- Section on Molecular Signal Transduction, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
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24
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Gomes DA, Rodrigues MA, Leite MF, Gomez MV, Varnai P, Balla T, Bennett AM, Nathanson MH. c-Met must translocate to the nucleus to initiate calcium signals. J Biol Chem 2007; 283:4344-51. [PMID: 18073207 DOI: 10.1074/jbc.m706550200] [Citation(s) in RCA: 122] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Hepatocyte growth factor (HGF) is important for cell proliferation, differentiation, and related activities. HGF acts through its receptor c-Met, which activates downstream signaling pathways. HGF binds to c-Met at the plasma membrane, where it is generally believed that c-Met signaling is initiated. Here we report that c-Met rapidly translocates to the nucleus upon stimulation with HGF. Ca(2+) signals that are induced by HGF result from phosphatidylinositol 4,5-bisphosphate hydrolysis and inositol 1,4,5-trisphosphate formation within the nucleus rather than within the cytoplasm. Translocation of c-Met to the nucleus depends upon the adaptor protein Gab1 and importin beta1, and formation of Ca(2+) signals in turn depends upon this translocation. HGF may exert its particular effects on cells because it bypasses signaling pathways in the cytoplasm to directly activate signaling pathways in the nucleus.
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Affiliation(s)
- Dawidson A Gomes
- Department of Internal Medicine and Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520-8019, USA
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25
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Abstract
The membrane phospholipid phosphatidylinositol 4,5-bisphosphate [PtdIns(4,5)P2 or PIP2] regulates many ion channels. There are conflicting reports on the effect of PtdIns(4,5)P2 on transient receptor potential vanilloid 1 (TRPV1) channels. We show that in excised patches PtdIns(4,5)P2 and other phosphoinositides activate and the PIP2 scavenger poly-Lys inhibits TRPV1. TRPV1 currents undergo desensitization on exposure to high concentrations of capsaicin in the presence of extracellular Ca2+. We show that in the presence of extracellular Ca2+, capsaicin activates phospholipase C (PLC) in TRPV1-expressing cells, inducing depletion of both PtdIns(4,5)P2 and its precursor PtdIns(4)P (PIP). The PLC inhibitor U73122 and dialysis of PtdIns(4,5)P2 or PtdIns(4)P through the patch pipette inhibited desensitization of TRPV1, indicating that Ca2+-induced activation of PLC contributes to desensitization of TRPV1 by depletion of PtdIns(4,5)P2 and PtdIns(4)P. Selective conversion of PtdIns(4,5)P2 to PtdIns(4)P by a rapamycin-inducible PIP2 5-phosphatase did not inhibit TRPV1 at high capsaicin concentrations, suggesting a significant role for PtdIns(4)P in maintaining channel activity. Currents induced by low concentrations of capsaicin and moderate heat, however, were potentiated by conversion of PtdIns(4,5)P2 to PtdIns(4)P. Increasing PtdIns(4,5)P2 levels by coexpressing phosphatidylinositol-4-phosphate 5-kinase inhibited TRPV1 at low but not at saturating capsaicin concentrations. These data show that at low capsaicin concentrations and other moderate stimuli, PtdIns(4,5)P2 partially inhibits TRPV1 in a cellular context, but this effect is likely to be indirect, because it is not detectable in excised patches. We conclude that phosphoinositides have both inhibitory and activating effects on TRPV1, resulting in complex and distinct regulation at various stimulation levels.
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Affiliation(s)
- Viktor Lukacs
- Department of Pharmacology and Physiology, University of Medicine and Dentistry of New Jersey–New Jersey Medical School, Newark, New Jersey 07103, and
| | - Baskaran Thyagarajan
- Department of Pharmacology and Physiology, University of Medicine and Dentistry of New Jersey–New Jersey Medical School, Newark, New Jersey 07103, and
| | - Peter Varnai
- Endocrinology and Reproduction Research Branch, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892
| | - Andras Balla
- Endocrinology and Reproduction Research Branch, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892
| | - Tamas Balla
- Endocrinology and Reproduction Research Branch, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892
| | - Tibor Rohacs
- Department of Pharmacology and Physiology, University of Medicine and Dentistry of New Jersey–New Jersey Medical School, Newark, New Jersey 07103, and
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26
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Abstract
ARNO is a soluble guanine nucleotide exchange factor (GEF) for the Arf family of GTPases. Although in biochemical assays ARNO prefers Arf1 over Arf6 as a substrate, its localization in cells at the plasma membrane (PM) suggests an interaction with Arf6. In this study, we found that ARNO activated Arf1 in HeLa and COS-7 cells resulting in the recruitment of Arf1 on to dynamic PM ruffles. By contrast, Arf6 was activated less by ARNO than EFA6, a canonical Arf6 GEF. Remarkably, Arf6 in its GTP-bound form recruited ARNO to the PM and the two proteins could be immunoprecipitated. ARNO binding to Arf6 was not mediated through the catalytic Sec7 domain, but via the pleckstrin homology (PH) domain. Active Arf6 also bound the PH domain of Grp1, another ARNO family member. This interaction was direct and required both inositol phospholipids and GTP. We propose a model of sequential Arf activation at the PM whereby Arf6-GTP recruits ARNO family GEFs for further activation of other Arf isoforms.
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Affiliation(s)
- Lee Ann Cohen
- *Laboratory of Cell Biology, National Heart, Lung, and Blood Institute, and
| | - Akira Honda
- *Laboratory of Cell Biology, National Heart, Lung, and Blood Institute, and
| | - Peter Varnai
- Endocrinology and Reproduction Research Branch, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892
| | - Fraser D. Brown
- *Laboratory of Cell Biology, National Heart, Lung, and Blood Institute, and
| | - Tamas Balla
- Endocrinology and Reproduction Research Branch, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892
| | - Julie G. Donaldson
- *Laboratory of Cell Biology, National Heart, Lung, and Blood Institute, and
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27
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Cohen LA, Varnai P, Balla T, Donaldson JG. Complexity of ARF Function in the Cell Periphery. FASEB J 2007. [DOI: 10.1096/fasebj.21.5.a617-d] [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: 11/11/2022]
Affiliation(s)
- Lee Ann Cohen
- LCB, NHLBI, NIHRoom 2505, Bldg 50, 50 South DriveBethesdaMD20892
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Varnai P, Thyagarajan B, Rohacs T, Balla T. Rapidly inducible changes in phosphatidylinositol 4,5-bisphosphate levels influence multiple regulatory functions of the lipid in intact living cells. J Cell Biol 2006; 175:377-82. [PMID: 17088424 PMCID: PMC2064515 DOI: 10.1083/jcb.200607116] [Citation(s) in RCA: 280] [Impact Index Per Article: 15.6] [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: 07/24/2006] [Accepted: 10/05/2006] [Indexed: 11/25/2022] Open
Abstract
Rapamycin (rapa)-induced heterodimerization of the FRB domain of the mammalian target of rapa and FKBP12 was used to translocate a phosphoinositide 5-phosphatase (5-ptase) enzyme to the plasma membrane (PM) to evoke rapid changes in phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P(2)) levels. Rapa-induced PM recruitment of a truncated type IV 5-ptase containing only the 5-ptase domain fused to FKBP12 rapidly decreased PM PtdIns(4,5)P(2) as monitored by the PLCdelta1PH-GFP fusion construct. This decrease was paralleled by rapid termination of the ATP-induced Ca(2+) signal and the prompt inactivation of menthol-activated transient receptor potential melastatin 8 (TRPM8) channels. Depletion of PM PtdIns(4,5)P(2) was associated with a complete blockade of transferrin uptake and inhibition of epidermal growth factor internalization. None of these changes were observed upon rapa-induced translocation of an mRFP-FKBP12 fusion protein that was used as a control. These data demonstrate that rapid inducible depletion of PM PtdIns(4,5)P(2) is a powerful tool to study the multiple regulatory roles of this phospholipid and to study differential sensitivities of various processes to PtdIns(4,5)P(2) depletion.
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Affiliation(s)
- Peter Varnai
- Endocrinology and Reproduction Research Branch, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
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Abstract
Angiotensin II (Ang II) receptors of the AT1 subtype are coupled to heterotrimeric G nucleotide-binding proteins, G(q/11), to activate phospholipase C-beta isoforms with production of inositol 1,4,5-trisphosphate (InsP3) and diacylglycerol. The resultant release of intracellular Ca2+ and increased Ca2+ influx are major determinants of several acute cellular responses initiated by Ang II, including secretion of aldosterone from the adrenal cortex and smooth muscle contraction. However, cellular events related to more prolonged effects of Ang II, such as hypertrophic and hyperplastic responses, are triggered by intracellular signaling cascades that are less dependent on Ca2+ signals. The Ang II-induced activation of Raf-1 kinase, p42 MAP-kinase and c-fos expression in response to Ang II in adrenal glomerulosa cells does not require Ca2+ influx. Moreover, the dose-response relationships for Raf-1 activation, MAP-kinase activation and mitogenesis show significantly higher sensitivity to Ang II than the InsP3, Ca2+-release and aldosterone secretory responses. The sensitivities of both Raf-1 kinase and MAP-kinase stimulation by Ang II to the inhibitors of phosphoinositide kinases, wortmannin and LY 294002, suggest that inositol phospholipids may play a role in these activation events unrelated to their role in Ca2+ signaling. To investigate the changes of various inositides after stimulation at the single cell level, fluorescent probes were developed in which pleckstrin homology domains with distinct binding specificities to inositol phospholipids were fused to the green fluorescent protein and expressed in NIH 3T3 cells. The use of these probes revealed heterogeneity of the inositol lipid pools and their complex relationship to Ca2+ signals. The use of these tools will help to further clarify the complex role of these lipids in initiating Ca2+-dependent and -independent signaling responses.
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Affiliation(s)
- T Balla
- Endocrinology and Reproduction Research Branch, National Institutes of Health, Bethesda, MD 20892, USA.
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Varnai P, Demaurex N, Jaconi M, Schlegel W, Lew DP, Krause KH. Highly co-operative Ca2+ activation of intermediate-conductance K+ channels in granulocytes from a human cell line. J Physiol 1993; 472:373-90. [PMID: 7511688 PMCID: PMC1160492 DOI: 10.1113/jphysiol.1993.sp019952] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
1. To study Ca(2+)-activated K+ currents in dimethyl sulphoxide (DMSO)-differentiated HL-60 cells (HL-60 granulocytes), we have combined the patch clamp technique with microfluorimetric measurements of the cytosolic free Ca2+ concentration ([Ca2+]i). 2. Elevations of [Ca2+]i induced by the receptor agonist N-formyl-L-methionyl-L-phenylalanine (f-MLP), by cellular spreading or by the Ca2+ ionophore ionomycin, activated whole-cell currents. The kinetics of the current elevations closely paralleled the kinetics of the elevations in [Ca2+]i. Cellular spreading induced oscillations in [Ca2+]i and parallel oscillatory changes in the amplitude of the recorded currents. 3. The reversal potential of the Ca(2+)-activated current was a function of the extracellular K+ concentration (56.1 mV per log [K+]), demonstrating that the underlying conductance was selective for K+. 4. The current was blocked by charybdotoxin, but insensitive to apamin. 5. The whole-cell current was inwardly rectifying. No time-dependent activation or inactivation of the current could be observed within the range of voltages tested (-100 to +100 mV). 6. The dependence of the current amplitude on the measured [Ca2+]i revealed a half-maximal activation at approximately 350 nM [Ca2+]i, and a highly co-operative activation by [Ca2+]i with an apparent Hill coefficient of approximately 8. Neither the half-maximal activation by [Ca2+]i nor the apparent Hill coefficient depended on the voltage, and they were identical for Ca2+ elevations caused by the ionophore and the receptor agonist. 7. Analysis of Ca(2+)-activated single-channel events in cell-attached recordings revealed an inwardly rectifying K+ channel with a slope conductance of 35 pS. Fluctuation analysis of the Ca(2+)-activated whole-cell current suggested an underlying single-channel conductance of a similar size (28 pS). 8. In summary, we describe a charybdotoxin-sensitive, intermediate-conductance Ca(2+)-activated K+ channel in HL-60 granulocytes. The characteristics of the Ca2+ activation of this current (i.e. sensitivity to submicromolar [Ca2+]i, high co-operativity and voltage independence) are similar to the Ca2+ activation of the apamin-sensitive small-conductance K+ channel. Our results also suggest that [Ca2+]i elevations are the predominant, if not the only, activators of this channel during physiological stimulation of HL-60 granulocytes.
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Affiliation(s)
- P Varnai
- Infectious Diseases Division, University Hospital, Geneva, Switzerland
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Demaurex N, Schlegel W, Varnai P, Mayr G, Lew DP, Krause KH. Regulation of Ca2+ influx in myeloid cells. Role of plasma membrane potential, inositol phosphates, cytosolic free [Ca2+], and filling state of intracellular Ca2+ stores. J Clin Invest 1992; 90:830-9. [PMID: 1522237 PMCID: PMC329937 DOI: 10.1172/jci115958] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
To study the mediation of Ca2+ influx by second messengers in myeloid cells, we have combined the whole-cell patch clamp technique with microfluorimetric measurements of [Ca2+]i. Me2SO-differentiated HL-60 cells were loaded with the fluorescent Ca2+ indicator Indo-1, allowed to adhere to glass slides, and patch-clamped. Receptor agonists and Ca(2+)-ATPase inhibitors were applied by superfusion and inositol phosphates by microperfusion through the patch pipette. In voltage-clamped cells, [Ca2+]i elevations with a sustained phase could be induced by (a) the chemoattractant receptor agonist FMLP, (b) the Ca(2+)-releasing second messenger myo-inositol(1,4,5)trisphosphate [Ins(1,4,5)P3], as well as its nonmetabolizable analogues, and (c) the Ca(2+)-ATPase inhibitor cyclopiazonic acid, which depletes intracellular Ca2+ stores. In the absence of extracellular Ca2+, responses to all stimuli were short-lasting, monophasic transients; however, subsequent addition of Ca2+ to the extracellular medium led to an immediate [Ca2+]i increase. In all cases, the sustained phase of the [Ca2+]i elevations could be inhibited by millimolar concentrations of extracellular Ni2+, and its amplitude could be decreased by depolarization of the plasma membrane. Thus, the sustained phase of the Ca2+ elevations was due to Ca2+ influx through a pathway sensitive to the electrical driving force and to Ni2+. No Ca2+ influx could be observed after (a) plasma membrane depolarization in resting cells, (b) an imposed [Ca2+]i transient independent of receptor activation, or (c) microperfusion of myo-inositol(1,3,4,5)tetrahisphosphate (Ins(1,3,4,5)P4). Also, Ins(1,3,4,5)P4 did not have additive effects when co-perfused with a submaximal concentration of Ins(1,4,5)P3. Our results suggest that, in myeloid cells, activation of chemoattractant receptors induces an electrogenic, Ni(2+)-sensitive Ca2+ influx via generation of Ins(1,4,5)P3. Ins(1,4,5)P3 might activate Ca2+ influx directly, or by depletion of intracellular Ca2+ stores, but not via [Ca2+]i increase or Ins(1,3,4,5)P4 generation.
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Affiliation(s)
- N Demaurex
- Infectious Diseases Division, University Hospital Geneva, Switzerland
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