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96 results on '"VIB [Belgium]"'

1. Supramolecular assembly of the Escherichia coli LdcI upon acid stress

Author: Grégory Effantin, Jean-Philippe Kleman, Megghane Baulard, Maria Bacia-Verloop, Dominique Bourgeois, Karine Huard, Virgile Adam, Angélique Fraudeau, Jan Felix, Clarissa Liesche, Irina Gutsche, Matthew Jessop, Ambroise Desfosses, Institut de biologie structurale (IBS - UMR 5075), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA), Unit for Structural Biology, VIB-UGent Center for Inflammation Research [Gand, Belgique] (IRC), VIB [Belgium]-VIB [Belgium], The cryoelectron microscopy platform, The M4D Cell Imaging Platform, The nanobody generation platform of the AFMB laboratory, ANR-10-INBS-0005,FRISBI,Infrastructure Française pour la Biologie Structurale Intégrée(2010), ANR-10-LABX-0049,GRAL,Grenoble Alliance for Integrated Structural Cell Biology(2010), European Project: grant no. 647784, European Project: ALTF441-2017, and European Project: 789385,RespViRALI
Subjects: DYNAMICS, DOMAINS, Cryo-electron microscopy, lysine decarboxylase, ORGANIZATION, medicine.disease_cause, Supramolecular assembly, 03 medical and health sciences, LdcI, REVEALS, Extracellular, medicine, ENZYMATIC-ACTIVITIES, SMLM, Escherichia coli, BACTERIAL-CELL BIOLOGY, 030304 developmental biology, 0303 health sciences, Multidisciplinary, Lysine decarboxylase, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], 030306 microbiology, Chemistry, Biology and Life Sciences, LOCALIZATION, Negative stain, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Cytosol, Biophysics, cryo-EM, VISUALIZATION, COMPLEXES, Function (biology)
Abstract: International audience; Pathogenic and commensal bacteria often have to resist the harsh acidity of the host stomach. The inducible lysine decarboxylase LdcI buffers the cytosol and the local extracellular environment to ensure enterobacterial survival at low pH. Here, we investigate the acid stress-response regulation of Escherichia coli LdcI by combining biochemical and biophysical characterization with negative stain and cryoelectron microscopy (cryo-EM) and wide-field and superresolution fluorescence imaging. Due to deleterious effects of fluorescent protein fusions on native LdcI decamers, we opt for three-dimensional localization of nanobody-labeled endogenous wild-type LdcI in acid-stressed E. coli cells and show that it organizes into distinct patches at the cell periphery. Consistent with recent hypotheses that in vivo clustering of metabolic enzymes often reflects their polymerization as a means of stimulus-induced regulation, we show that LdcI assembles into filaments in vitro at physiologically relevant low pH. We solve the structures of these filaments and of the LdcI decamer formed at neutral pH by cryo-EM and reveal the molecular determinants of LdcI polymerization, confirmed by mutational analysis. Finally, we propose a model for LdcI function inside the enterobacterial cell, providing a structural and mechanistic basis for further investigation of the role of its supramolecular organization in the acid stress response.
Published: 2021

2. Hepatitis C virus sequence divergence preserves p7 viroporin structural and dynamic features

Author: Latifah Almanea, Juan H. Bolivar, Nicole Zitzmann, François Dehez, Nicole Holzmann, Chris Chipot, Jolyon K. Claridge, Jason R. Schnell, Benjamin P. Oestringer, Oxford Glycobiology Institute, University of Oxford [Oxford], Department of Biochemistry [Oxford], Immunocore Limited, Structural Biology Brussels (SBB), Vrije Universiteit Brussel (VUB), Structural Biology Research Center, VIB, 1050 Brussels, Belgium, VIB-VUB Center for Structural Biology [Bruxelles], VIB [Belgium]-VIB [Belgium], Laboratoire International Associé (LIA), University of Illinois at Urbana-Champaign [Urbana], University of Illinois System-University of Illinois System-Centre National de la Recherche Scientifique (CNRS), Department of Physics [Illinois at Urbana-Champaign, USA], University of Illinois System-University of Illinois System, Laboratoire de Physique et Chimie Théoriques (LPCT), and Institut de Chimie du CNRS (INC)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Genotype, Hepatitis C virus, lcsh:Medicine, Hepacivirus, Viral Nonstructural Proteins, medicine.disease_cause, Endoplasmic Reticulum, Ion Channels, Protein Structure, Secondary, Article, Viroporin Proteins, Viroporin, 03 medical and health sciences, Viral Proteins, medicine, Humans, Secretion, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Amino Acid Sequence, lcsh:Science, Protein secondary structure, Ion channel, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Genetics, 0303 health sciences, Multidisciplinary, Chemistry, Endoplasmic reticulum, lcsh:R, 030302 biochemistry & molecular biology, Hepatitis C, 3. Good health, [SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, Transmembrane domain, lcsh:Q, Molecular modelling, Solution-state NMR
Abstract: The hepatitis C virus (HCV) viroporin p7 oligomerizes to form ion channels, which are required for the assembly and secretion of infectious viruses. The 63-amino acid p7 monomer has two putative transmembrane domains connected by a cytosolic loop, and has both N- and C- termini exposed to the endoplasmic reticulum (ER) lumen. NMR studies have indicated differences between p7 structures of distantly related HCV genotypes. A critical question is whether these differences arise from the high sequence variation between the different isolates and if so, how the divergent structures can support similar biological functions. Here, we present a side-by-side characterization of p7 derived from genotype 1b (isolate J4) in the detergent 6-cyclohexyl-1-hexylphosphocholine (Cyclofos-6) and p7 derived from genotype 5a (isolate EUH1480) in n-dodecylphosphocholine (DPC). The 5a isolate p7 in conditions previously associated with a disputed oligomeric form exhibits secondary structure, dynamics, and solvent accessibility broadly like those of the monomeric 1b isolate p7. The largest differences occur at the start of the second transmembrane domain, which is destabilized in the 5a isolate. The results show a broad consensus among the p7 variants that have been studied under a range of different conditions and indicate that distantly related HCVs preserve key features of structure and dynamics.
Published: 2019

3. Protein crystallization promotes type 2 immunity and is reversible by antibody treatment

Author: K. Verschueren, Emma Persson, Helena Catharine Aegerter, Ann Dansercoer, H. De Haard, Kim Deswarte, Michael A. Saunders, Kenneth Verstraete, Delphine Gras, Ines Heyndrickx, Claus Bachert, Pascal Chanez, Jean-Michel Percier, Hamida Hammad, Christophe Blanchetot, Elien Gevaert, Bart N. Lambrecht, Amanda Gonçalves, H. Van Gorp, Savvas N. Savvides, Laboratory for Protein Biochemistry and Biomolecular Engineering, Department of Biochemistry, Physiology and Microbiology, Universiteit Gent = Ghent University [Belgium] (UGENT), Centre de Recherche en Cancérologie Nantes-Angers (CRCNA), Centre Hospitalier Universitaire d'Angers (CHU Angers), PRES Université Nantes Angers Le Mans (UNAM)-PRES Université Nantes Angers Le Mans (UNAM)-Hôtel-Dieu de Nantes-Institut National de la Santé et de la Recherche Médicale (INSERM)-Hôpital Laennec-Centre National de la Recherche Scientifique (CNRS)-Faculté de Médecine d'Angers-Centre hospitalier universitaire de Nantes (CHU Nantes), VIB Inflammation Research Center [Ghent, Belgium], Unit for Structural Biology, VIB-UGent Center for Inflammation Research [Gand, Belgique] (IRC), VIB [Belgium]-VIB [Belgium], Centre recherche en CardioVasculaire et Nutrition = Center for CardioVascular and Nutrition research (C2VN), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Ghent University Hospital, Institut Municipal d'Investigacio Medica [Barcelona] (IMIM), GOG2318N FWO/OPR2017004401, Swedish Research Council 2014-6852, Ghent University BOF/DOC2017005501, FWO Flanders1515516N FWO/PDO/108, Interuniversity Attraction Poles grant P7/30, Universiteit Gent = Ghent University (UGENT), and Pulmonary Medicine
Subjects: 0301 basic medicine, Multidisciplinary, biology, Chemistry, [SDV]Life Sciences [q-bio], Eosinophil, Immunoglobulin E, Acquired immune system, Molecular biology, Epitope, 3. Good health, 03 medical and health sciences, 030104 developmental biology, 0302 clinical medicine, Immune system, medicine.anatomical_structure, 030228 respiratory system, Humanized mouse, biology.protein, medicine, Major basic protein, Antibody
Abstract: A crystal-clear ingredient for allergy? Charcot-Leyden crystals (CLCs) are formed from the eosinophil granule protein galectin-10 (Gal10) and found in severe eosinophil-associated diseases like asthma and chronic rhinosinusitis. Whether CLCs actively contribute to disease pathogenesis is unknown. Persson et al. found that lab-grown Gal10 crystals are biosimilar to CLCs (see the Perspective by Allen and Sutherland). When given to mice, the crystals acted as a type 2 adjuvant, mimicking many of the features of human asthma. In contrast, a Gal10 mutein unable to crystallize had no effect. Antibodies against epitopes crucial for Gal10 autocrystallization could dissolve both in vitro–generated Gal10 crystals and patient-derived CLCs. Furthermore, these anti-Gal10 antibodies reversed the effects of Gal10 crystals in a humanized mouse model of asthma, suggesting a potential therapeutic approach for crystallopathies more broadly. Science , this issue p. eaaw4295 ; see also p. 738
Published: 2019

4. Neutrophils enhance early Trypanosoma brucei infection onset

Author: Marie Malissen, Guy Caljon, Carl De Trez, Fabienne Tacchini-Cottier, Stefan Magez, Jo A. Van Ginderachter, Dorien Mabille, Benoit Stijlemans, Patrick De Baetselier, Massimiliano Mazzone, Jan Van Den Abbeele, Cellular and Molecular Immunology (VIB), Vrije Universiteit Brussel (VUB), Laboratory of Myeloid Cell Immunology, Flanders Interuniversity Institute for Biotechnology (VIB), Vlaams Interuniversitair Instituut voor Biotechnologie, Department of Biochemistry, Université de Lausanne (UNIL)-WHO Collaborating Center for Research and Training in Immunology, Centre d'Immunologie de Marseille - Luminy (CIML), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU), Structural Biology Research Center, VIB, 1050 Brussels, Belgium, VIB-VUB Center for Structural Biology [Bruxelles], VIB [Belgium]-VIB [Belgium], Vrije Universiteit Brussel - Myeloid Cell immunology Laboratory, Laboratory of cellular & Molecular Immunology [Vrije Universiteit Brussel], Cellular and Molecular Immunology, Department of Bio-engineering Sciences, Vriendenkring VUB, Université de Lausanne = University of Lausanne (UNIL)-WHO Collaborating Center for Research and Training in Immunology, and Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Chemokine CXCL5, Chemokine, GLOSSINA-MORSITANS, HOST, Neutrophils, Chemokine CXCL1, Interleukin-1beta, CATTLE, lcsh:Medicine, Parasitemia, Mice, Medicine and Health Sciences, SAND FLIES, lcsh:Science, AFRICAN TRYPANOSOMES, CONGOLENSE, Multidisciplinary, biology, FLIES, Dermis, Interleukin-10, 3. Good health, Multidisciplinary Sciences, CXCL1, Science & Technology - Other Topics, [SDV.IMM]Life Sciences [q-bio]/Immunology, Engineering sciences. Technology, Tsetse Flies, Trypanosoma brucei brucei, TSETSE-FLY, Trypanosoma brucei, Neutropenia, DENDRITIC CELLS, Article, Microbiology, Proinflammatory cytokine, 03 medical and health sciences, Animals, Gene Expression Regulation, Insect Bites and Stings, Insect Vectors, Interleukin-6, Luminescent Measurements, Trypanosomiasis, African, Trypanosomiasis, parasitic diseases, medicine, LOCAL SKIN REACTIONS, Biology, Science & Technology, lcsh:R, African, Biology and Life Sciences, medicine.disease, Leishmania, biology.organism_classification, 030104 developmental biology, SHEEP, general, biology.protein, lcsh:Q, LEISHMANIASIS
Abstract: In this study, Trypanosoma brucei was naturally transmitted to mice through the bites of infected Glossina morsitans tsetse flies. Neutrophils were recruited rapidly to the bite site, whereas monocytes were attracted more gradually. Expression of inflammatory cytokines (il1b, il6), il10 and neutrophil chemokines (cxcl1, cxcl5) was transiently up-regulated at the site of parasite inoculation. Then, a second influx of neutrophils occurred that coincided with the previously described parasite retention and expansion in the ear dermis. Congenital and experimental neutropenia models, combined with bioluminescent imaging, indicate that neutrophils do not significantly contribute to dermal parasite control and elicit higher systemic parasitemia levels during the infection onset. Engulfment of parasites by neutrophils in the skin was rarely observed and was restricted to parasites with reduced motility/viability, whereas live parasites escaped phagocytosis. To our knowledge, this study represents the first description of a trypanosome infection promoting role of early innate immunological reactions following an infective tsetse fly bite. Our data indicate that the trypanosome is not hindered in its early development and benefits from the host innate responses with the neutrophils being important regulators of the early infection, as already demonstrated for the sand fly transmitted Leishmania parasite.
Published: 2018

5. Structural basis of GM-CSF and IL-2 sequestration by the viral decoy receptor GIF

Author: Felix, Jan, Kandiah, Eaazhisai, De Munck, Steven, Bloch, Yehudi, Van Zundert, Gydo C P, Pauwels, Kris, Dansercoer, Ann, Novanska, Katka, Read, Randy J., Bonvin, Alexandre M J J, Vergauwen, Bjorn, Verstraete, Kenneth, Gutsche, Irina, Savvides, Savvas N., Sub NMR Spectroscopy, NMR Spectroscopy, Sub NMR Spectroscopy, NMR Spectroscopy, Laboratory for Protein Biochemistry and Biomolecular Engineering, Department of Biochemistry, Physiology and Microbiology, Universiteit Gent = Ghent University (UGENT), Institut de biologie structurale (IBS - UMR 5075 ), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Bijvoet Center for Biomolecular Research [Utrecht], Utrecht University [Utrecht], Structural Biology Research Center, VIB, 1050 Brussels, Belgium, VIB-VUB Center for Structural Biology [Bruxelles], VIB [Belgium]-VIB [Belgium], Masaryk University [Brno] (MUNI), Department of Haematology, University of Cambridge [UK] (CAM), beamlines P14 and P12 of the EMBL at PETRA3-DESY (Hamburg, Germany), Proxima 2 and SWING at SOLEIL French National Synchrotron (Gif-sur-Yvette, France), research fellowships from Research Foundation Flanders (FWO, Belgium), pre-doctoral research fellows of the Flemish Agency for Innovation and Entrepreneurship (VLAIO), FWO research grants G0597.10, G0643.07N, and G0B7912N, infrastructure grant AUGE-11-029 from the Hercules Foundation (Belgium), and the Flanders Institute for Biotechnology (VIB), Grenoble Instruct center (ISBG, UMS 3518 CNRS-CEA-UJF-EMBL), ANR-10-INBS-0005,FRISBI,Infrastructure Française pour la Biologie Structurale Intégrée(2010), ANR-10-LABX-0049,GRAL,Grenoble Alliance for Integrated Structural Cell Biology(2010), Universiteit Gent = Ghent University [Belgium] (UGENT), Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Read, Randy J [0000-0001-8273-0047], Apollo - University of Cambridge Repository, Department of Bio-engineering Sciences, and Faculty of Sciences and Bioengineering Sciences
Subjects: Models, Molecular, 0301 basic medicine, Chemistry(all), viruses, medicine.medical_treatment, General Physics and Astronomy, CHEMOKINE-BINDING-PROTEIN, Poxviridae Infections, Plasma protein binding, Crystallography, X-Ray, medicine.disease_cause, Biochemistry, Medicine and Health Sciences, CRYSTAL-STRUCTURE, skin and connective tissue diseases, Receptor, INTERLEUKIN-2, Parapoxvirus, Multidisciplinary, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], INHIBITOR, Orf virus, COLONY-STIMULATING FACTOR, VACCINIA VIRUS, 3. Good health, Cell biology, Molecular mimicry, Cytokine, Host-Pathogen Interactions, Mammalia, Cytokines, ddc:500, Decoy, Protein Binding, Viral protein, Science, chemical and pharmacologic phenomena, Biology, Physics and Astronomy(all), Article, General Biochemistry, Genetics and Molecular Biology, Viral Proteins, 03 medical and health sciences, Immune system, medicine, Humans, X-ray crystallography, COMPLEX, COWPOX VIRUS, Biochemistry, Genetics and Molecular Biology(all), Poxviridae, HEK 293 cells, Granulocyte-Macrophage Colony-Stimulating Factor, General Chemistry, biochemical phenomena, metabolism, and nutrition, Virology, biological factors, HEK293 Cells, 030104 developmental biology, kinetics, Multiprotein Complexes, Interleukin-2, SYSTEM, Genetics and Molecular Biology(all)
Abstract: Subversion of the host immune system by viruses is often mediated by molecular decoys that sequester host proteins pivotal to mounting effective immune responses. The widespread mammalian pathogen parapox Orf virus deploys GIF, a member of the poxvirus immune evasion superfamily, to antagonize GM-CSF (granulocyte macrophage colony-stimulating factor) and IL-2 (interleukin-2), two pleiotropic cytokines of the mammalian immune system. However, structural and mechanistic insights into the unprecedented functional duality of GIF have remained elusive. Here we reveal that GIF employs a dimeric binding platform that sequesters two copies of its target cytokines with high affinity and slow dissociation kinetics to yield distinct complexes featuring mutually exclusive interaction footprints. We illustrate how GIF serves as a competitive decoy receptor by leveraging binding hotspots underlying the cognate receptor interactions of GM-CSF and IL-2, without sharing any structural similarity with the cytokine receptors. Our findings contribute to the tracing of novel molecular mimicry mechanisms employed by pathogenic viruses., Viruses often subvert the host immune system using molecular decoys to prevent an effective immune response. Here, the authors examine the structural details of the viral decoy receptor GIF and its antagnosim of GM-CSF and IL-2.
Published: 2016

6. DisProt 7.0 : a major update of the database of disordered proteins

Author: Edoardo Salladini, Eva Schad, Antoine Schramm, Fiorella Tonello, Francesco Tabaro, A. Keith Dunker, Mauricio Macossay-Castillo, Sandra Macedo-Ribeiro, Per Warholm, Norman E. Davey, Maria Cristina Aspromonte, Jordi Pujols, Emanuela Leonardi, Beáta Szabó, Marco Necci, Konstantinos D. Tsirigos, Ivan Mičetić, Salvador Ventura, Wim F. Vranken, Giovanni Minervini, Radoslav Davidovic, Federica Quaglia, Attila Meszaros, Vladimir N. Uversky, Agnes Tantos, Lajos Kalmar, Nikoletta Murvai, Nevena Veljkovic, Peter Tompa, Tamas Lazar, Sonia Longhi, Arne Elofsson, Alessandra Gasparini, Damiano Piovesan, Silvio C. E. Tosatto, Daniel B. Roche, Zsuzsanna Dosztányi, Andrey V. Kajava, András Hatos, Christopher J. Oldfield, Università degli Studi di Padova = University of Padua (Unipd), Institute of Medical Technology and Tampere University Hospital, University of Tampere [Finland], Indiana University School of Medicine, Indiana University System, Conway Institute of Biomolecular & Biomedical Research, University College Dublin [Dublin] (UCD), Vinča Institute of Nuclear Sciences, University of Belgrade [Belgrade], Biophysics Research Group [Budapest] (ELTE-MTA 'Lendület'), Hungarian Academy of Sciences (MTA), Stockholm University, Centre de recherche en Biologie cellulaire de Montpellier (CRBM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Computationnelle (IBC), Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), ITMO University [Russia], University of Cambridge [UK] (CAM), Structural Biology Brussels (SBB), Vrije Universiteit Brussel (VUB), Structural Biology Research Center, VIB, 1050 Brussels, Belgium, VIB-VUB Center for Structural Biology [Bruxelles], VIB [Belgium]-VIB [Belgium], Instituto de Biologia Molecular e Celular (IBMC), Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona (UAB), Architecture et fonction des macromolécules biologiques (AFMB), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Interuniversity Institute of Bioinformatics in Brussels (IB2), Université libre de Bruxelles (ULB)-Vrije Universiteit Brussel (VUB), Institute of Cytology of the Russian Academy of Science (St. Petersburg), Morsani College of Medicine, Department of Pediatrics, University of South Florida [Tampa] (USF), COST Action BM1405 NGP-net, ELIXIR-IIB (elixir-italy.org), ‘Lend ̈ulet’ Grant from the Hungarian Academyof Sciences [LP2014-16 to Z.D.], Hungarian Scientific Re-search Fund [OTKA K 108798 to Z.D.], AIRC ResearchFellowship (to D.P.), Spanish Ministerio de Educaci ́on Cul-tura i Deporte PhD Fellowship (to J.P.), Mexican Na-tional Council for Science and Technology (CONACYT)PhD Fellowship [215503 to M.M.-C.], Grant PortoNeu-roDRIve@i3S funded by Norte Portugal Regional Opera-tional Programme (NORTE 2020), under the PORTUGAL2020 Partnership Agreement, through the European Re-gional Development Fund (ERDF) (to S.M.-R.), DirectionG ́en ́erale des Arm ́ees and Aix-Marseille University PhDFellowship (to E.Sa.), OTKA Grant [PD-OTKA 108772 toE.Sc.], French Ministry of National Education, Researchand Technology PhD Fellowship (to A.S.), Ministry of Ed-ucation, Science and Technological Development of the Re-public of Serbia [173001, 173049 to N.V., R.D.], ICREA-Academia Award (to S.V.), Odysseus Grant from ResearchFoundation Flanders (FWO) [G.0029.12 to P.T.], AIRC IGGrant [17753 to S.T., in part], Italian Ministry of Health[GR-2011-02347754 to E.L., S.T., GR-2011-02346845 toS.T.], Swedish Research Council Grant [VR-NT 2012-5046to A.E.]. Computational resources were provided by theSwedish National Infrastructure for Computing (SNIC)at NSC. Funding for open access charge: COST ActionBM1405 NGP-net, Universita degli Studi di Padova, University of Padova and INFN Padova, Centre de recherche en Biologie Cellulaire (CRBM), Université Montpellier 1 (UM1)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Department of Veterinary Medicine, University of Cambridge, Cambridge, UK, Vrije Universiteit [Brussels] (VUB), Universitat Autònoma de Barcelona [Barcelona] (UAB), CNR Institute of Neuroscience, University of Padova, Interuniversity Institute of Bioinformatics in Brussels [ULB], Université Libre de Bruxelles [Bruxelles] (ULB), University of South Florida (USF), Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Université Montpellier 1 (UM1), Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS), and Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA)
Subjects: 0301 basic medicine, Protein Conformation, Classification scheme, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Computational biology, Biology, Intrinsically disordered proteins, computer.software_genre, Crystallography, X-Ray, 03 medical and health sciences, Text mining, Protein structure, Research community, Fluorescence Resonance Energy Transfer, Genetics, Database Issue, Animals, Humans, Databases, Protein, Biological sciences, Nuclear Magnetic Resonance, Biomolecular, ComputingMilieux_MISCELLANEOUS, 030102 biochemistry & molecular biology, Database, business.industry, Généralités, Intrinsically Disordered Proteins, 030104 developmental biology, Förster resonance energy transfer, Forms and Records Control, Erratum, business, computer, Forecasting
Abstract: The Database of Protein Disorder (DisProt, URL: www.disprot.org) has been significantly updated and upgraded since its last major renewal in 2007. The current release holds information on more than 800 entries of IDPs/IDRs, i.e. intrinsically disordered proteins or regions that exist and function without a well-defined three-dimensional structure. We have re-curated previous entries to purge DisProt from conflicting cases, and also upgraded the functional classification scheme to reflect continuous advance in the field in the past 10 years or so. We define IDPs as proteins that are disordered along their entire sequence, i.e. entirely lack structural elements, and IDRs as regions that are at least five consecutive residues without well-defined structure. We base our assessment of disorder strictly on experimental evidence, such as X-ray crystallography and nuclear magnetic resonance (primary techniques) and a broad range of other experimental approaches (secondary techniques). Confident and ambiguous annotations are highlighted separately. DisProt 7.0 presents classified knowledge regarding the experimental characterization and functional annotations of IDPs/IDRs, and is intended to provide an invaluable resource for the research community for a better understanding structural disorder and for developing better computational tools for studying disordered proteins., SCOPUS: ar.j, info:eu-repo/semantics/published
Published: 2016

7. From TNF-induced signaling to NADPH oxidase enzyme activity: Methods to investigate protein complexes involved in regulated cell death modalities

Author: Maria Ladik, Hana Valenta, Marie Erard, Peter Vandenabeele, Franck B. Riquet, Universiteit Gent = Ghent University (UGENT), VIB-UGent Center for Inflammation Research [Gand, Belgique] (IRC), VIB [Belgium], Institut de Chimie Physique (ICP), Institut de Chimie du CNRS (INC)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Physique des Lasers, Atomes et Molécules - UMR 8523 (PhLAM), and Université de Lille-Centre National de la Recherche Scientifique (CNRS)
Subjects: [SDV]Life Sciences [q-bio]
Abstract: International audience; The formation of molecular complexes is a key feature of intracellular signaling pathways which governs to the initiation and execution of dedicated cellular processes. Tumor Necrosis Factor (TNF) and Reactive Oxygen Species (ROS) function as signaling molecules and are both involved in balancing cell fate decision between cell survival or cell demise. As master regulators of cell signaling, they are also instrumental in controlling various cellular processes towards tissue homeostasis, innate immunity and inflammation. Interestingly, TNF and ROS are interlinked and involved in regulating each other’s production via the engagement of molecular signaling complexes. This relationship calls for detailed reviewing of both TNF-induced and ROS-producing molecular complexes in the context of regulated cell death (RCD) modalities. Here, we outline biotechnological approaches that were used to investigate the TNF- and, concerning ROS, the NADPH oxidase-related molecular complexes with an emphasis on different regulated cell death modalities. This systematic review highlights how the cell death field has benefited from both biochemical and live-cell fluorescence imaging approaches. This knowledge and established workflows are highly generalizable, can be of a broader use for any protein-complex studies, and well suited for addressing new challenges in signaling dynamics. These will help understand molecular signaling complexes as ensembles organized into signaling platforms, most likely the key sites of signaling dynamics integration toward cell fate regulation.
Published: 2023
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8. Generation of a Nanobody Targeting the Paraflagellar Rod Protein of Trypanosomes

Author: Serge Muldermans, Bart Devreese, Stefan Magez, Philippe Bastin, Emmanuel Obishakin, Isabel Vandenberghe, Benoit Stijlemans, Julien Santi-Rocca, Cellular and Molecular Immunology (VIB), Vrije Universiteit Brussel (VUB), Structural Biology Research Center, VIB, 1050 Brussels, Belgium, VIB-VUB Center for Structural Biology [Bruxelles], VIB [Belgium]-VIB [Belgium], Laboratory of Myeloid Cell Immunology, Flanders Interuniversity Institute for Biotechnology (VIB), Biologie Cellulaire des Trypanosomes, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Department of Biochemistry and Microbiology, Universiteit Gent = Ghent University [Belgium] (UGENT), This work was supported by the European Union/FP7 Nanotryp (FP7-HEALTH 2007-2.3.4-1) and the Fund for Scientific Research Flanders (FWO). Work at the Institut Pasteur was funded by a French Government Investissement d'Avenir program, Laboratoire d'Excellence 'Integrative Biology of Emerging Infectious Diseases' (ANR-10-LABX-62- IBEID), the Institut Carnot Maladies Infectieuses and the Fondation pour la Recherche Médicale. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript., ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), European Project: 223048,EC:FP7:HEALTH,FP7-HEALTH-2007-B,NANOTRYP(2009), Cellular and Molecular Immunology, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), and Universiteit Gent = Ghent University (UGENT)
Subjects: Phage display, Protozoan Proteins, Antigen Processing and Recognition, Epitope, Zoonoses, Trypanosomes, Medicine and Health Sciences, Bio-panning techniques, RNA, Small Interfering, VIVAX, CONGOLENSE, Multidisciplinary, biology, DOMAIN ANTIBODY FRAGMENTS, DETECTION ENZYME IMMUNOASSAYS, Vaccination and Immunization, Trypanocidal Agents, Recombinant Proteins, nanobodies, 3. Good health, Infectious Diseases, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Veterinary Diseases, Flagella, INFECTIONS, Trypanosome-specific antigen, Medicine, RNA Interference, phage display, Immunoglobulin Heavy Chains, Camelids, New World, Research Article, Biotechnology, Trypanosoma, Infectious Disease Control, medicine.drug_class, Science, Immunology, Molecular Sequence Data, Biophysics, Bioengineering, Antigens, Protozoan, TSETSE-FLY, Monoclonal antibody, Antigen, Trypanosomiasis, medicine, Animals, FLAGELLUM, Amino Acid Sequence, Immunodiagnostics, Paraflagellar rod protein (PFR1), Biology and Life Sciences, BRUCEI, Trypanosoma evansi, Veterinary Parasitology, biology.organism_classification, Virology, Vector-Borne Diseases, Bionanotechnology, RNA, Parasitology, Veterinary Science, Sequence Alignment, Single-Chain Antibodies, AFRICAN TRYPANOSOMIASIS
Abstract: International audience; Trypanosomes are protozoan parasites that cause diseases in humans and livestock for which no vaccines are available. Disease eradication requires sensitive diagnostic tools and efficient treatment strategies. Immunodiagnostics based on antigen detection are preferable to antibody detection because the latter cannot differentiate between active infection and cure. Classical monoclonal antibodies are inaccessible to cryptic epitopes (based on their size-150 kDa), costly to produce and require cold chain maintenance, a condition that is difficult to achieve in trypanosomiasis endemic regions, which are mostly rural. Nanobodies are recombinant, heat-stable, small-sized (15 kDa), antigen-specific, single-domain, variable fragments derived from heavy chain-only antibodies in camelids. Because of numerous advantages over classical antibodies, we investigated the use of nanobodies for the targeting of trypanosome-specific antigens and diagnostic potential. An alpaca was immunized using lysates of Trypanosoma evansi. Using phage display and bio-panning techniques, a cross-reactive nanobody (Nb392) targeting all trypanosome species and isolates tested was selected. Imunoblotting, immunofluorescence microscopy, immunoprecipitation and mass spectrometry assays were combined to identify the target recognized. Nb392 targets paraflagellar rod protein (PFR1) of T. evansi, T. brucei, T. congolense and T. vivax. Two different RNAi mutants with defective PFR assembly (PFR2(RNAi) and KIF9B(RNAi)) were used to confirm its specificity. In conclusion, using a complex protein mixture for alpaca immunization, we generated a highly specific nanobody (Nb392) that targets a conserved trypanosome protein, i.e., PFR1 in the flagella of trypanosomes. Nb392 is an excellent marker for the PFR and can be useful in the diagnosis of trypanosomiasis. In addition, as demonstrated, Nb392 can be a useful research or PFR protein isolation tool.
Published: 2014

9. BRASSINOSTEROID INSENSITIVE1 internalization can occur independent of ligand binding

Author: Lucas Alves Neubus Claus, Derui Liu, Ulrich Hohmann, Nemanja Vukašinović, Roman Pleskot, Jing Liu, Alexei Schiffner, Yvon Jaillais, Guang Wu, Sebastian Wolf, Daniël Van Damme, Michael Hothorn, Eugenia Russinova, Universiteit Gent = Ghent University (UGENT), Shandong Agricultural University (SDAU), VIB [Belgium], Université de Genève = University of Geneva (UNIGE), Austrian Academy of Sciences (OeAW), Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Czech Academy of Sciences [Prague] (CAS), Shaanxi Normal University (SNNU), Universitätsklinikum Tübingen - University Hospital of Tübingen, Eberhard Karls Universität Tübingen = Eberhard Karls University of Tuebingen, Reproduction et développement des plantes (RDP), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Center for Plant Systems Biology (PSB Center), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), and École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL)
Subjects: PERCEPTION, ligand-binding, RECEPTOR, Physiology, PROTEINS, ENDOCYTOSIS, Biology and Life Sciences, Plant Science, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, DEGRADATION, EXTRACELLULAR DOMAIN, BRI1, brassinosteroids, non-canonical, [SDE]Environmental Sciences, Genetics, KINASE, endocytosis, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, TRAFFICKING
Abstract: The brassinosteroid (BR) hormone and its plasma membrane (PM) receptor BR INSENSITIVE1 (BRI1) are one of the best-studied receptor–ligand pairs for understanding the interplay between receptor endocytosis and signaling in plants. BR signaling is mainly determined by the PM pool of BRI1, whereas BRI1 endocytosis ensures signal attenuation. As BRs are ubiquitously distributed in the plant, the tools available to study the BRI1 function without interference from endogenous BRs are limited. Here, we designed a BR binding-deficient Arabidopsis (Arabidopsis thaliana) mutant based on protein sequence-structure analysis and homology modeling of members of the BRI1 family. This tool allowed us to re-examine the BRI1 endocytosis and signal attenuation model. We showed that despite impaired phosphorylation and ubiquitination, BR binding-deficient BRI1 internalizes similarly to the wild type form. Our data indicate that BRI1 internalization relies on different endocytic machineries. In addition, the BR binding-deficient mutant provides opportunities to study non-canonical ligand-independent BRI1 functions.
Published: 2023

10. Wheat germ in vitro translation to produce one of the most toxic sodium channel specific toxins

Author: Wael Gad, Khadija Wahni, Rahma Ben-Abderrazek, Joris Messens, Serge Muyldermans, Didier Vertommen, Balkiss Bouhaouala-Zahar, Department of Bio-engineering Sciences, Structural Biology Brussels, Cellular and Molecular Immunology, Ultrastructure, Brussels Center for Redox Biology, 1050 Brussels, Belgium, Brussels Center for Redox Biology, Structural Biology Research Center, VIB, 1050 Brussels, Belgium, VIB-VUB Center for Structural Biology [Bruxelles], VIB [Belgium]-VIB [Belgium], Structural Biology Brussels (SBB), Vrije Universiteit Brussel (VUB), Laboratoire des Venins et Biomolécules Thérapeutiques - Laboratory of Venoms and Therapeutic Biomolecules (LR11IPT08), Institut Pasteur de Tunis, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), de Duve Institute, Université Catholique de Louvain = Catholic University of Louvain (UCL), Cellular and Molecular Immunology, Vrije Universiteit Brussel, 1050 Brussels, Belgium, Université de Tunis El Manar (UTM), This work was made possible by financial support from Vlaams Instituute Voor Biotechnologie (VIB) and the Flanders Hercules Foundation [grant number HERC16]. J.M. and S.M. are group leaders at the VIB.W.G. is supported by the European Student ExchangeProgramme ‘Erasmus Mundus ECW II’ [grant number 141085-EM-12008-BE-ERA Mundus – ECW]. D.V. is ‘collaborateur logistique of the FNRS-FRS Belgium’ R.B.A. is a Post-Doc in the group of B.B.Z. B.B.Z. is ‘scorpion venoms and antivenoms’ group leader at the IPT, and UCL - SSS/DDUV - Institut de Duve
Subjects: Male, [SDV]Life Sciences [q-bio], lcsh:Life, lcsh:QR1-502, QSOX, Quiescin sulfhydryl oxidase, Scorpion Venoms, Venom, medicine.disease_cause, hQSOX1b, human quiescin-sulphhydryl oxidase, Biochemistry, Median lethal dose, lcsh:Microbiology, GST, glutathione S-transferase, Sodium Channels, law.invention, Mice, law, WGE, wheat germ embryo, wheat germ extract, Triticum, Glutathione Transferase, PDI, protein disulphide isomerase, Scorpion toxin, biology, Research Support, Non-U.S. Gov't, [SDV.BA]Life Sciences [q-bio]/Animal biology, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, LD50, median lethal dose, 3. Good health, IMAC, immobilized metal-ion-affinity chromatography, i.c.v., intracerebroventricular, [SDV.TOX]Life Sciences [q-bio]/Toxicology, Recombinant DNA, NbAahII10, Androctonus australis hector nanobody 10, Androctonus australis, Molecular Sequence Data, Biophysics, In Vitro Techniques, S2, TEV, tobacco etch virus, Scorpions, dromedary, Journal Article, medicine, Animals, Amino Acid Sequence, Molecular Biology, Escherichia coli, single-domain antibody, Original Paper, Toxin, Aah, Androctonus australis hector, Cell Biology, biology.organism_classification, rAahII, recombinant AahII, AahII, lcsh:QH501-531, CBB, Coomassie Brilliant Blue, Peptides, anti-venom, CDR1, complementary-determining region 1, recombinant protein
Abstract: Envenoming following scorpion sting is a common emergency in many parts of the world. During scorpion envenoming, highly toxic small polypeptides of the venom diffuse rapidly within the victim causing serious medical problems. The exploration of toxin structure-function relationship would benefit from the generation of soluble recombinant scorpion toxins in Escherichia coli. We developed an in vitro wheat germ translation system for the expression of the highly toxic Aah (Androctonus australis hector)II protein that requires the proper formation of four disulphide bonds. Soluble, recombinant N-terminal GST (glutathione S-transferase)-tagged AahII toxin is obtained in this in vitro translation system. After proteolytic removal of the GST-tag, purified rAahII (recombinant AahII) toxin, which contains two extra amino acids at its N terminal relative to the native AahII, is highly toxic after i.c.v. (intracerebroventricular) injection in Swiss mice. An LD50 (median lethal dose)-value of 10 ng (or 1.33 pmol), close to that of the native toxin (LD50 of 3 ng) indicates that the wheat germ in vitro translation system produces properly folded and biological active rAahII. In addition, NbAahII10 (Androctonus australis hector nanobody 10), a camel single domain antibody fragment, raised against the native AahII toxin, recognizes its cognate conformational epitope on the recombinant toxin and neutralizes the toxicity of purified rAahII upon injection in mice., A wheat germ embryo derived cell-free translation system expresses a biologically active, highly toxic scorpion venom protein that is fully neutralized by a camel single domain antibody fragment raised against the native scorpion toxin.
Published: 2014

11. Astrocyte-targeted gene delivery of interleukin 2 specifically increases brain-resident regulatory T cell numbers and protects against pathological neuroinflammation

Author: Lidia Yshii, Emanuela Pasciuto, Pascal Bielefeld, Loriana Mascali, Pierre Lemaitre, Marika Marino, James Dooley, Lubna Kouser, Stijn Verschoren, Vasiliki Lagou, Hannelore Kemps, Pascal Gervois, Antina de Boer, Oliver T. Burton, Jérôme Wahis, Jens Verhaert, Samar H. K. Tareen, Carlos P. Roca, Kailash Singh, Carly E. Whyte, Axelle Kerstens, Zsuzsanna Callaerts-Vegh, Suresh Poovathingal, Teresa Prezzemolo, Keimpe Wierda, Amy Dashwood, Junhua Xie, Elien Van Wonterghem, Eline Creemers, Meryem Aloulou, Willy Gsell, Oihane Abiega, Sebastian Munck, Roosmarijn E. Vandenbroucke, Annelies Bronckaers, Robin Lemmens, Bart De Strooper, Ludo Van Den Bosch, Uwe Himmelreich, Carlos P. Fitzsimons, Matthew G. Holt, Adrian Liston, Pasciuto, Emanuela [0000-0002-5391-9585], Marino, Marika [0000-0001-6773-6176], Dooley, James [0000-0003-3154-4708], Verschoren, Stijn [0000-0001-6733-3481], Kemps, Hannelore [0000-0001-9248-1697], Gervois, Pascal [0000-0002-8320-1320], Burton, Oliver T [0000-0003-3884-7373], Singh, Kailash [0000-0002-6771-7757], Whyte, Carly E [0000-0001-6556-6855], Callaerts-Vegh, Zsuzsanna [0000-0001-9091-2078], Dashwood, Amy [0000-0002-4340-377X], Gsell, Willy [0000-0001-7334-6107], Vandenbroucke, Roosmarijn E [0000-0002-8327-620X], Liston, Adrian [0000-0002-6272-4085], Apollo - University of Cambridge Repository, Benson-Rumiz, Alicia, Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), University of Amsterdam [Amsterdam] (UvA), The Babraham Institute [Cambridge, UK], Brunel University London [Uxbridge], Hasselt University (UHasselt), Institut des Neurosciences Cellulaires et Intégratives (INCI), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), VIB [Belgium], VIB-UGent Center for Inflammation Research [Gand, Belgique] (IRC), Universiteit Gent = Ghent University (UGENT), Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), University Hospitals Leuven [Leuven], University College of London [London] (UCL), Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto = University of Porto, Pasciuto, Emanuela/0000-0002-5391-9585, Aloulou, Meryem/0000-0003-4590-230X, Dooley, James/0000-0003-3154-4708, Verschoren, Stijn/0000-0001-6733-3481, Kemps, Hannelore/0000-0001-9248-1697, Marino, Marika/0000-0001-6773-6176, Lemaitre, Pierre/0000-0003-0687-8685, Structural and Functional Plasticity of the nervous system (SILS, FNWI), SILS Other Research (FNWI), and Instituto de Investigação e Inovação em Saúde
Subjects: EXPRESSION, Immunology, Neuroimmunology, 631/250/127/1213, THERAPY, T-Lymphocytes, Regulatory, MICROGLIA, Mice, Medicine and Health Sciences, Immunology and Allergy, Animals, Humans, Interleukin-2 / genetics, REPAIR, Biological Products, [SDV.MHEP] Life Sciences [q-bio]/Human health and pathology, Interleukins, article, Biology and Life Sciences, 631/250/371, Brain, 631/250/251, REG-CELLS, Regulatory T cells, Astrocytes, 631/250/1619/554/1898/1271, Neuroinflammatory Diseases, Interleukin-2, Immunotherapy, SYSTEM, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology, PACKAGE
Abstract: The ability of immune-modulating biologics to prevent and reverse pathology has transformed recent clinical practice. Full utility in the neuroinflammation space, however, requires identification of both effective targets for local immune modulation and a delivery system capable of crossing the blood-brain barrier. The recent identification and characterization of a small population of regulatory T (Treg) cells resident in the brain presents one such potential therapeutic target. Here, we identified brain interleukin 2 (IL-2) levels as a limiting factor for brain-resident Treg cells. We developed a gene-delivery approach for astrocytes, with a small-molecule on-switch to allow temporal control, and enhanced production in reactive astrocytes to spatially direct delivery to inflammatory sites. Mice with brain-specific IL-2 delivery were protected in traumatic brain injury, stroke and multiple sclerosis models, without impacting the peripheral immune system. These results validate brain-specific IL-2 gene delivery as effective protection against neuroinflammation, and provide a versatile platform for delivery of diverse biologics to neuroinflammatory patients. The work was supported by the VIB, an ERC Consolidator Grant TissueTreg (to A.L.), an ERC Proof of Concept Grant TreatBrainDamage (to A.L.), an ERC Starting Grant AstroFunc (to M.G.H.), an ERC Proof of Concept Grant AD-VIP (to M.G.H.), FWO Research Grant 1513616N (to M.G.H.), Thierry Latran Foundation Grant SOD-VIP (to M.G.H.), an ERNAET Chair (H2020-WIDESPREAD-2018-2020-6; NCBio: 951923; to M.G.H.), FWO Research Grants 1503420N (to E.P.) and 1513020N (to J.W.), an SAO-FRA pilot grant (20190032, to E.P.), and the Biotechnology and Biological Sciences Research Council through Institute Strategic Program Grant funding BBS/E/B/000C0427 and BBS/E/B/000C0428, and the Biotechnology and Biological Sciences Research Council Core Capability Grant to the Babraham Institute. E.P., V.L., M.M., P.G., J.W. and A.d.B. were supported by fellowships from the FWO. R.L. is a senior clinical investigator of FWO Flanders. P.B., O.A. and C.P.F. were supported by an ERA-NET-NEURON grant EJTC 2016 to C.P.F. and by the Netherlands Organization for Scientific research (NWO). The authors acknowledge the important contributions of J. Haughton (VIB) for mouse husbandry, M. Rincon (VIB) for advice on AAV design and production, K. Vennekens for technical support, P. -A. Penttila and the KUL FACS Core, J. Wouters and the KUL Molecular Small Animal Imaging Center (MoSAIC), S. Walker and the Babraham Institute Imaging Core, the VIB Bio-Imaging Core, the VIB Single Cell Sequencing Core, and R. Breedijk, M. Hink and the Leeuwenhoek Center for Advanced Microscopy at the University of Amsterdam.
Published: 2022

12. Prion Fibrillization Is Mediated by a Native Structural Element That Comprises Helices H2 and H3

Author: Human Rezaei, A. Pastore, Céline Chapuis, Kris Pauwels, Zhou Xu, Stéphanie Prigent, Cesira de Chiara, Miquel Adrover, Structural Biology Research Center, VIB, 1050 Brussels, Belgium, VIB-VUB Center for Structural Biology [Bruxelles], VIB [Belgium]-VIB [Belgium], Unité de recherche Virologie et Immunologie Moléculaires (VIM), Institut National de la Recherche Agronomique (INRA), Biologie Computationnelle et Quantitative = Laboratory of Computational and Quantitative Biology (LCQB), Institut de Biologie Paris Seine (IBPS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Molecular Structure, The National Institute for Medical Research, Unité de recherche Virologie et Immunologie Moléculaires (VIM (UR 0892)), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Paris Seine (IBPS), and Sorbonne Université (SU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Circular dichroism, Amyloid, Protein Denaturation, Protein Folding, Magnetic Resonance Spectroscopy, Prions, Protein Conformation, [SDV]Life Sciences [q-bio], Sequence (biology), Biology, Biochemistry, 03 medical and health sciences, 0302 clinical medicine, Protein structure, Escherichia coli, Animals, Humans, Prion protein, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], Molecular Biology, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, Sheep, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Circular Dichroism, Genetic Variation, Neurodegenerative Diseases, Cell Biology, Protein tertiary structure, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], [SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, Kinetics, Microscopy, Electron, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], Membrane protein, Biophysics, Chromatography, Gel, Thermodynamics, Protein folding, [SDV.NEU]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC], 030217 neurology & neurosurgery, Molecular Biophysics
Abstract: Aggregation and misfolding of the prion protein (PrP) are thought to be the cause of a family of lethal neurodegenerative diseases affecting humans and other animals. Although the structures of PrP from several species have been solved, still little is known about the mechanisms that lead to the misfolded species. Here, we show that the region of PrP comprising the hairpin formed by the helices H2 and H3 is a stable independently folded unit able to retain its secondary and tertiary structure also in the absence of the rest of the sequence. We also prove that the isolated H2H3 is highly fibrillogenic and forms amyloid fibers morphologically similar to those obtained for the full-length protein. Fibrillization of H2H3 but not of full-length PrP is concomitant with formation of aggregates. These observations suggest a "banana-peeling" mechanism for misfolding of PrP in which H2H3 is the aggregation seed that needs to be first exposed to promote conversion from a helical to a beta-rich structure.
Published: 2010

13. Nlrp3 inflammasome activation in macrophages suffices for inducing autoinflammation in mice

Author: Ulrika C. Frising, Maria Giulia Doglio, Van Loo Geert, Silvia Ribo, Bernard Malissen, Andy Wullaert, Ghent University Hospital, VIB-UGent Center for Inflammation Research [Gand, Belgique] (IRC), VIB [Belgium], Centre d'Immunologie de Marseille - Luminy (CIML), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre d'Immunophénomique (CIPHE), and University of Antwerp (UA)
Subjects: EXPRESSION, Nlrp3, cryopyrin-associated periodic syndromes, Inflammasomes, [SDV]Life Sciences [q-bio], Interleukin-1beta, macrophage, interleukin-1 beta, Biochemistry, Mice, inflammasome, NLR Family, Pyrin Domain-Containing 3 Protein, Medicine and Health Sciences, Genetics, Animals, HETEROGENEITY, Biology, MUTATION, Molecular Biology, Inflammation, integumentary system, Macrophages, Biology and Life Sciences, Articles, Cryopyrin-Associated Periodic Syndromes, CIAS1, Chemistry, CELLS, Human medicine
Abstract: Cryopyrin-associated periodic syndromes (CAPS) are a spectrum of autoinflammatory disorders caused by gain-of-function NLRP3 mutant proteins that form hyperactive inflammasomes leading to overproduction of the pro-inflammatory cytokines IL-1 beta and IL-18. Expressing the murine gain-of-function Nlrp3(A350V) mutant selectively in neutrophils recapitulates several autoinflammatory features of human CAPS, but the potential contribution of macrophage inflammasome hyperactivation to CAPS development is poorly defined. Here, we show that expressing Nlrp3(A350V) in macrophages is sufficient for driving severe multi-organ autoinflammation leading to perinatal lethality in mice. In addition, we show that macrophages contribute to autoinflammation also in adult mice, as depleting macrophages in mice ubiquitously expressing Nlrp3(A350V) significantly diminishes splenic and hepatic IL-1 beta production. Interestingly, inflammation induced by macrophage-selective Nlrp3(A350V) expression does not provoke an influx of mature neutrophils, while neutrophil influx is still occurring in macrophage-depleted mice with body-wide Nlrp3(A350V) expression. These observations identify macrophages as important cellular drivers of CAPS in mice and support a cooperative cellular model of CAPS development in which macrophages and neutrophils act independently of each other in propagating severe autoinflammation.
Published: 2022

14. Operational tolerance after hematopoietic stem cell transplantation is characterized by distinct transcriptional, phenotypic, and metabolic signatures

Author: Laetitia Dubouchet, Helena Todorov, Ruth Seurinck, Nicolas Vallet, Sofie Van Gassen, Aurélien Corneau, Catherine Blanc, Habib Zouali, Anne Boland, Jean-François Deleuze, Brian Ingram, Regis Peffault de Latour, Yvan Saeys, Gérard Socié, David Michonneau, Immunologie humaine, physiopathologie & immunothérapie (HIPI (UMR_S_976 / U976)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), VIB-UGent Center for Inflammation Research [Gand, Belgique] (IRC), VIB [Belgium], Universiteit Gent = Ghent University (UGENT), Unité Mixte de Service Production et Analyse de données en Sciences de la vie et en Santé (PASS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), Cytométrie Pitié-Salpêtrière (PASS-CYPS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), Centre d'Etude du Polymorphisme Humain (CEPH), Institut Universitaire d'Hématologie (IUH), Université Paris Diderot - Paris 7 (UPD7)-Université Paris Diderot - Paris 7 (UPD7)-Fondation Jean Dausset-Université Paris Cité (UPCité), Centre National de Recherche en Génomique Humaine (CNRGH), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Metabolon INC, Hopital Saint-Louis [AP-HP] (AP-HP), and Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)
Subjects: EXPRESSION, IDENTIFICATION, [SDV]Life Sciences [q-bio], MATCHED UNRELATED DONORS, Hematopoietic Stem Cell Transplantation, Biology and Life Sciences, General Medicine, T REGULATORY CELLS, CHRONIC GVHD, KIDNEY, HLA Antigens, CYTOMETRY, THROMBOTIC MICROANGIOPATHY, B-CELLS, VERSUS-HOST-DISEASE, Immune Tolerance, Medicine and Health Sciences, Humans, Transplantation Tolerance
Abstract: The mechanisms underlying operational tolerance after hematopoietic stem cell transplantation in humans are poorly understood. We studied two independent cohorts of patients who underwent allogeneic hematopoietic stem cell transplantation from human leukocyte antigen–identical siblings. Primary tolerance was associated with long-lasting reshaping of the recipients’ immune system compared to their healthy donors with an increased proportion of regulatory T cell subsets and decreased T cell activation, proliferation, and migration. Transcriptomics profiles also identified a role for nicotinamide adenine dinucleotide biosynthesis in the regulation of immune cell functions. We then compared individuals with operational tolerance and nontolerant recipients at the phenotypic, transcriptomic, and metabolomic level. We observed alterations centered on CD38+-activated T and B cells in nontolerant patients. In tolerant patients, cell subsets with regulatory functions were prominent. RNA sequencing analyses highlighted modifications in the tolerant patients’ transcriptomic profiles, particularly with overexpression of the ectoenzymeNT5E(encoding CD73), which could counterbalance CD38 enzymatic functions by producing adenosine. Further, metabolomic analyses suggested a central role of androgens in establishing operational tolerance. These data were confirmed using an integrative approach to evaluating the immune landscape associated with operational tolerance. Thus, balance between a CD38-activated immune state and CD73-related production of adenosine may be a key regulator of operational tolerance.
Published: 2022

15. Plasma membrane perforation by GSDME during apoptosis-driven secondary necrosis

Author: Elke De Schutter, Jana Ramon, Benjamin Pfeuty, Caroline De Tender, Stephan Stremersch, Koen Raemdonck, Ken Op de Beeck, Wim Declercq, Franck B. Riquet, Kevin Braeckmans, Peter Vandenabeele, VIB [Belgium], Universiteit Gent = Ghent University (UGENT), Laboratoire de Physique des Lasers, Atomes et Molécules - UMR 8523 (PhLAM), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Vakgroep Toegepaste Wiskunde en Informatica [Gent] (Department of Applied Mathematics, Computer Science and Statistics), Université de Lille, Universiteit Gent = Ghent University [UGENT], Laboratoire de Physique des Lasers, Atomes et Molécules - UMR 8523 [PhLAM], and Vakgroep Toegepaste Wiskunde en Informatica [Gent] [Department of Applied Mathematics, Computer Science and Statistics]
Subjects: Cell death, CLEARANCE, Cell Membrane Permeability, Membrane permeabilization, Apoptosis, [SDV.BC.BC]Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC], GASDERMIN-D, PYROPTOSIS, Cell Line, Influx, Efflux, 03 medical and health sciences, Cellular and Molecular Neuroscience, DELIVERY, Mice, Necrosis, 0302 clinical medicine, Gasdermins, Medicine and Health Sciences, Animals, Dextrans, Molecular Biology, Biology, 030304 developmental biology, Pharmacology, Cell Nucleus, 0303 health sciences, NANOBUBBLES, CLEAVAGE, Cell Membrane, Biology and Life Sciences, Cell Biology, PHOTOPORATION, Molecular Weight, Chemistry, Kinetics, CELL-DEATH, Receptors, Estrogen, 030220 oncology & carcinogenesis, Molecular Medicine, SECRETION, Nanoparticles, Original Article, Human medicine
Abstract: Secondary necrosis has long been perceived as an uncontrolled process resulting in total lysis of the apoptotic cell. Recently, it was shown that progression of apoptosis to secondary necrosis is regulated by Gasdermin E (GSDME), which requires activation by caspase-3. Although the contribution of GSDME in this context has been attributed to its pore-forming capacity, little is known about the kinetics and size characteristics of this. Here we report on the membrane permeabilizing features of GSDME by monitoring the influx and efflux of dextrans of different sizes into/from anti-Fas-treated L929sAhFas cells undergoing apoptosis-driven secondary necrosis. We found that GSDME accelerates cell lysis measured by SYTOX Blue staining but does not affect the exposure of phosphatidylserine on the plasma membrane. Furthermore, loss of GSDME expression clearly hampered the influx of fluorescently labeled dextrans while the efflux happened independently of the presence or absence of GSDME expression. Importantly, both in- and efflux of dextrans were dependent on their molecular weight. Altogether, our results demonstrate that GSDME regulates the passage of compounds together with other plasma membrane destabilizing subroutines. Supplementary Information The online version contains supplementary material available at 10.1007/s00018-021-04078-0.
Published: 2022

16. Prediction of protein assemblies, the next frontier: The CASP14-CAPRI experiment

Author: Xiaoqin Zou, Théo Mauri, Hang Shi, Shaowen Zhu, Justas Dapkūnas, Yuanfei Sun, Didier Barradas-Bautista, Raphael A. G. Chaleil, Ragul Gowthaman, Sohee Kwon, Xianjin Xu, Zuzana Jandova, Genki Terashi, Ryota Ashizawa, Petras J. Kundrotas, Shuang Zhang, Tunde Aderinwale, Jian Liu, Sandor Vajda, Paul A. Bates, Jianlin Cheng, Daisuke Kihara, Luis A. Rodríguez-Lumbreras, Carlos A. Del Carpio Muñoz, Liming Qiu, Guillaume Brysbaert, Jorge Roel-Touris, Česlovas Venclovas, Tereza Clarence, Rui Yin, Amar Singh, Patryk A. Wesołowski, Rafał Ślusarz, Adam Liwo, Guangbo Yang, Agnieszka S. Karczyńska, Yoshiki Harada, Sergei Kotelnikov, Yuya Hanazono, Charlotte W. van Noort, Marc F. Lensink, Jonghun Won, Adam K. Sieradzan, Israel Desta, Xufeng Lu, Charles Christoffer, Anna Antoniak, Taeyong Park, Sheng-You Huang, Tsukasa Nakamura, Brian G. Pierce, Usman Ghani, Yang Shen, Luigi Cavallo, Chaok Seok, Hao Li, Nurul Nadzirin, Ghazaleh Taherzadeh, Jacob Verburgt, Rodrigo V. Honorato, Artur Giełdoń, Jeffrey J. Gray, Dima Kozakov, Ming Liu, Shan Chang, Eiichiro Ichiishi, Manon Réau, Rui Duan, Francesco Ambrosetti, Johnathan D. Guest, Juan Fernández-Recio, Alexandre M. J. J. Bonvin, Ilya A. Vakser, Farhan Quadir, Yumeng Yan, Ren Kong, Sameer Velankar, Sergei Grudinin, Mateusz Kogut, Mikhail Ignatov, Yasuomi Kiyota, Hyeonuk Woo, Shoshana J. Wodak, Ameya Harmalkar, Shinpei Kobayashi, Panagiotis I. Koukos, Zhen Cao, Kliment Olechnovič, Cezary Czaplewski, Xiao Wang, Agnieszka G. Lipska, Kathryn A. Porter, Peicong Lin, Emilia A. Lubecka, Nasser Hashemi, Bin Liu, Mayuko Takeda-Shitaka, Karolina Zięba, Dzmitry Padhorny, Zhuyezi Sun, Daipayan Sarkar, Romina Oliva, Andrey Alekseenko, Siri Camee van Keulen, Mireia Rosell, Raj S. Roy, Brian Jiménez-García, Jinsol Yang, Martyna Maszota-Zieleniak, Cancer Research UK, Department of Energy and Climate Change (UK), European Commission, Institut National de Recherche en Informatique et en Automatique (France), Medical Research Council (UK), Japan Society for the Promotion of Science, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), National Institute of General Medical Sciences (US), National Institutes of Health (US), National Natural Science Foundation of China, National Science Foundation (US), Unité de Glycobiologie Structurale et Fonctionnelle (UGSF), Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, Biomolecular Modelling Laboratory [London], The Francis Crick Institute [London], Jiangsu University of Technology [Changzhou], Department of Electrical Engineering and Computer Science [Columbia] (EECS), University of Missouri [Columbia] (Mizzou), University of Missouri System-University of Missouri System, Institute for Data Science and Informatics [Columbia], University of Gdańsk (UG), Faculty of Electronics, Telecommunications and Informatics [GUT Gdańsk] (ETI), Gdańsk University of Technology (GUT), Medical University of Gdańsk, Graduate School of Medical Sciences [Nagoya], Nagoya City University [Nagoya, Japan], International University of Health and Welfare Hospital (IUHW Hospital), Department of Chemical and Biomolecular Engineering [Baltimore], Johns Hopkins University (JHU), Bijvoet Center of Biomolecular Research [Utrecht], Utrecht University [Utrecht], Stony Brook University [SUNY] (SBU), State University of New York (SUNY), Innopolis University, Boston University [Boston] (BU), Russian Academy of Sciences [Moscow] (RAS), Barcelona Supercomputing Center - Centro Nacional de Supercomputacion (BSC - CNS), Universidad de La Rioja (UR), Algorithms for Modeling and Simulation of Nanosystems (NANO-D), Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire Jean Kuntzmann (LJK), Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA), Données, Apprentissage et Optimisation (DAO), Laboratoire Jean Kuntzmann (LJK), Université Grenoble Alpes (UGA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Huazhong University of Science and Technology [Wuhan] (HUST), Indiana University - Purdue University Indianapolis (IUPUI), Indiana University System, Graduate School of Information Sciences [Sendaï], Tohoku University [Sendai], National Institutes for Quantum and Radiological Science and Technology (QST), University of Maryland [Baltimore], King Abdullah University of Science and Technology (KAUST), University of Naples Federico II, Texas A&M University [Galveston], Seoul National University [Seoul] (SNU), Kitasato University, University of Kansas [Lawrence] (KU), Vilnius University [Vilnius], University of Missouri System, VIB-VUB Center for Structural Biology [Bruxelles], VIB [Belgium], Sub NMR Spectroscopy, Sub Overig UiLOTS, Sub Mathematics Education, NMR Spectroscopy, Université de Lille, CNRS, Unité de Glycobiologie Structurale et Fonctionnelle (UGSF) - UMR 8576, European Bioinformatics Institute [Hinxton] [EMBL-EBI], Department of Electrical Engineering and Computer Science [Columbia] [EECS], Faculty of Chemistry [Univ Gdańsk], Faculty of Electronics, Telecommunications and Informatics [GUT Gdańsk] [ETI], International University of Health and Welfare Hospital [IUHW Hospital], Johns Hopkins University [JHU], Stony Brook University [SUNY] [SBU], Department of Biomedical Engineering [Boston], Instituto de Ciencias de la Vid y el Vino [ICVV], Huazhong University of Science and Technology [Wuhan] [HUST], Indiana University - Purdue University Indianapolis [IUPUI], National Institutes for Quantum and Radiological Science and Technology [QST], King Abdullah University of Science and Technology [KAUST], Università degli Studi di Napoli 'Parthenope' = University of Naples [PARTHENOPE], Seoul National University [Seoul] [SNU], University of Kansas [Lawrence] [KU], University of Missouri [Columbia] [Mizzou], Unité de Glycobiologie Structurale et Fonctionnelle - UMR 8576 (UGSF), Université de Lille-Centre National de la Recherche Scientifique (CNRS), University of Naples Federico II = Università degli studi di Napoli Federico II, European Project: 675728,H2020,H2020-EINFRA-2015-1,BioExcel(2015), European Project: 823830,H2020-EU.1.4.1.3. Development, deployment and operation of ICT-based e-infrastructures, H2020-EU.1.4. EXCELLENT SCIENCE - Research Infrastructures ,BioExcel-2(2019), European Project: 777536,H2020-EU.1.4.1.3. Development, deployment and operation of ICT-based e-infrastructures, and H2020-EU.1.4. EXCELLENT SCIENCE - Research Infrastructures,EOSC-hub(2018)
Subjects: Models, Molecular, blind prediction, CAPRI, CASP, docking, oligomeric state, protein assemblies, protein complexes, protein docking, protein–protein interaction, template-based modeling, Computer science, [SDV]Life Sciences [q-bio], Machine learning, computer.software_genre, Biochemistry, Article, protein-protein interaction, 03 medical and health sciences, Sequence Analysis, Protein, Structural Biology, Server, Protein Interaction Domains and Motifs, Molecular Biology, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, Binding Sites, business.industry, 030302 biochemistry & molecular biology, Computational Biology, Proteins, 3. Good health, Molecular Docking Simulation, Artificial intelligence, business, computer, Software
Abstract: We present the results for CAPRI Round 50, the fourth joint CASP-CAPRI protein assembly prediction challenge. The Round comprised a total of twelve targets, including six dimers, three trimers, and three higher-order oligomers. Four of these were easy targets, for which good structural templates were available either for the full assembly, or for the main interfaces (of the higher-order oligomers). Eight were difficult targets for which only distantly related templates were found for the individual subunits. Twenty-five CAPRI groups including eight automatic servers submitted ~1250 models per target. Twenty groups including six servers participated in the CAPRI scoring challenge submitted ~190 models per target. The accuracy of the predicted models was evaluated using the classical CAPRI criteria. The prediction performance was measured by a weighted scoring scheme that takes into account the number of models of acceptable quality or higher submitted by each group as part of their five top-ranking models. Compared to the previous CASP-CAPRI challenge, top performing groups submitted such models for a larger fraction (70–75%) of the targets in this Round, but fewer of these models were of high accuracy. Scorer groups achieved stronger performance with more groups submitting correct models for 70–80% of the targets or achieving high accuracy predictions. Servers performed less well in general, except for the MDOCKPP and LZERD servers, who performed on par with human groups. In addition to these results, major advances in methodology are discussed, providing an informative overview of where the prediction of protein assemblies currently stands., Cancer Research UK, Grant/Award Number: FC001003; Changzhou Science and Technology Bureau, Grant/Award Number: CE20200503; Department of Energy and Climate Change, Grant/Award Numbers: DE-AR001213, DE-SC0020400, DE-SC0021303; H2020 European Institute of Innovation and Technology, Grant/Award Numbers: 675728, 777536, 823830; Institut national de recherche en informatique et en automatique (INRIA), Grant/Award Number: Cordi-S; Lietuvos Mokslo Taryba, Grant/Award Numbers: S-MIP-17-60, S-MIP-21-35; Medical Research Council, Grant/Award Number: FC001003; Japan Society for the Promotion of Science KAKENHI, Grant/Award Number: JP19J00950; Ministerio de Ciencia e Innovación, Grant/Award Number: PID2019-110167RB-I00; Narodowe Centrum Nauki, Grant/Award Numbers: UMO-2017/25/B/ST4/01026, UMO-2017/26/M/ST4/00044, UMO-2017/27/B/ST4/00926; National Institute of General Medical Sciences, Grant/Award Numbers: R21GM127952, R35GM118078, RM1135136, T32GM132024; National Institutes of Health, Grant/Award Numbers: R01GM074255, R01GM078221, R01GM093123, R01GM109980, R01GM133840, R01GN123055, R01HL142301, R35GM124952, R35GM136409; National Natural Science Foundation of China, Grant/Award Number: 81603152; National Science Foundation, Grant/Award Numbers: AF1645512, CCF1943008, CMMI1825941, DBI1759277, DBI1759934, DBI1917263, DBI20036350, IIS1763246, MCB1925643; NWO, Grant/Award Number: TOP-PUNT 718.015.001; Wellcome Trust, Grant/Award Number: FC001003
Published: 2021

17. Efficacy of a tight-control and treat-to-target strategy in axial spondyloarthritis: results of the open-label, pragmatic, cluster-randomised TICOSPA trial

Author: Molto, Anna, López-Medina, Clementina, Van den Bosch, Filip E, Boonen, Annelies, Webers, Casper, Dernis, Emanuelle, van Gaalen, Floris A, Soubrier, Martin, Claudepierre, Pascal, Baillet, Athan, Starmans-Kool, Mirian, Spoorenberg, Anneke, Jacques, Peggy, Carron, Philippe, Joos, Rik, Lenaerts, Jan, Gossec, Laure, Pouplin, Sophie, Ruyssen-Witrand, Adeline, Sparsa, Laetitia, van Tubergen, Astrid, van der Heijde, Désirée, Dougados, Maxime, Service de rhumatologie [CHU Cochin], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Cochin [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Equipe 4 : ECaMO - Épidémiologie clinique appliquée aux maladies rhumatismales et musculo-squelettiques (CRESS - U1153), Centre de Recherche Épidémiologie et Statistique Sorbonne Paris Cité (CRESS (U1153 / UMR_A_1125 / UMR_S_1153)), Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université (HESAM)-HESAM Université (HESAM)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPC)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université (HESAM)-HESAM Université (HESAM)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPC)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Ghent University Hospital, Maastricht University [Maastricht], Centre Hospitalier Le Mans (CH Le Mans), Leiden University Medical Center (LUMC), CHU Clermont-Ferrand, Epidemiology in Dermatology and Evaluation in Therapeutics (EpiDermE), Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), CHU Henri Mondor, University Medical Center Groningen [Groningen] (UMCG), VIB-UGent Center for Inflammation Research [Gand, Belgique] (IRC), VIB [Belgium], Ziekenhuis Netwerk Antwerpen (ZNA), Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), Service de Rhumatologie [CHU Pitié Salpêtrière], CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées, Maastricht University Medical Centre (MUMC), Hôpital Cochin [AP-HP], Conservatoire National des Arts et Métiers [CNAM] (CNAM)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Conservatoire National des Arts et Métiers [CNAM] (CNAM)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Sorbonne Université (SU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Service de rhumatologie [CHU Pitié Salpêtrière] (GRC-08 EEMOIS), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), RS: CAPHRI - R3 - Functioning, Participating and Rehabilitation, Interne Geneeskunde, MUMC+: MA Reumatologie (9), MUMC+: MA Med Staf Artsass Interne Geneeskunde (9), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)
Subjects: [SDV]Life Sciences [q-bio], Immunology, Genetics and Molecular Biology, IMPROVEMENT, RECOMMENDATIONS, Rheumatology, Spondyloarthritis, Spondylarthritis, therapeutics, Humans, Immunology and Allergy, DISEASE-ACTIVITY SCORE, CRITERIA, Spondylitis, Ankylosing, ASAS, Biology and Life Sciences, healthcare, ANKYLOSING-SPONDYLITIS, spondylitis, outcome and process assessment, ABILITY, RHEUMATOID-ARTHRITIS, ankylosing, PSORIATIC-ARTHRITIS, General Biochemistry, ADALIMUMAB
Abstract: Objectives To compare the benefits of a tight-control/treat-to-target strategy (TC/T2T) in axial spondyloarthritis (axSpA) with those of usual care (UC). Methods Pragmatic, prospective, cluster-randomised, controlled, open, 1-year trial (NCT03043846). 18 centres were randomised (1:1). Patients met Axial Spondylo Arthritis International Society (ASAS) criteria for axSpA, had an Ankylosing Spondylitis Disease Activity Score (ASDAS) ≥2.1, received non-optimal treatment by non-steroidal anti-inflammatory drugs and were biologic-naive. Interventions (1) TC/T2T: visits every 4 weeks and prespecified strategy based on treatment intensification until achieving target (ie, ASDAS
Published: 2021

18. Les nesprines, des protéines de l’enveloppe nucléaire, contrôlent mécaniquement différentes transitions épithélio-mésenchymateuses

Author: Louis Laurent, François Sipieter, Nicolas Borghi, Université de Lille, VIB-UGent Center for Inflammation Research [Gand, Belgique] (IRC), VIB [Belgium], Universiteit Gent = Ghent University [Belgium] (UGENT), Institut Jacques Monod UMR 7592 Université Paris Diderot and CNRS, 75205 Paris cedex 13, Universiteit Gent = Ghent University (UGENT), Institut Jacques Monod (IJM (UMR_7592)), and Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)
Subjects: 0303 health sciences, 03 medical and health sciences, 0302 clinical medicine, [SDV]Life Sciences [q-bio], General Medicine, 030217 neurology & neurosurgery, General Biochemistry, Genetics and Molecular Biology, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology
Abstract: International audience; No abstract available
Published: 2021

19. Nucleation of protein mesocrystals via oriented attachment

Author: Nani Van Gerven, Rick R. M. Joosten, Wai Li Ling, Alexander E. S. Van Driessche, Nico A. J. M. Sommerdijk, Mike Sleutel, Maria Bacia, Institut des Sciences de la Terre (ISTerre), Institut national des sciences de l'Univers (INSU - CNRS)-Institut de recherche pour le développement [IRD] : UR219-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Gustave Eiffel-Université Grenoble Alpes (UGA), VIB-VUB Center for Structural Biology [Bruxelles], VIB [Belgium], Department of Chemical Engineering and Chemistry [Eindhoven], Eindhoven University of Technology [Eindhoven] (TU/e), Institut de biologie structurale (IBS - UMR 5075), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA), Department of Biochemistry, Department of Molecular Biology, Faculty of Science, Radboud University, Radboud Institute for Molecular Life Sciences (RIMLS), 6525GA Nijmegen, the Netherlands, Department of Molecular Biology, Radboud Institute for Molecular Life Sciences (RIMLS), Oncode Institute, Radboud University, Nijmegen, the Netherland, Structural Biology Brussels (SBB), Vrije Universiteit Brussel (VUB), ANR-10-INBS-0005,FRISBI,Infrastructure Française pour la Biologie Structurale Intégrée(2010), ANR-17-EURE-0003,CBH-EUR-GS,CBH-EUR-GS(2017), Centre National de la Recherche Scientifique (CNRS)-PRES Université de Grenoble-Université Joseph Fourier - Grenoble 1 (UJF)-Institut Français des Sciences et Technologies des Transports, de l'Aménagement et des Réseaux (IFSTTAR)-Institut national des sciences de l'Univers (INSU - CNRS)-Institut de recherche pour le développement [IRD] : UR219-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry]), Institut national des sciences de l'Univers (INSU - CNRS)-Institut de recherche pour le développement [IRD] : UR219-Université Grenoble Alpes (UGA)-Université Gustave Eiffel-Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry]), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institute for Complex Molecular Systems, Materials and Interface Chemistry, Physical Chemistry, Department of Bio-engineering Sciences, and Structural Biology Brussels
Subjects: 0301 basic medicine, Models, Molecular, Chemistry(all), Nucleation, General Physics and Astronomy, Nanoparticle, Crystallography, X-Ray, 01 natural sciences, law.invention, MESH: Recombinant Proteins, law, Crystallization, Aldose-Ketose Isomerases, MESH: Crystallization, Multidisciplinary, MESH: Kinetics, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Self-assembly, Nanocrystalline material, Recombinant Proteins, MESH: Cryoelectron Microscopy, Protein crystallization, MESH: Models, Molecular, Materials science, Science, Nanotechnology, Physics and Astronomy(all), 010402 general chemistry, Molecular resolution, General Biochemistry, Genetics and Molecular Biology, Article, 03 medical and health sciences, MESH: Nanostructures, Point Mutation, [CHIM]Chemical Sciences, MESH: Particle Size, Particle Size, MESH: Aldose-Ketose Isomerases, MESH: Point Mutation, Biochemistry, Genetics and Molecular Biology(all), Cryoelectron Microscopy, Proteins, General Chemistry, MESH: Crystallography, X-Ray, 0104 chemical sciences, Nanostructures, Kinetics, 030104 developmental biology, Phase transitions and critical phenomena, Nanocrystal, [SDU]Sciences of the Universe [physics], Nanomedicine Radboud Institute for Molecular Life Sciences [Radboudumc 19]
Abstract: Self-assembly of proteins holds great promise for the bottom-up design and production of synthetic biomaterials. In conventional approaches, designer proteins are pre-programmed with specific recognition sites that drive the association process towards a desired organized state. Although proven effective, this approach poses restrictions on the complexity and material properties of the end-state. An alternative, hierarchical approach that has found wide adoption for inorganic systems, relies on the production of crystalline nanoparticles that become the building blocks of a next-level assembly process driven by oriented attachment (OA). As it stands, OA has not yet been observed for protein systems. Here we employ cryo-transmission electron microscopy (cryoEM) in the high nucleation rate limit of protein crystals and map the self-assembly route at molecular resolution. We observe the initial formation of facetted nanocrystals that merge lattices by means of OA alignment well before contact is made, satisfying non-trivial symmetry rules in the process. As these nanocrystalline assemblies grow larger we witness imperfect docking events leading to oriented aggregation into mesocrystalline assemblies. These observations highlight the underappreciated role of the interaction between crystalline nuclei, and the impact of OA on the crystallization process of proteins., Past studies on protein nucleation have focused on the routes that molecules follow towards a crystalline cluster, while possible interactions that may occur between nuclei have not been investigated. Here, the authors show that in the high supersaturation limit such interactions dominate the nucleation process in the form of inter-nucleus docking driving by oriented attachment.
Published: 2021

20. Intestinal cDC1 drive cross-tolerance to epithelial-derived antigen via induction of FoxP3 + CD8 + T regs

Author: Luisa Klotz, Aaron Silva-Sanchez, Troy D. Randall, Knut Kotarsky, Simon Tavernier, Cristina Gomez-Casado, Thorsten Joeris, Bernard Malissen, Petra Holmkvist, William W. Agace, Allan McI. Mowat, Department of Health Technology, Technical University of Denmark, Danmarks Tekniske Universitet = Technical University of Denmark (DTU), Lund University [Lund], Ghent University Hospital, VIB-UGent Center for Inflammation Research [Gand, Belgique] (IRC), VIB [Belgium], University of Alabama at Birmingham, department od Medicine, University Hospital Münster - Universitaetsklinikum Muenster [Germany] (UKM), University of Alabama at Birmingham - Department of Medicine, University of Glasgow - Institute of Infection, Immunity and Inflammation, Centre d'Immunologie de Marseille - Luminy (CIML), and Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Chemistry, [SDV]Life Sciences [q-bio], T cell, education, Immunology, Retinoic acid, CCR9, FOXP3, hemic and immune systems, chemical and pharmacologic phenomena, General Medicine, Epithelium, Cell biology, chemistry.chemical_compound, medicine.anatomical_structure, Antigen, medicine, health care economics and organizations, Homeostasis, CD8
Abstract: Although CD8+ T cell tolerance to tissue-specific antigen (TSA) is essential for host homeostasis, the mechanisms underlying peripheral cross-tolerance and whether they may differ between tissue sites remain to be fully elucidated. Here, we demonstrate that peripheral cross-tolerance to intestinal epithelial cell (IEC)–derived antigen involves the generation and suppressive function of FoxP3+CD8+ T cells. FoxP3+CD8+ Treg generation was dependent on intestinal cDC1, whose absence led to a break of tolerance and epithelial destruction. Mechanistically, intestinal cDC1-derived PD-L1, TGFβ, and retinoic acid contributed to the generation of gut-tropic CCR9+CD103+FoxP3+CD8+ Tregs. Last, CD103-deficient CD8+ T cells lacked tolerogenic activity in vivo, indicating a role for CD103 in FoxP3+CD8+ Treg function. Our results describe a role for FoxP3+CD8+ Tregs in cross-tolerance in the intestine for which development requires intestinal cDC1.
Published: 2021

21. Guidelines for the use of flow cytometry and cell sorting in immunological studies (second edition)

Author: Lara Gibellini, Sussan Nourshargh, Susanna Cardell, Wlodzimierz Maslinski, Mar Felipo-Benavent, Florian Mair, Hans-Martin Jäck, Lilly Lopez, Klaus Warnatz, John Trowsdale, Diana Ordonez, Marcus Eich, William Hwang, Anne Cooke, Dirk Mielenz, Alberto Orfao, Winfried F. Pickl, Vladimir Benes, Alice Yue, T. Vincent Shankey, Maria Tsoumakidou, Virginia Litwin, Gelo Victoriano Dela Cruz, Andrea Cavani, Sara De Biasi, Larissa Nogueira Almeida, Jonathan J M Landry, Claudia Haftmann, Charlotte Esser, Ana Cumano, Anneke Wilharm, Francesco Dieli, Rudi Beyaert, Alessio Mazzoni, Burkhard Ludewig, Carlo Pucillo, Dirk H. Busch, Joe Trotter, Stipan Jonjić, Marc Veldhoen, Josef Spidlen, Aja M. Rieger, Dieter Adam, Srijit Khan, Todd A. Fehniger, Giuseppe Matarese, Maximilien Evrard, Christian Maueröder, Steffen Schmitt, Kristin A. Hogquist, Barry Moran, Raghavendra Palankar, Markus Feuerer, S Schmid, Susann Rahmig, Amy E. Lovett-Racke, James V. Watson, Megan K. Levings, Susanne Melzer, Dinko Pavlinic, Christopher M. Harpur, Christina Stehle, A. Graham Pockley, Toshinori Nakayama, Attila Tárnok, Juhao Yang, Michael Lohoff, Paulo Vieira, Francisco Sala-de-Oyanguren, Christian Kurts, Anastasia Gangaev, Alfonso Blanco, Hans Scherer, Regine J. Dress, Bruno Silva-Santos, Kiyoshi Takeda, Bimba F. Hoyer, Ilenia Cammarata, Daryl Grummitt, Isabel Panse, Günnur Deniz, Bianka Baying, Friederike Ebner, Esther Schimisky, Leo Hansmann, Thomas Kamradt, Edwin van der Pol, Daniel Scott-Algara, Anna Iannone, Giorgia Alvisi, Sebastian R. Schulz, Francesco Liotta, Irmgard Förster, Beatriz Jávega, Hans-Peter Rahn, Caetano Reis e Sousa, Livius Penter, Xuetao Cao, David P. Sester, Keisuke Goda, Peter Wurst, Iain B. McInnes, Ricardo T. Gazzinelli, Federica Piancone, Gerald Willimsky, Yotam Raz, Pärt Peterson, Wolfgang Fritzsche, Yvonne Samstag, Martin Büscher, Thomas Schüler, Susanne Hartmann, Robert J. Wilkinson, Anna E. S. Brooks, Steven L. C. Ketelaars, Catherine Sautès-Fridman, Anna Rubartelli, Petra Bacher, Katja Kobow, Marco A. Cassatella, Andrea Hauser, Henrik E. Mei, Kilian Schober, Silvia Della Bella, Graham Anderson, Michael D. Ward, Garth Cameron, Sebastian Lunemann, Katharina Kriegsmann, Katarzyna M. Sitnik, Brice Gaudilliere, Chantip Dang-Heine, Marcello Pinti, Paul Klenerman, Frank A. Schildberg, Joana Barros-Martins, Laura G. Rico, Hanlin Zhang, Christian Münz, Thomas Dörner, Jakob Zimmermann, Andrea M. Cooper, Jonni S. Moore, Andreas Diefenbach, Yanling Liu, Wolfgang Bauer, Tobit Steinmetz, Katharina Pracht, Leonard Tan, Peter K. Jani, Alan M. Stall, Petra Hoffmann, Christine S. Falk, Jasmin Knopf, Simon Fillatreau, Hans-Dieter Volk, Luis E. Muñoz, David L. Haviland, William W. Agace, Jonathan Rebhahn, Ljiljana Cvetkovic, Mohamed Trebak, Jordi Petriz, Mario Clerici, Diether J. Recktenwald, Anders Ståhlberg, Tristan Holland, Helen M. McGuire, Sa A. Wang, Christian Kukat, Thomas Kroneis, Laura Cook, Wan Ting Kong, Xin M. Wang, Britta Engelhardt, Pierre Coulie, Genny Del Zotto, Sally A. Quataert, Kata Filkor, Gabriele Multhoff, Bartek Rajwa, Federica Calzetti, Hans Minderman, Cosima T. Baldari, Jens Geginat, Hervé Luche, Gert Van Isterdael, Linda Schadt, Sophia Urbanczyk, Giovanna Borsellino, Liping Yu, Dale I. Godfrey, Achille Anselmo, Rachael C. Walker, Andreas Grützkau, David W. Hedley, Birgit Sawitzki, Silvia Piconese, Maria Yazdanbakhsh, Burkhard Becher, Ramon Bellmas Sanz, Michael Delacher, Hyun-Dong Chang, Immanuel Andrä, Hans-Gustaf Ljunggren, José-Enrique O'Connor, Ahad Khalilnezhad, Sharon Sanderson, Federico Colombo, Götz R. A. Ehrhardt, Inga Sandrock, Enrico Lugli, Christian Bogdan, James B. Wing, Susann Müller, Tomohiro Kurosaki, Derek Davies, Ester B. M. Remmerswaal, Kylie M. Quinn, Christopher A. Hunter, Andreas Radbruch, Timothy P. Bushnell, Anna Erdei, Sabine Adam-Klages, Pascale Eede, Van Duc Dang, Rieke Winkelmann, Thomas Korn, Gemma A. Foulds, Dirk Baumjohann, Matthias Schiemann, Manfred Kopf, Jan Kisielow, Lisa Richter, Jochen Huehn, Gloria Martrus, Alexander Scheffold, Jessica G. Borger, Sidonia B G Eckle, John Bellamy Foster, Anna Katharina Simon, Alicia Wong, Mübeccel Akdis, Gisa Tiegs, Toralf Kaiser, James McCluskey, Anna Vittoria Mattioli, Aaron J. Marshall, Hui-Fern Koay, Eva Orlowski-Oliver, Anja E. Hauser, J. Paul Robinson, Jay K. Kolls, Luca Battistini, Mairi McGrath, Jane L. Grogan, Natalio Garbi, Timothy Tree, Kingston H. G. Mills, Stefan H. E. Kaufmann, Wolfgang Schuh, Ryan R. Brinkman, Tim R. Mosmann, Vincenzo Barnaba, Andreas Dolf, Lorenzo Cosmi, Bo Huang, Andreia C. Lino, Baerbel Keller, René A. W. van Lier, Alexandra J. Corbett, Paul S. Frenette, Pleun Hombrink, Helena Radbruch, Sofie Van Gassen, Olivier Lantz, Lorenzo Moretta, Désirée Kunkel, Kirsten A. Ward-Hartstonge, Armin Saalmüller, Leslie Y. T. Leung, Salvador Vento-Asturias, Paola Lanuti, Alicia Martínez-Romero, Sarah Warth, Zhiyong Poon, Diana Dudziak, Andrea Cossarizza, Kovit Pattanapanyasat, Konrad von Volkmann, Jessica P. Houston, Agnès Lehuen, Andrew Filby, Pratip K. Chattopadhyay, Stefano Casola, Annika Wiedemann, Hannes Stockinger, Jürgen Ruland, Arturo Zychlinsky, Claudia Waskow, Katrin Neumann, Ari Waisman, Lucienne Chatenoud, Sudipto Bari, Kamran Ghoreschi, David W. Galbraith, Yvan Saeys, Hamida Hammad, Andrea Gori, Miguel López-Botet, Gabriel Núñez, Sabine Ivison, Michael Hundemer, Dorothea Reimer, Mark C. Dessing, Günter J. Hämmerling, Rudolf A. Manz, Tomas Kalina, Jonas Hahn, Holden T. Maecker, Hendy Kristyanto, Martin S. Davey, Henning Ulrich, Michael L. Dustin, Takashi Saito, Yousuke Takahama, Milena Nasi, Johanna Huber, Jürgen Wienands, Paolo Dellabona, Andreas Schlitzer, Michael D. Leipold, Kerstin H. Mair, Christian Peth, Immo Prinz, Chiara Romagnani, José M. González-Navajas, Josephine Schlosser, Marina Saresella, Matthias Edinger, Dirk Brenner, Nicole Baumgarth, Rikard Holmdahl, Fang-Ping Huang, Guadalupe Herrera, Malte Paulsen, Gergely Toldi, Luka Cicin-Sain, Reiner Schulte, Christina E. Zielinski, Thomas Winkler, Christoph Goettlinger, Philip E. Boulais, Jennie H M Yang, Antonio Celada, Heike Kunze-Schumacher, Julia Tornack, Florian Ingelfinger, Jenny Mjösberg, Andy Riddell, Leonie Wegener, Thomas Höfer, Christoph Hess, James P. Di Santo, Anna E. Oja, J. Kühne, Willem van de Veen, Mary Bebawy, Alberto Mantovani, Bart Everts, Giovanna Lombardi, Laura Maggi, Anouk von Borstel, Pia Kvistborg, Elisabetta Traggiai, A Ochel, Nima Aghaeepour, Charles-Antoine Dutertre, Matthieu Allez, Thomas Höllt, Wenjun Ouyang, Regina Stark, Maries van den Broek, Shimon Sakaguchi, Paul K. Wallace, Silvano Sozzani, Francesca LaRosa, Annette Oxenius, Malgorzata J. Podolska, Ivana Marventano, Wilhelm Gerner, Oliver F. Wirz, Britta Frehse, Gevitha Ravichandran, Martin Herrmann, Carl S. Goodyear, Gary Warnes, Helen Ferry, Stefan Frischbutter, Tim R. Radstake, Salomé LeibundGut-Landmann, Yi Zhao, Axel Schulz, Angela Santoni, Pablo Engel, Daniela C. Hernández, Andreas Acs, Cristiano Scottà, Francesco Annunziato, Thomas Weisenburger, Wolfgang Beisker, Sue Chow, Fritz Melchers, Daniel E. Speiser, Immanuel Kwok, Florent Ginhoux, Dominic A. Boardman, Natalie Stanley, Carsten Watzl, Marie Follo, Erik Lubberts, Andreas Krueger, Susanne Ziegler, Göran K. Hansson, David Voehringer, Antonia Niedobitek, Eleni Christakou, Lai Guan Ng, Sabine Baumgart, Nicholas A Gherardin, Antonio Cosma, Orla Maguire, Jolene Bradford, Daniel Schraivogel, Linda Quatrini, Stephen D. Miller, Rheumatology, Università degli Studi di Modena e Reggio Emilia (UNIMORE), Deutsches Rheuma-ForschungsZentrum (DRFZ), Deutsches Rheuma-ForschungsZentrum, Swiss Institute of Allergy and Asthma Research (SIAF), Universität Zürich [Zürich] = University of Zurich (UZH), Institut de Recherche Saint-Louis - Hématologie Immunologie Oncologie (Département de recherche de l’UFR de médecine, ex- Institut Universitaire Hématologie-IUH) (IRSL), Université de Paris (UP), Ecotaxie, microenvironnement et développement lymphocytaire (EMily (UMR_S_1160 / U1160)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP), Department of Internal Medicine, Università degli Studi di Firenze = University of Florence [Firenze] (UNIFI)-DENOTHE Center, Institute of Clinical Molecular Biology, Kiel University, Department of Life Sciences [Siena, Italy], Università degli Studi di Siena = University of Siena (UNISI), Institut Pasteur, Fondation Cenci Bolognetti - Istituto Pasteur Italia, Fondazione Cenci Bolognetti, Réseau International des Instituts Pasteur (RIIP), Dulbecco Telethon Institute/Department of Biology, Caprotec Bioanalytics GmbH, International Occultation Timing Association European Section (IOTA ES), International Occultation Timing Association European Section, European Molecular Biology Laboratory [Heidelberg] (EMBL), VIB-UGent Center for Inflammation Research [Gand, Belgique] (IRC), VIB [Belgium], Fondazione Santa Lucia (IRCCS), Department of Immunology, Chinese Academy of Medical Sciences, FIRC Institute of Molecular Oncology Foundation, IFOM, Istituto FIRC di Oncologia Molecolare (IFOM), Institut Necker Enfants-Malades (INEM - UM 111 (UMR 8253 / U1151)), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Department of Physiopatology and Transplantation, University of Milan (DEPT), University of Milan, Monash University [Clayton], Institut des Maladies Emergentes et des Thérapies Innovantes (IMETI), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Institute of Cellular Pathology, Université Catholique de Louvain = Catholic University of Louvain (UCL), Lymphopoïèse (Lymphopoïèse (UMR_1223 / U1223 / U-Pasteur_4)), Institut Pasteur [Paris]-Université Paris Diderot - Paris 7 (UPD7)-Institut National de la Santé et de la Recherche Médicale (INSERM), Experimental Immunology Unit, Dept. of Oncology, DIBIT San Raffaele Scientific Institute, Immunité Innée - Innate Immunity, Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur [Paris], Charité - UniversitätsMedizin = Charité - University Hospital [Berlin], Department of Biopharmacy [Bruxelles, Belgium] (Institute for Medical Immunology IMI), Université libre de Bruxelles (ULB), Charité Hospital, Humboldt-Universität zu Berlin, Agency for science, technology and research [Singapore] (A*STAR), Laboratory of Molecular Immunology and the Howard Hughes Institute, Rockefeller University [New York], Kennedy Institute of Rheumatology [Oxford, UK], Imperial College London, Theodor Kocher Institute, University of Bern, Leibniz Research Institute for Environmental Medicine [Düsseldorf, Germany] ( IUF), Université Lumière - Lyon 2 (UL2), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), University of Edinburgh, Integrative Biology Program [Milano], Istituto Nazionale Genetica Molecolare [Milano] (INGM), Singapore Immunology Network (SIgN), Biomedical Sciences Institute (BMSI), Universitat de Barcelona (UB), Rheumatologie, Cell Biology, Department of medicine [Stockholm], Karolinska Institutet [Stockholm]-Karolinska University Hospital [Stockholm], Department for Internal Medicine 3, Institute for Clinical Immunology, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), Delft University of Technology (TU Delft), Medical Inflammation Research, Karolinska Institutet [Stockholm], Department of Photonics Engineering [Lyngby], Technical University of Denmark [Lyngby] (DTU), Dpt of Experimental Immunology [Braunschweig], Helmholtz Centre for Infection Research (HZI), Department of Internal Medicine V, Universität Heidelberg [Heidelberg], Department of Histology and Embryology, University of Rijeka, Freiburg University Medical Center, Nuffield Dept of Clinical Medicine, University of Oxford [Oxford]-NIHR Biomedical Research Centre, Institute of Integrative Biology, Molecular Biomedicine, Berlin Institute of Health (BIH), Laboratory for Lymphocyte Differentiation, RIKEN Research Center, Institutes of Molecular Medicine and Experimental Immunology, University of Bonn, Immunité et cancer (U932), Institut Curie [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Cochin (IC UM3 (UMR 8104 / U1016)), Department of Surgery [Vancouver, BC, Canada] (Child and Family Research Institute), University of British Columbia (UBC)-Child and Family Research Institute [Vancouver, BC, Canada], College of Food Science and Technology [Shangai], Shanghai Ocean University, Institute for Medical Microbiology and Hygiene, University of Marburg, King‘s College London, Erasmus University Medical Center [Rotterdam] (Erasmus MC), Centre d'Immunophénomique (CIPHE), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Brustzentrum Kantonsspital St. Gallen, Immunotechnology Section, Vaccine Research Center, National Institutes of Health [Bethesda] (NIH)-National Institute of Allergy and Infectious Diseases, Heinrich Pette Institute [Hamburg], Università degli Studi di Firenze = University of Florence [Firenze] (UNIFI), Department of Immunology and Cell Biology, Mario Negri Institute, Laboratory of Molecular Medicine and Biotechnology, Don C. Gnocchi ONLUS Foundation, Institute of Translational Medicine, Klinik für Dermatologie, Venerologie und Allergologie, School of Biochemistry and Immunology, Department of Medicine Huddinge, Karolinska Institutet [Stockholm]-Karolinska University Hospital [Stockholm]-Lipid Laboratory, Università di Genova, Dipartimento di Medicina Sperimentale, Department of Environmental Microbiology, Helmholtz Zentrum für Umweltforschung = Helmholtz Centre for Environmental Research (UFZ), Department of Radiation Oncology [Munich], Ludwig-Maximilians-Universität München (LMU), Centre de Recherche Publique- Santé, Université du Luxembourg (Uni.lu), William Harvey Research Institute, Barts and the London Medical School, University of Michigan [Ann Arbor], University of Michigan System, Centro de Investigacion del Cancer (CSIC), Universitario de Salamanca, Molecular Pathology [Tartu, Estonia], University of Tartu, Hannover Medical School [Hannover] (MHH), Centre d'Immunologie de Marseille - Luminy (CIML), Monash Biomedicine Discovery Institute, Cytometry Laboratories and School of Veterinary Medicine, Purdue University [West Lafayette], Data Mining and Modelling for Biomedicine [Ghent, Belgium], VIB Center for Inflammation Research [Ghent, Belgium], Laboratory for Cell Signaling, RIKEN Research Center for Allergy and Immunology, RIKEN Research Center for Allergy and Immunology, Osaka University [Osaka], Università degli Studi di Roma 'La Sapienza' = Sapienza University [Rome], Centre de Recherche des Cordeliers (CRC (UMR_S_1138 / U1138)), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Université de Paris (UP), Institute of Medical Immunology [Berlin, Germany], FACS and Array Core Facility, Johannes Gutenberg - Universität Mainz (JGU), Otto-von-Guericke University [Magdeburg] (OVGU), SUPA School of Physics and Astronomy [University of St Andrews], University of St Andrews [Scotland]-Scottish Universities Physics Alliance (SUPA), Biologie Cellulaire des Lymphocytes - Lymphocyte Cell Biology, Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), General Pathology and Immunology (GPI), University of Brescia, Université de Lausanne (UNIL), Terry Fox Laboratory, BC Cancer Agency (BCCRC)-British Columbia Cancer Agency Research Centre, Department of Molecular Immunology, Medizinische Universität Wien = Medical University of Vienna, Dept. Pediatric Cardiology, Universität Leipzig [Leipzig], Universitaetsklinikum Hamburg-Eppendorf = University Medical Center Hamburg-Eppendorf [Hamburg] (UKE), Center for Cardiovascular Sciences, Albany Medical College, Dept Pathol, Div Immunol, University of Cambridge [UK] (CAM), Department of Information Technology [Gent], Universiteit Gent, Department of Plant Systems Biology, Department of Plant Biotechnology and Genetics, Universiteit Gent = Ghent University [Belgium] (UGENT), Division of Molecular Immunology, Institute for Immunology, Department of Geological Sciences, University of Oregon [Eugene], Centers for Disease Control and Prevention [Atlanta] (CDC), Centers for Disease Control and Prevention, University of Colorado [Colorado Springs] (UCCS), FACS laboratory, Cancer Research, London, Cancer Research UK, Regeneration in Hematopoiesis and Animal Models of Hematopoiesis, Faculty of Medicine, Dresden University of Technology, Barbara Davis Center for Childhood Diabetes (BDC), University of Colorado Anschutz [Aurora], School of Computer and Electronic Information [Guangxi University], Guangxi University [Nanning], School of Materials Science and Engineering, Nanyang Technological University [Singapour], Max Planck Institute for Infection Biology (MPIIB), Max-Planck-Gesellschaft, Work in the laboratory of Dieter Adam is supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)—Projektnummer 125440785 – SFB 877, Project B2.Petra Hoffmann, Andrea Hauser, and Matthias Edinger thank BD Biosciences®, San José, CA, USA, and SKAN AG, Bale, Switzerland for fruitful cooperation during the development, construction, and installation of the GMP‐compliant cell sorting equipment and the Bavarian Immune Therapy Network (BayImmuNet) for financial support.Edwin van der Pol and Paola Lanuti acknowledge Aleksandra Gąsecka M.D. for excellent experimental support and Dr. Rienk Nieuwland for textual suggestions. This work was supported by the Netherlands Organisation for Scientific Research – Domain Applied and Engineering Sciences (NWO‐TTW), research program VENI 15924.Jessica G Borger, Kylie M Quinn, Mairi McGrath, and Regina Stark thank Francesco Siracusa and Patrick Maschmeyer for providing data.Larissa Nogueira Almeida was supported by DFG research grant MA 2273/14‐1. Rudolf A. Manz was supported by the Excellence Cluster 'Inflammation at Interfaces' (EXC 306/2).Susanne Hartmann and Friederike Ebner were supported by the German Research Foundation (GRK 2046).Hans Minderman was supported by NIH R50CA211108.This work was funded by the Deutsche Forschungsgemeinschaft through the grant TRR130 (project P11 and C03) to Thomas H. Winkler.Ramon Bellmàs Sanz, Jenny Kühne, and Christine S. Falk thank Jana Keil and Kerstin Daemen for excellent technical support. The work was funded by the Germany Research Foundation CRC738/B3 (CSF).The work by the Mei laboratory was supported by German Research Foundation Grant ME 3644/5‐1 and TRR130 TP24, the German Rheumatism Research Centre Berlin, European Union Innovative Medicines Initiative ‐ Joint Undertaking ‐ RTCure Grant Agreement 777357, the Else Kröner‐Fresenius‐Foundation, German Federal Ministry of Education and Research e:Med sysINFLAME Program Grant 01ZX1306B and KMU‐innovativ 'InnoCyt', and the Leibniz Science Campus for Chronic Inflammation (http://www.chronische-entzuendung.org).Axel Ronald Schulz, Antonio Cosma, Sabine Baumgart, Brice Gaudilliere, Helen M. McGuire, and Henrik E. Mei thank Michael D. Leipold for critically reading the manuscript.Christian Kukat acknowledges support from the ISAC SRL Emerging Leaders program.John Trowsdale received funding from the European Research Council under the European Union's Horizon 2020 research and innovation program (Grant Agreement 695551)., European Project: 7728036(1978), Università degli Studi di Modena e Reggio Emilia = University of Modena and Reggio Emilia (UNIMORE), Université Paris Cité (UPCité), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), Università degli Studi di Firenze = University of Florence (UniFI)-DENOTHE Center, Università degli Studi di Milano = University of Milan (UNIMI), Institut Pasteur [Paris] (IP)-Université Paris Diderot - Paris 7 (UPD7)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM), Humboldt University Of Berlin, Leibniz Research Institute for Environmental Medicine [Düsseldorf, Germany] (IUF), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Danmarks Tekniske Universitet = Technical University of Denmark (DTU), Universität Heidelberg [Heidelberg] = Heidelberg University, Universitäts Klinikum Freiburg = University Medical Center Freiburg (Uniklinik), University of Oxford-NIHR Biomedical Research Centre, Universität Bonn = University of Bonn, Università degli Studi di Firenze = University of Florence (UniFI), Università degli studi di Genova = University of Genoa (UniGe), Universidad de Salamanca, Università degli Studi di Roma 'La Sapienza' = Sapienza University [Rome] (UNIROMA), École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Université Paris Cité (UPCité), Johannes Gutenberg - Universität Mainz = Johannes Gutenberg University (JGU), Otto-von-Guericke-Universität Magdeburg = Otto-von-Guericke University [Magdeburg] (OVGU), Université de Lausanne = University of Lausanne (UNIL), Universität Leipzig, Universiteit Gent = Ghent University (UGENT), HZI,Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7,38124 Braunschweig, Germany., Cossarizza, A., Chang, H. -D., Radbruch, A., Acs, A., Adam, D., Adam-Klages, S., Agace, W. W., Aghaeepour, N., Akdis, M., Allez, M., Almeida, L. N., Alvisi, G., Anderson, G., Andra, I., Annunziato, F., Anselmo, A., Bacher, P., Baldari, C. T., Bari, S., Barnaba, V., Barros-Martins, J., Battistini, L., Bauer, W., Baumgart, S., Baumgarth, N., Baumjohann, D., Baying, B., Bebawy, M., Becher, B., Beisker, W., Benes, V., Beyaert, R., Blanco, A., Boardman, D. A., Bogdan, C., Borger, J. G., Borsellino, G., Boulais, P. E., Bradford, J. A., Brenner, D., Brinkman, R. R., Brooks, A. E. S., Busch, D. H., Buscher, M., Bushnell, T. P., Calzetti, F., Cameron, G., Cammarata, I., Cao, X., Cardell, S. L., Casola, S., Cassatella, M. A., Cavani, A., Celada, A., Chatenoud, L., Chattopadhyay, P. K., Chow, S., Christakou, E., Cicin-Sain, L., Clerici, M., Colombo, F. S., Cook, L., Cooke, A., Cooper, A. M., Corbett, A. J., Cosma, A., Cosmi, L., Coulie, P. G., Cumano, A., Cvetkovic, L., Dang, V. D., Dang-Heine, C., Davey, M. S., Davies, D., De Biasi, S., Del Zotto, G., Dela Cruz, G. V., Delacher, M., Della Bella, S., Dellabona, P., Deniz, G., Dessing, M., Di Santo, J. P., Diefenbach, A., Dieli, F., Dolf, A., Dorner, T., Dress, R. J., Dudziak, D., Dustin, M., Dutertre, C. -A., Ebner, F., Eckle, S. B. G., Edinger, M., Eede, P., Ehrhardt, G. R. A., Eich, M., Engel, P., Engelhardt, B., Erdei, A., Esser, C., Everts, B., Evrard, M., Falk, C. S., Fehniger, T. A., Felipo-Benavent, M., Ferry, H., Feuerer, M., Filby, A., Filkor, K., Fillatreau, S., Follo, M., Forster, I., Foster, J., Foulds, G. A., Frehse, B., Frenette, P. S., Frischbutter, S., Fritzsche, W., Galbraith, D. W., Gangaev, A., Garbi, N., Gaudilliere, B., Gazzinelli, R. T., Geginat, J., Gerner, W., Gherardin, N. A., Ghoreschi, K., Gibellini, L., Ginhoux, F., Goda, K., Godfrey, D. I., Goettlinger, C., Gonzalez-Navajas, J. M., Goodyear, C. S., Gori, A., Grogan, J. L., Grummitt, D., Grutzkau, A., Haftmann, C., Hahn, J., Hammad, H., Hammerling, G., Hansmann, L., Hansson, G., Harpur, C. M., Hartmann, S., Hauser, A., Hauser, A. E., Haviland, D. L., Hedley, D., Hernandez, D. C., Herrera, G., Herrmann, M., Hess, C., Hofer, T., Hoffmann, P., Hogquist, K., Holland, T., Hollt, T., Holmdahl, R., Hombrink, P., Houston, J. P., Hoyer, B. F., Huang, B., Huang, F. -P., Huber, J. E., Huehn, J., Hundemer, M., Hunter, C. A., Hwang, W. Y. K., Iannone, A., Ingelfinger, F., Ivison, S. M., Jack, H. -M., Jani, P. K., Javega, B., Jonjic, S., Kaiser, T., Kalina, T., Kamradt, T., Kaufmann, S. H. E., Keller, B., Ketelaars, S. L. C., Khalilnezhad, A., Khan, S., Kisielow, J., Klenerman, P., Knopf, J., Koay, H. -F., Kobow, K., Kolls, J. K., Kong, W. T., Kopf, M., Korn, T., Kriegsmann, K., Kristyanto, H., Kroneis, T., Krueger, A., Kuhne, J., Kukat, C., Kunkel, D., Kunze-Schumacher, H., Kurosaki, T., Kurts, C., Kvistborg, P., Kwok, I., Landry, J., Lantz, O., Lanuti, P., Larosa, F., Lehuen, A., LeibundGut-Landmann, S., Leipold, M. D., Leung, L. Y. T., Levings, M. K., Lino, A. C., Liotta, F., Litwin, V., Liu, Y., Ljunggren, H. -G., Lohoff, M., Lombardi, G., Lopez, L., Lopez-Botet, M., Lovett-Racke, A. E., Lubberts, E., Luche, H., Ludewig, B., Lugli, E., Lunemann, S., Maecker, H. T., Maggi, L., Maguire, O., Mair, F., Mair, K. H., Mantovani, A., Manz, R. A., Marshall, A. J., Martinez-Romero, A., Martrus, G., Marventano, I., Maslinski, W., Matarese, G., Mattioli, A. V., Maueroder, C., Mazzoni, A., Mccluskey, J., Mcgrath, M., Mcguire, H. M., Mcinnes, I. B., Mei, H. E., Melchers, F., Melzer, S., Mielenz, D., Miller, S. D., Mills, K. H. G., Minderman, H., Mjosberg, J., Moore, J., Moran, B., Moretta, L., Mosmann, T. R., Muller, S., Multhoff, G., Munoz, L. E., Munz, C., Nakayama, T., Nasi, M., Neumann, K., Ng, L. G., Niedobitek, A., Nourshargh, S., Nunez, G., O'Connor, J. -E., Ochel, A., Oja, A., Ordonez, D., Orfao, A., Orlowski-Oliver, E., Ouyang, W., Oxenius, A., Palankar, R., Panse, I., Pattanapanyasat, K., Paulsen, M., Pavlinic, D., Penter, L., Peterson, P., Peth, C., Petriz, J., Piancone, F., Pickl, W. F., Piconese, S., Pinti, M., Pockley, A. G., Podolska, M. J., Poon, Z., Pracht, K., Prinz, I., Pucillo, C. E. M., Quataert, S. A., Quatrini, L., Quinn, K. M., Radbruch, H., Radstake, T. R. D. J., Rahmig, S., Rahn, H. -P., Rajwa, B., Ravichandran, G., Raz, Y., Rebhahn, J. A., Recktenwald, D., Reimer, D., Reis e Sousa, C., Remmerswaal, E. B. M., Richter, L., Rico, L. G., Riddell, A., Rieger, A. M., Robinson, J. P., Romagnani, C., Rubartelli, A., Ruland, J., Saalmuller, A., Saeys, Y., Saito, T., Sakaguchi, S., Sala-de-Oyanguren, F., Samstag, Y., Sanderson, S., Sandrock, I., Santoni, A., Sanz, R. B., Saresella, M., Sautes-Fridman, C., Sawitzki, B., Schadt, L., Scheffold, A., Scherer, H. U., Schiemann, M., Schildberg, F. A., Schimisky, E., Schlitzer, A., Schlosser, J., Schmid, S., Schmitt, S., Schober, K., Schraivogel, D., Schuh, W., Schuler, T., Schulte, R., Schulz, A. R., Schulz, S. R., Scotta, C., Scott-Algara, D., Sester, D. P., Shankey, T. V., Silva-Santos, B., Simon, A. K., Sitnik, K. M., Sozzani, S., Speiser, D. E., Spidlen, J., Stahlberg, A., Stall, A. M., Stanley, N., Stark, R., Stehle, C., Steinmetz, T., Stockinger, H., Takahama, Y., Takeda, K., Tan, L., Tarnok, A., Tiegs, G., Toldi, G., Tornack, J., Traggiai, E., Trebak, M., Tree, T. I. M., Trotter, J., Trowsdale, J., Tsoumakidou, M., Ulrich, H., Urbanczyk, S., van de Veen, W., van den Broek, M., van der Pol, E., Van Gassen, S., Van Isterdael, G., van Lier, R. A. W., Veldhoen, M., Vento-Asturias, S., Vieira, P., Voehringer, D., Volk, H. -D., von Borstel, A., von Volkmann, K., Waisman, A., Walker, R. V., Wallace, P. K., Wang, S. A., Wang, X. M., Ward, M. D., Ward-Hartstonge, K. A., Warnatz, K., Warnes, G., Warth, S., Waskow, C., Watson, J. V., Watzl, C., Wegener, L., Weisenburger, T., Wiedemann, A., Wienands, J., Wilharm, A., Wilkinson, R. J., Willimsky, G., Wing, J. B., Winkelmann, R., Winkler, T. H., Wirz, O. F., Wong, A., Wurst, P., Yang, J. H. M., Yang, J., Yazdanbakhsh, M., Yu, L., Yue, A., Zhang, H., Zhao, Y., Ziegler, S. M., Zielinski, C., Zimmermann, J., Zychlinsky, A., UCL - SSS/DDUV - Institut de Duve, UCL - SSS/DDUV/GECE - Génétique cellulaire, Netherlands Organization for Scientific Research, German Research Foundation, European Commission, European Research Council, Repositório da Universidade de Lisboa, CCA - Imaging and biomarkers, Experimental Immunology, AII - Infectious diseases, AII - Inflammatory diseases, Biomedical Engineering and Physics, ACS - Atherosclerosis & ischemic syndromes, and Landsteiner Laboratory
Subjects: 0301 basic medicine, Consensus, Immunology, Consensu, Cell Separation, Biology, Article, Flow cytometry, 03 medical and health sciences, 0302 clinical medicine, Guidelines, Allergy and Immunology, medicine, Cell separation, Immunology and Allergy, Humans, guidelines, flow cytometry, immunology, medicine.diagnostic_test, BIOMEDICINE AND HEALTHCARE. Basic Medical Sciences, Cell sorting, Flow Cytometry, Cell selection, Data science, 3. Good health, 030104 developmental biology, Phenotype, [SDV.IMM]Life Sciences [q-bio]/Immunology, BIOMEDICINA I ZDRAVSTVO. Temeljne medicinske znanosti, 030215 immunology, Human
Abstract: All authors: Andrea Cossarizza Hyun‐Dong Chang Andreas Radbruch Andreas Acs Dieter Adam Sabine Adam‐Klages William W. Agace Nima Aghaeepour Mübeccel Akdis Matthieu Allez Larissa Nogueira Almeida Giorgia Alvisi Graham Anderson Immanuel Andrä Francesco Annunziato Achille Anselmo Petra Bacher Cosima T. Baldari Sudipto Bari Vincenzo Barnaba Joana Barros‐Martins Luca Battistini Wolfgang Bauer Sabine Baumgart Nicole Baumgarth Dirk Baumjohann Bianka Baying Mary Bebawy Burkhard Becher Wolfgang Beisker Vladimir Benes Rudi Beyaert Alfonso Blanco Dominic A. Boardman Christian Bogdan Jessica G. Borger Giovanna Borsellino Philip E. Boulais Jolene A. Bradford Dirk Brenner Ryan R. Brinkman Anna E. S. Brooks Dirk H. Busch Martin Büscher Timothy P. Bushnell Federica Calzetti Garth Cameron Ilenia Cammarata Xuetao Cao Susanna L. Cardell Stefano Casola Marco A. Cassatella Andrea Cavani Antonio Celada Lucienne Chatenoud Pratip K. Chattopadhyay Sue Chow Eleni Christakou Luka Čičin‐Šain Mario Clerici Federico S. Colombo Laura Cook Anne Cooke Andrea M. Cooper Alexandra J. Corbett Antonio Cosma Lorenzo Cosmi Pierre G. Coulie Ana Cumano Ljiljana Cvetkovic Van Duc Dang Chantip Dang‐Heine Martin S. Davey Derek Davies Sara De Biasi Genny Del Zotto Gelo Victoriano Dela Cruz Michael Delacher Silvia Della Bella Paolo Dellabona Günnur Deniz Mark Dessing James P. Di Santo Andreas Diefenbach Francesco Dieli Andreas Dolf Thomas Dörner Regine J. Dress Diana Dudziak Michael Dustin Charles‐Antoine Dutertre Friederike Ebner Sidonia B. G. Eckle Matthias Edinger Pascale Eede Götz R.A. Ehrhardt Marcus Eich Pablo Engel Britta Engelhardt Anna Erdei Charlotte Esser Bart Everts Maximilien Evrard Christine S. Falk Todd A. Fehniger Mar Felipo‐Benavent Helen Ferry Markus Feuerer Andrew Filby Kata Filkor Simon Fillatreau Marie Follo Irmgard Förster John Foster Gemma A. Foulds Britta Frehse Paul S. Frenette Stefan Frischbutter Wolfgang Fritzsche David W. Galbraith Anastasia Gangaev Natalio Garbi Brice Gaudilliere Ricardo T. Gazzinelli Jens Geginat Wilhelm Gerner Nicholas A. Gherardin Kamran Ghoreschi Lara Gibellini Florent Ginhoux Keisuke Goda Dale I. Godfrey Christoph Goettlinger Jose M. González‐Navajas Carl S. Goodyear Andrea Gori Jane L. Grogan Daryl Grummitt Andreas Grützkau Claudia Haftmann Jonas Hahn Hamida Hammad Günter Hämmerling Leo Hansmann Goran Hansson Christopher M. Harpur Susanne Hartmann Andrea Hauser Anja E. Hauser David L. Haviland David Hedley Daniela C. Hernández Guadalupe Herrera Martin Herrmann Christoph Hess Thomas Höfer Petra Hoffmann Kristin Hogquist Tristan Holland Thomas Höllt Rikard Holmdahl Pleun Hombrink Jessica P. Houston Bimba F. Hoyer Bo Huang Fang‐Ping Huang Johanna E. Huber Jochen Huehn Michael Hundemer Christopher A. Hunter William Y. K. Hwang Anna Iannone Florian Ingelfinger Sabine M Ivison Hans‐Martin Jäck Peter K. Jani Beatriz Jávega Stipan Jonjic Toralf Kaiser Tomas Kalina Thomas Kamradt Stefan H. E. Kaufmann Baerbel Keller Steven L. C. Ketelaars Ahad Khalilnezhad Srijit Khan Jan Kisielow Paul Klenerman Jasmin Knopf Hui‐Fern Koay Katja Kobow Jay K. Kolls Wan Ting Kong Manfred Kopf Thomas Korn Katharina Kriegsmann Hendy Kristyanto Thomas Kroneis Andreas Krueger Jenny Kühne Christian Kukat Désirée Kunkel Heike Kunze‐Schumacher Tomohiro Kurosaki Christian Kurts Pia Kvistborg Immanuel Kwok Jonathan Landry Olivier Lantz Paola Lanuti Francesca LaRosa Agnès Lehuen Salomé LeibundGut‐Landmann Michael D. Leipold Leslie Y.T. Leung Megan K. Levings Andreia C. Lino Francesco Liotta Virginia Litwin Yanling Liu Hans‐Gustaf Ljunggren Michael Lohoff Giovanna Lombardi Lilly Lopez Miguel López‐Botet Amy E. Lovett‐Racke Erik Lubberts Herve Luche Burkhard Ludewig Enrico Lugli Sebastian Lunemann Holden T. Maecker Laura Maggi Orla Maguire Florian Mair Kerstin H. Mair Alberto Mantovani Rudolf A. Manz Aaron J. Marshall Alicia Martínez‐Romero Glòria Martrus Ivana Marventano Wlodzimierz Maslinski Giuseppe Matarese Anna Vittoria Mattioli Christian Maueröder Alessio Mazzoni James McCluskey Mairi McGrath Helen M. McGuire Iain B. McInnes Henrik E. Mei Fritz Melchers Susanne Melzer Dirk Mielenz Stephen D. Miller Kingston H.G. Mills Hans Minderman Jenny Mjösberg Jonni Moore Barry Moran Lorenzo Moretta Tim R. Mosmann Susann Müller Gabriele Multhoff Luis Enrique Muñoz Christian Münz Toshinori Nakayama Milena Nasi Katrin Neumann Lai Guan Ng Antonia Niedobitek Sussan Nourshargh Gabriel Núñez José‐Enrique O'Connor Aaron Ochel Anna Oja Diana Ordonez Alberto Orfao Eva Orlowski‐Oliver Wenjun Ouyang Annette Oxenius Raghavendra Palankar Isabel Panse Kovit Pattanapanyasat Malte Paulsen Dinko Pavlinic Livius Penter Pärt Peterson Christian Peth Jordi Petriz Federica Piancone Winfried F. Pickl Silvia Piconese Marcello Pinti A. Graham Pockley Malgorzata Justyna Podolska Zhiyong Poon Katharina Pracht Immo Prinz Carlo E. M. Pucillo Sally A. Quataert Linda Quatrini Kylie M. Quinn Helena Radbruch Tim R. D. J. Radstake Susann Rahmig Hans‐Peter Rahn Bartek Rajwa Gevitha Ravichandran Yotam Raz Jonathan A. Rebhahn Diether Recktenwald Dorothea Reimer Caetano Reis e Sousa Ester B.M. Remmerswaal Lisa Richter Laura G. Rico Andy Riddell Aja M. Rieger J. Paul Robinson Chiara Romagnani Anna Rubartelli Jürgen Ruland Armin Saalmüller Yvan Saeys Takashi Saito Shimon Sakaguchi Francisco Sala‐de‐Oyanguren Yvonne Samstag Sharon Sanderson Inga Sandrock Angela Santoni Ramon Bellmàs Sanz Marina Saresella Catherine Sautes‐Fridman Birgit Sawitzki Linda Schadt Alexander Scheffold Hans U. Scherer Matthias Schiemann Frank A. Schildberg Esther Schimisky Andreas Schlitzer Josephine Schlosser Stephan Schmid Steffen Schmitt Kilian Schober Daniel Schraivogel Wolfgang Schuh Thomas Schüler Reiner Schulte Axel Ronald Schulz Sebastian R. Schulz Cristiano Scottá Daniel Scott‐Algara David P. Sester T. Vincent Shankey Bruno Silva‐Santos Anna Katharina Simon Katarzyna M. Sitnik Silvano Sozzani Daniel E. Speiser Josef Spidlen Anders Stahlberg Alan M. Stall Natalie Stanley Regina Stark Christina Stehle Tobit Steinmetz Hannes Stockinger Yousuke Takahama Kiyoshi Takeda Leonard Tan Attila Tárnok Gisa Tiegs Gergely Toldi Julia Tornack Elisabetta Traggiai Mohamed Trebak Timothy I.M. Tree Joe Trotter John Trowsdale Maria Tsoumakidou Henning Ulrich Sophia Urbanczyk Willem van de Veen Maries van den Broek Edwin van der Pol Sofie Van Gassen Gert Van Isterdael René A.W. van Lier Marc Veldhoen Salvador Vento‐Asturias Paulo Vieira David Voehringer Hans‐Dieter Volk Anouk von Borstel Konrad von Volkmann Ari Waisman Rachael V. Walker Paul K. Wallace Sa A. Wang Xin M. Wang Michael D. Ward Kirsten A Ward‐Hartstonge Klaus Warnatz Gary Warnes Sarah Warth Claudia Waskow James V. Watson Carsten Watzl Leonie Wegener Thomas Weisenburger Annika Wiedemann Jürgen Wienands Anneke Wilharm Robert John Wilkinson Gerald Willimsky James B. Wing Rieke Winkelmann Thomas H. Winkler Oliver F. Wirz Alicia Wong Peter Wurst Jennie H. M. Yang Juhao Yang Maria Yazdanbakhsh Liping Yu Alice Yue Hanlin Zhang Yi Zhao Susanne Maria Ziegler Christina Zielinski Jakob Zimmermann Arturo Zychlinsky., These guidelines are a consensus work of a considerable number of members of the immunology and flow cytometry community. They provide the theory and key practical aspects of flow cytometry enabling immunologists to avoid the common errors that often undermine immunological data. Notably, there are comprehensive sections of all major immune cell types with helpful Tables detailing phenotypes in murine and human cells. The latest flow cytometry techniques and applications are also described, featuring examples of the data that can be generated and, importantly, how the data can be analysed. Furthermore, there are sections detailing tips, tricks and pitfalls to avoid, all written and peer‐reviewed by leading experts in the field, making this an essential research companion., This work was supported by the Netherlands Organisation for Scientific Research – Domain Applied and Engineering Sciences (NWO-TTW), research program VENI 15924. This work was funded by the Deutsche Forschungsgemeinschaft. European Union Innovative Medicines Initiative - Joint Undertaking - RTCure Grant Agreement 777357 and innovation program (Grant Agreement 695551).
Published: 2019

22. Minimal epitope for Mannitou IgM on paucimannose-carrying glycoproteins

Author: Ana Gimeno, Jesús Jiménez-Barbero, Stefania Robakiewicz, Sandra Delgado, Clarisse Bridot, Begoña Echeverria, Ann Dansercoer, Nicola G. A. Abrescia, Jérôme de Ruyck, Sonia Serna, Shubham Semwal, Mikel Azkargorta, Ruud H. P. Wilbers, Ana Ardá, Savvas N. Savvides, Diego Charro, Niels C. Reichardt, Kenneth Verstraete, Julie Bouckaert, Kim van Noort, Unité de Glycobiologie Structurale et Fonctionnelle UMR 8576 (UGSF), Institut National de la Recherche Agronomique (INRA)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Unité de Glycobiologie Structurale et Fonctionnelle (UGSF), Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centro de Investigación Cooperativa en Biomateriales (CIC biomaGUNE), Cell Biology and Stem Cells Unit (CICbioGUNE), Technologic Park of Bizkaia, VIB-UGent Center for Inflammation Research [Gand, Belgique] (IRC), VIB [Belgium], Wageningen University and Research [Wageningen] (WUR), Biomedical Research Networking Center in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Instituto de Salud Carlos III [Madrid] (ISC)-ministerio de ciencia e innovacion, Université de Lille-Centre National de la Recherche Scientifique (CNRS), Unité de Glycobiologie Structurale et Fonctionnelle - UMR 8576 (UGSF), Université de Lille, CNRS, Unité de Glycobiologie Structurale et Fonctionnelle (UGSF) - UMR 8576, Centro de Investigación Cooperativa en Biomateriales [CIC biomaGUNE], Cell Biology and Stem Cells Unit [CICbioGUNE], VIB-UGent Center for Inflammation Research [Gand, Belgique] [IRC], Wageningen University and Research [Wageningen] [WUR], Unité de Glycobiologie Structurale et Fonctionnelle UMR 8576 [UGSF], and Biomedical Research Networking Center in Bioengineering, Biomaterials and Nanomedicine [CIBER-BBN]
Subjects: [SDV]Life Sciences [q-bio], Mannose, Biochemistry, Epitope, Epitopes, Mice, chemistry.chemical_compound, 0302 clinical medicine, Mannitou, N-linked glycosylation, BINDING, Medicine and Health Sciences, AFFINITY, Mammals, chemistry.chemical_classification, 0303 health sciences, biology, PROLIFERATION, paucimannosidic epitopes, Schistosoma mansoni, N-GLYCOSYLATION, CANCER, 3. Good health, DNA-Binding Proteins, GLYCAN MICROARRAYS, 030220 oncology & carcinogenesis, N-glycan, Antibody, Glycan, core fucose, IgM, CORE FUCOSYLATION, 03 medical and health sciences, Antigen, Polysaccharides, Animals, Humans, Laboratorium voor Nematologie, Fucose, Glycoproteins, 030304 developmental biology, Membrane Proteins, Biology and Life Sciences, IgM binding, Immunoglobulin M, chemistry, ANTIBODIES, biology.protein, Laboratory of Nematology, Glycoprotein, ELASTASE
Abstract: Paucimannosidic glycans are restricted to the core structure [Man1–3GlcNAc2Fuc0–1] of N-glycans and are rarely found in mammalian tissues. Yet, especially [Man2-3GlcNAc2Fuc1] have been found significantly upregulated in tumors, including in colorectal and liver cancer. Mannitou IgM is a murine monoclonal antibody that was previously shown to recognize Man3GlcNAc2 with an almost exclusive selectivity. Here, we have sought the definition of the minimal glycan epitope of Mannitou IgM, initiated by screening on a newly designed paucimannosidic glycan microarray; among the best binders were Man3GlcNAc2 and its α1,6 core-fucosylated variant, Man3GlcNAc2Fuc1. Unexpectedly and in contrast to earlier findings, Man5GlcNAc2-type structures bind equally well and a large tolerance was observed for substitutions on the α1,6 arm. It was confirmed that any substitution on the single α1,3-linked mannose completely abolishes binding. Surface plasmon resonance for kinetic measurements of Mannitou IgM binding, either directly on the glycans or as presented on omega-1 and kappa-5 soluble egg antigens from the helminth parasite Schistosoma mansoni, showed submicromolar affinities. To characterize the epitope in greater and atomic detail, saturation transfer difference nuclear magnetic resonance spectroscopy was performed with the Mannitou antigen-binding fragment. The STD-NMR data demonstrated the strongest interactions with the aliphatic protons H1 and H2 of the α1–3-linked mannose and weaker imprints on its H3, H4 and H5 protons. In conclusion, Mannitou IgM binding requires a nonsubstituted α1,3-linked mannose branch of paucimannose also on proteins, making it a highly specific tool for the distinction of concurrent human tumor-associated carbohydrate antigens.
Published: 2021

23. ILC3s control splenic cDC homeostasis via lymphotoxin signaling

Author: Eric Vivier, Marco De Giovanni, Alexei V. Tumanov, Antonio Pires da Silva Baptista, Jason G. Cyster, Paula S. Norris, Carl De Trez, Gérard Eberl, Carl F. Ware, Yvan Saeys, Robin Browaeys, James P. Di Santo, Bart N. Lambrecht, Matthias Vanderkerken, Satoshi Fukuyama, Hamida Hammad, Charlotte L. Scott, VIB-UGent Center for Inflammation Research [Gand, Belgique] (IRC), VIB [Belgium], Universiteit Gent = Ghent University (UGENT), University of California [San Francisco] (UC San Francisco), University of California (UC), The University of Tokyo (UTokyo), Sanford Burnham Prebys Medical Discovery Institute, Microenvironnement et Immunité - Microenvironment and Immunity, Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM), Immunité Innée - Innate Immunity, Innate Pharma, Centre d'Immunologie de Marseille - Luminy (CIML), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), University of Texas Health Science Center, The University of Texas Health Science Center at Houston (UTHealth), Vrije Universiteit Brussel (VUB), Erasmus University Medical Center [Rotterdam] (Erasmus MC), M. Vanderkerken is supported by a fellowship from Fonds Wetenschappelijk Onderzoek Vlaanderen, A.P. Baptista is supported by a Marie-Sklodowska Curie Action fellowship as part of Horizon 2020, C.L. Scott is supported by the Fonds Wetenschappelijk Onderzoek Vlaanderen and a European Research Council starting grant, Y. Saeys is supported by the Fonds Wetenschappelijk Onderzoek Vlaanderen and the Marylou Ingram Scholar program, H. Hammad is supported by a research initiative grant from Ghent University, A.V. Tumanov is supported by grants from the National Institutes of Health (AI135574) and the Max and Minnie Tomerlin Voelcker Fund, and B.N. Lambrecht is supported by a European Research Council advanced grant, a research initiative grant from Ghent University, and an Excellence of Science research grant., Universiteit Gent = Ghent University [Belgium] (UGENT), University of California [San Francisco] (UCSF), University of California, Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU), Pulmonary Medicine, HUGOT, Bérengère, Department of Bio-engineering Sciences, and Cellular and Molecular Immunology
Subjects: 0301 basic medicine, BETA-RECEPTOR, SUBSETS, ZONE, Inbred C57BL, Medical and Health Sciences, Transgenic, Mice, 0302 clinical medicine, Immunologic, Group F, Receptors, Medicine and Health Sciences, Innate, Immunology and Allergy, R PACKAGE, Receptors, Immunologic, Lymphotoxin-alpha, Mice, Knockout, Innate lymphoid cell, Nuclear Receptor Subfamily 1, Group F, Member 3, Acquired immune system, 3. Good health, Cell biology, Infectious Diseases, medicine.anatomical_structure, B-CELLS, [SDV.IMM]Life Sciences [q-bio]/Immunology, Female, Signal transduction, Signal Transduction, EXPRESSION, [SDV.IMM] Life Sciences [q-bio]/Immunology, Nuclear Receptor Subfamily 1, Member 3, Lymphoid Tissue, Knockout, 1.1 Normal biological development and functioning, Innate Immunity and Inflammation, Immunology, INNATE LYMPHOID-CELLS, Mice, Transgenic, Spleen, Biology, Vaccine Related, 03 medical and health sciences, Immune system, SUBCAPSULAR SINUS MACROPHAGES, Underpinning research, Lymphotoxin beta Receptor, Biodefense, medicine, Animals, Prevention, Immunity, Brief Definitive Report, Biology and Life Sciences, IN-VITRO, Dendritic Cells, Immunity, Innate, Mice, Inbred C57BL, CONVENTIONAL DENDRITIC CELLS, Emerging Infectious Diseases, Good Health and Well Being, 030104 developmental biology, Lymphotoxin, Cell Adhesion Molecules, 030217 neurology & neurosurgery, Conventional Dendritic Cell, Homeostasis
Abstract: Conventional dendritic cells (cDCs) bridge antigen detection to the induction of adaptive immunity, playing crucial roles in host defense. Vanderkerken, Baptista, et al. show that LTα1β2-expressing ILC3s, together with B cells, control the size of the splenic cDC compartment and cDC2 differentiation., The spleen contains a myriad of conventional dendritic cell (cDC) subsets that protect against systemic pathogen dissemination by bridging antigen detection to the induction of adaptive immunity. How cDC subsets differentiate in the splenic environment is poorly understood. Here, we report that LTα1β2-expressing Rorgt+ ILC3s, together with B cells, control the splenic cDC niche size and the terminal differentiation of Sirpα+CD4+Esam+ cDC2s, independently of the microbiota and of bone marrow pre-cDC output. Whereas the size of the splenic cDC niche depended on lymphotoxin signaling only during a restricted time frame, the homeostasis of Sirpα+CD4+Esam+ cDC2s required continuous lymphotoxin input. This latter property made Sirpα+CD4+Esam+ cDC2s uniquely susceptible to pharmacological interventions with LTβR agonists and antagonists and to ILC reconstitution strategies. Together, our findings demonstrate that LTα1β2-expressing Rorgt+ ILC3s drive splenic cDC differentiation and highlight the critical role of ILC3s as perpetual regulators of lymphoid tissue homeostasis.
Published: 2021

24. Immune Monitoring in Melanoma and Urothelial Cancer Patients Treated with Anti-PD-1 Immunotherapy and SBRT Discloses Tumor Specific Immune Signatures

Author: Sylvie Rottey, Mathieu Spaas, Simon J. Tavernier, Liesbeth Ferdinande, Karel Decaestecker, Annelies Demeyer, Sofie Van Gassen, Piet Ost, Annabel Meireson, Lieve Brochez, Vibeke Kruse, Benjamin Hennart, Filomeen Haerynck, Jo Van Dorpe, Nora Sundahl, Delphine Allorge, Yvan Saeys, CHU Lille, Institut Pasteur de Lille, Université de Lille, Universiteit Gent = Ghent University [UGENT], IMPact de l'Environnement Chimique sur la Santé humaine (IMPECS) - ULR 4483, Ghent University Hospital, Vlaams Instituut voor Biotechnologie [Ghent, Belgique] [VIB], VIB-UGent Center for Inflammation Research [Gand, Belgique] [IRC], Impact de l'environnement chimique sur la santé humaine - ULR 4483 [IMPECS], Universiteit Gent = Ghent University (UGENT), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), VIB-UGent Center for Inflammation Research [Gand, Belgique] (IRC), VIB [Belgium], Impact de l'environnement chimique sur la santé humaine - ULR 4483 (IMPECS), and Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)
Subjects: EXPRESSION, PD-L1, 0301 basic medicine, Oncology, Cancer Research, medicine.medical_specialty, Myeloid, immune monitoring, [SDV]Life Sciences [q-bio], medicine.medical_treatment, MONOTHERAPY, MULTICENTER, Pembrolizumab, immunotherapy, anti-PD-1, melanoma, urothelial cancer, blood biomarkers, THERAPY, Article, 03 medical and health sciences, 0302 clinical medicine, Internal medicine, Medicine and Health Sciences, medicine, Progression-free survival, Neutrophil to lymphocyte ratio, PEMBROLIZUMAB, RC254-282, biology, business.industry, Melanoma, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, Biology and Life Sciences, NIVOLUMAB, Immunotherapy, medicine.disease, FDA APPROVAL, 030104 developmental biology, medicine.anatomical_structure, 030220 oncology & carcinogenesis, T-CELLS, biology.protein, Nivolumab, BURDEN, business
Abstract: Simple Summary Currently available biomarkers for response to checkpoint inhibitors are incomplete and predominantly focus on tumor tissue analysis e.g., tumor mutational burden, programmed cell death-ligand 1 (PD-L1) expression. Biomarkers in peripheral blood would allow a more dynamic monitoring and could offer a way for sequential adaptation of treatment strategy. We conducted an in-depth analysis of baseline and on-treatment systemic immune features in a cohort of stage III/IV melanoma and stage IV urothelial cancer (UC) patients treated with anti-programmed cell death-1 (anti-PD-1) therapy combined with stereotactic body radiotherapy (SBRT) in a similar regimen/schedule. Baseline immunity was clearly different between these two cohorts, indicating a less active immune landscape in UC patients. This study also detected signatures of proliferation in the CD8+ T-cell compartment pre-treatment and early after anti-PD-1 initiation that were positively correlated with clinical outcome in both tumor types. In addition our data support the biological relevance of PD-1/PD-L1 expression on circulating immune cell subsets, especially in melanoma. Abstract (1) Background: Blockade of the PD-1/PD-L1 pathway has revolutionized the oncology field in the last decade. However, the proportion of patients experiencing a durable response is still limited. In the current study, we performed an extensive immune monitoring in patients with stage III/IV melanoma and stage IV UC who received anti-PD-1 immunotherapy with SBRT. (2) Methods: In total 145 blood samples from 38 patients, collected at fixed time points before and during treatment, were phenotyped via high-parameter flow cytometry, luminex assay and UPLC-MS/MS. (3) Results: Baseline systemic immunity in melanoma and UC patients was different with a more prominent myeloid compartment and a higher neutrophil to lymphocyte ratio in UC. Proliferation (Ki67+) of CD8+ T-cells and of the PD-1+/PD-L1+ CD8+ subset at baseline correlated with progression free survival in melanoma. In contrast a higher frequency of PD-1/PD-L1 expressing non-proliferating (Ki67−) CD8+ and CD4+ T-cells before treatment was associated with worse outcome in melanoma. In UC, the expansion of Ki67+ CD8+ T-cells and of the PD-L1+ subset relative to tumor burden correlated with clinical outcome. (4) Conclusion: This study reveals a clearly different immune landscape in melanoma and UC at baseline, which may impact immunotherapy response. Signatures of proliferation in the CD8+ T-cell compartment prior to and early after anti-PD-1 initiation were positively correlated with clinical outcome in both cohorts. PD-1/PD-L1 expression on circulating immune cell subsets seems of clinical relevance in the melanoma cohort.
Published: 2021

25. Megabodies expand the nanobody toolkit for protein structure determination by single-particle cryo-EM

Author: Alexandre Wohlkonig, Hugues Nury, Baptiste Fischer, Tomasz Uchański, Eleftherios Zarkadas, Philip N. Ward, Thomas Zögg, Wim F. Vranken, Uriel López-Sánchez, Han Remaut, Jan Steyaert, S. Masiulis, A. Radu Aricescu, Valentina Kalichuk, Els Pardon, Andrija Sente, Miriam Weckener, James H. Naismith, Department of Bio-engineering Sciences, Structural Biology Brussels, Basic (bio-) Medical Sciences, Chemistry, Informatics and Applied Informatics, VIB-VUB Center for Structural Biology [Bruxelles], and VIB [Belgium]
Subjects: Scaffold protein, Models, Molecular, Materials science, Cryo-electron microscopy, Protein Conformation, [SDV]Life Sciences [q-bio], Immunoglobulin domain, Yeast display, Biochemistry, Article, 03 medical and health sciences, Protein structure, Humans, Molecular Biology, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, Molecular Structure, Resolution (electron density), Cryoelectron Microscopy, Cell Biology, Single-Domain Antibodies, Receptors, GABA-A, Lipids, Single Molecule Imaging, Structural biology, Membrane protein, Multiprotein Complexes, Biophysics, Single-Cell Analysis, Biotechnology
Abstract: Nanobodies are popular and versatile tools for structural biology. They have a compact single immunoglobulin domain organization, bind target proteins with high affinities while reducing their conformational heterogeneity and stabilize multi-protein complexes. Here we demonstrate that engineered nanobodies can also help overcome two major obstacles that limit the resolution of single-particle cryo-electron microscopy reconstructions: particle size and preferential orientation at the water-air interfaces. We have developed and characterized constructs, termed megabodies, by grafting nanobodies onto selected protein scaffolds to increase their molecular weight while retaining the full antigen-binding specificity and affinity. We show that the megabody design principles are applicable to different scaffold proteins and recognition domains of compatible geometries and are amenable for efficient selection from yeast display libraries. Moreover, we demonstrate that megabodies can be used to obtain three-dimensional reconstructions for membrane proteins that suffer from severe preferential orientation or are otherwise too small to allow accurate particle alignment.
Published: 2021

26. Genome-wide association study of Alzheimer's disease CSF biomarkers in the EMIF-AD Multimodal Biomarker Discovery dataset

Author: Pablo Martinez-Lage, Ulf Andreasson, Richard Dobson, Ellis Niemantsverdriet, Fabian Kilpert, Mikel Tainta, Michael Wittig, Mara ten Kate, Simon Lovestone, Lars Bertram, Henrik Zetterberg, Stephanie J.B. Vos, Dmitry Prokopenko, Frederik Barkhof, Jolien Schaeverbeke, Philip Scheltens, Shengjun Hong, Jill C. Richardson, Olivier Blin, Valerija Dobricic, Pieter Jelle Visser, Silvy Gabel, Cristina Legido-Quigley, Giovanni B. Frisoni, Johannes Streffer, Isabel Sala, Sebastiaan Engelborghs, José Luis Molinuevo, Andre Franke, Alberto Lleó, Isabelle Bos, Rudolph E. Tanzi, Lorena Rami, Kristel Sleegers, Betty M. Tijms, Régis Bordet, Charlotte E. Teunissen, Petronella Kettunen, Rik Vandenberghe, Julius Popp, Isabelle Cleynen, Gwendoline Peyratout, Kaj Blennow, Anders Wallin, Christine Van Broeckhoven, Psychiatrie & Neuropsychologie, RS: MHeNs - R1 - Cognitive Neuropsychiatry and Clinical Neuroscience, Alzheimers Dis Neuroimaging Initia, Universität zu Lübeck = University of Lübeck [Lübeck], Massachusetts General Hospital [Boston], Maastricht University [Maastricht], Vrije Universiteit Amsterdam [Amsterdam] (VU), University of Gothenburg (GU), Sahlgrenska University Hospital [Gothenburg], Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), University Hospitals Leuven [Leuven], University of Antwerp (UA), Vrije Universiteit Brussel (VUB), Université de Genève = University of Geneva (UNIGE), Istituto Centro San Giovanni di Dio Fatebenefratelli, Partenaires INRAE, Institut de Neurosciences des Systèmes (INS), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), GlaxoSmithKline [Stevenage, UK] (GSK), GlaxoSmithKline [Headquarters, London, UK] (GSK), CHU Lille, Université de Lille, Clinic Barcelona Hospital Universitari, University of Oxford, Centro de Investigacion Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III [Madrid] (ISC), Geneva University Hospital (HUG), Lausanne University Hospital, Center for Research and Advanced Therapies CITA-Alzheimer Foundation [San Sebastián], King‘s College London, University College of London [London] (UCL), Steno Diabetes Center, VIB [Belgium], Amsterdam UMC - Amsterdam University Medical Center, UCL Institute of Neurology, Queen Square [London], UK Dementia Research Institute (UK DRI), UCB BioPharma [Braine l’Alleud, Belgium], Christian-Albrechts University of Kiel, University of Oslo (UiO), Alzheimer's Disease Neuroimaging Initiative (ADNI), Amsterdam Neuroscience - Neurodegeneration, Neurology, Laboratory Medicine, Radiology and nuclear medicine, Clinical sciences, Neuroprotection & Neuromodulation, and Pathologic Biochemistry and Physiology
Subjects: 0301 basic medicine, Male, Genome-wide association study, 0302 clinical medicine, RISK VARIANTS, Biomarker discovery, MIF-AD Multimodal Biomarker Discovery dataset, Psychiatry, Alzheimer's disease, Psychiatry and Mental health, Female, Life Sciences & Biomedicine, SUSCEPTIBILITY LOCI, Neuroscience(all), Single-nucleotide polymorphism, Genomics, tau Proteins, Computational biology, Biology, Molecular neuroscience, elderly, Article, lcsh:RC321-571, 03 medical and health sciences, Cellular and Molecular Neuroscience, Alzheimer Disease, medicine, Dementia, SNP, Humans, CSF biomarkers, lcsh:Neurosciences. Biological psychiatry. Neuropsychiatry, Biological Psychiatry, Aged, Amyloid beta-Peptides, Science & Technology, business.industry, [SCCO.NEUR]Cognitive science/Neuroscience, Neurodegenerative disorder, medicine.disease, Personalized medicine, Genetic architecture, Peptide Fragments, 030104 developmental biology, Human medicine, TAU, business, 030217 neurology & neurosurgery, Biomarkers, dementia, Genome-Wide Association Study
Abstract: Alzheimer’s disease (AD) is the most prevalent neurodegenerative disorder and the most common form of dementia in the elderly. Susceptibility to AD is considerably determined by genetic factors which hitherto were primarily identified using case–control designs. Elucidating the genetic architecture of additional AD-related phenotypic traits, ideally those linked to the underlying disease process, holds great promise in gaining deeper insights into the genetic basis of AD and in developing better clinical prediction models. To this end, we generated genome-wide single-nucleotide polymorphism (SNP) genotyping data in 931 participants of the European Medical Information Framework Alzheimer’s Disease Multimodal Biomarker Discovery (EMIF-AD MBD) sample to search for novel genetic determinants of AD biomarker variability. Specifically, we performed genome-wide association study (GWAS) analyses on 16 traits, including 14 measures derived from quantifications of five separate amyloid-beta (Aβ) and tau-protein species in the cerebrospinal fluid (CSF). In addition to confirming the well-established effects of apolipoprotein E (APOE) on diagnostic outcome and phenotypes related to Aβ42, we detected novel potential signals in the zinc finger homeobox 3 (ZFHX3) for CSF-Aβ38 and CSF-Aβ40 levels, and confirmed the previously described sex-specific association between SNPs in geminin coiled-coil domain containing (GMNC) and CSF-tau. Utilizing the results from independent case–control AD GWAS to construct polygenic risk scores (PRS) revealed that AD risk variants only explain a small fraction of CSF biomarker variability. In conclusion, our study represents a detailed first account of GWAS analyses on CSF-Aβ and -tau-related traits in the EMIF-AD MBD dataset. In subsequent work, we will utilize the genomics data generated here in GWAS of other AD-relevant clinical outcomes ascertained in this unique dataset.
Published: 2020

27. Maize specialized metabolome networks reveal organ-preferential mixed glycosides

Author: Ruben Vanholme, Claudiu Niculaes, John Ralph, Hoon Kim, Atsushi Fukushima, Rebecca Dauwe, Wout Boerjan, Sandrien Desmet, Kris Morreel, Geert Goeminne, Yvan Saeys, Kevin Verstaen, Department of plant Biotechnology and Bioinformatics, Universiteit Gent = Ghent University (UGENT), Flanders Institute for Biotechnology, VIB-UGent Center for Inflammation Research [Gand, Belgique] (IRC), VIB [Belgium], Biologie des Plantes et Innovation - UR UPJV 3900 (BIOPI), Université de Picardie Jules Verne (UPJV)-Transfrontalière BioEcoAgro - UMR 1158 (BioEcoAgro), Université d'Artois (UA)-Université de Liège-Université de Picardie Jules Verne (UPJV)-Université du Littoral Côte d'Opale (ULCO)-Université de Lille-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-JUNIA (JUNIA), Université catholique de Lille (UCL)-Université catholique de Lille (UCL)-Université d'Artois (UA)-Université de Liège-Université du Littoral Côte d'Opale (ULCO)-Université de Lille-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-JUNIA (JUNIA), Université catholique de Lille (UCL)-Université catholique de Lille (UCL), Department of Pharmacy, and Research Institute of Life Pharmaceutical Sciences, Sunchon National University, Suncheon 57922, Republic of Korea, John Innes Centre [Norwich], Biotechnology and Biological Sciences Research Council (BBSRC), RIKEN Center for Sustainable Resource Science [Yokohama] (RIKEN CSRS), RIKEN - Institute of Physical and Chemical Research [Japon] (RIKEN), Center for Plant Systems Biology (PSB Center), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), University of Wisconsin-Madison, and Department of Plant Systems Biology, VIB, and Department of Plant Biotechnology and Bioinformatics
Subjects: Agriculture and Food Sciences, PREDICTION, Systems biology, [SDV]Life Sciences [q-bio], Biophysics, DIVERSITY, Spectral metadata analysis, Computational biology, Biochemistry, Zea mays, ANNOTATION, Specialized metabolism, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, Structural Biology, Arabidopsis, Genetics, Metabolome, Glycosyl, AUXIN BIOSYNTHESIS, ComputingMethodologies_COMPUTERGRAPHICS, 030304 developmental biology, chemistry.chemical_classification, 0303 health sciences, Phenylpropanoid, biology, Mass spectrometry, IDENTIFICATION, ELUCIDATION, Glycoside, Biology and Life Sciences, MASS-SPECTROMETRY, biology.organism_classification, ARABIDOPSIS, Computer Science Applications, ddc, Metabolic pathway, chemistry, 030220 oncology & carcinogenesis, Acyltransferase, FRAGMENTATION, PHENYLACETIC ACID, TP248.13-248.65, Research Article, Biotechnology
Abstract: Graphical abstract, Despite the scientific and economic importance of maize, little is known about its specialized metabolism. Here, five maize organs were profiled using different reversed-phase liquid chromatography-mass spectrometry methods. The resulting spectral metadata, combined with candidate substrate-product pair (CSPP) networks, allowed the structural characterization of 427 of the 5,420 profiled compounds, including phenylpropanoids, flavonoids, benzoxazinoids, and auxin-related compounds, among others. Only 75 of the 427 compounds were already described in maize. Analysis of the CSPP networks showed that phenylpropanoids are present in all organs, whereas other metabolic classes are rather organ-enriched. Frequently occurring CSPP mass differences often corresponded with glycosyl- and acyltransferase reactions. The interplay of glycosylations and acylations yields a wide variety of mixed glycosides, bearing substructures corresponding to the different biochemical classes. For example, in the tassel, many phenylpropanoid and flavonoid-bearing glycosides also contain auxin-derived moieties. The characterized compounds and mass differences are an important step forward in metabolic pathway discovery and systems biology research. The spectral metadata of the 5,420 compounds is publicly available (DynLib spectral database, https://bioit3.irc.ugent.be/dynlib/).
Published: 2020

28. Dominant-negative mutations in human IL6ST underlie hyper-IgE syndrome

Author: Vivien, Béziat, Simon J, Tavernier, Yin-Huai, Chen, Cindy S, Ma, Marie, Materna, Arian, Laurence, Jens, Staal, Dominik, Aschenbrenner, Lisa, Roels, Lisa, Worley, Kathleen, Claes, Lisa, Gartner, Lisa A, Kohn, Marieke, De Bruyne, Klaus, Schmitz-Abe, Louis-Marie, Charbonnier, Sevgi, Keles, Justine, Nammour, Natasha, Vladikine, Majistor Raj Luxman, Maglorius Renkilaraj, Yoann, Seeleuthner, Mélanie, Migaud, Jérémie, Rosain, Mohamed, Jeljeli, Bertrand, Boisson, Eva, Van Braeckel, Jill A, Rosenfeld, Hongzheng, Dai, Lindsay C, Burrage, David R, Murdock, Bart N, Lambrecht, Véronique, Avettand-Fenoel, Tiphanie P, Vogel, Charles R, Esther, Sule, Haskologlu, Figen, Dogu, Peter, Ciznar, David, Boutboul, Marie, Ouachée-Chardin, Jean, Amourette, Marie-Noëlle, Lebras, Clément, Gauvain, Colas, Tcherakian, Aydan, Ikinciogullari, Rudi, Beyaert, Laurent, Abel, Joshua D, Milner, Bodo, Grimbacher, Louis-Jean, Couderc, Manish J, Butte, Alexandra F, Freeman, Émilie, Catherinot, Claire, Fieschi, Talal A, Chatila, Stuart G, Tangye, Holm H, Uhlig, Filomeen, Haerynck, Jean-Laurent, Casanova, Anne, Puel, St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller University [New York], Imagine - Institut des maladies génétiques (IHU) (Imagine - U1163), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP), Laboratory of Human Genetics of Infectious Diseases (Necker Branch - INSERM U1163), Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Ghent University Hospital, VIB-UGent Center for Inflammation Research [Gand, Belgique] (IRC), VIB [Belgium], Center for Medical Genetics [Ghent], John Radcliffe Hospital [Oxford University Hospital], University of Oxford [Oxford], Garvan Institute of Medical Research [Darlinghurst, Australia], St. Vincent’s Clinical School, Faculty of Medicine, University of New South Wales [Sydney] (UNSW), University of California, Boston Children's Hospital, Harvard Medical School [Boston] (HMS), Necmettin Erbakan University [Konya, Turquie], Hôpital Cochin [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Baylor College of Medicine (BCM), Baylor University, Laboratoire de Virologie [CHU Necker], CHU Necker - Enfants Malades [AP-HP], University of North Carolina [Chapel Hill] (UNC), University of North Carolina System (UNC), Ankara University School of Medicine [Turkey], Comenius University in Bratislava, Service d'Immunopathologie [Hôpital Saint-Louis, Paris], Hopital Saint-Louis [AP-HP] (AP-HP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Université de Paris (UP), Unité d'Hémato-Immunologie pédiatrique [Hôpital Robert Debré, Paris], Service d'Immuno-hématologie pédiatrique [Hôpital Robert Debré, Paris], Hôpital Robert Debré-Hôpital Robert Debré, Groupe Hospitalier Artois-Ternois Centre Hospitalier d’Arras, Service de pneumologie [Hôpital Foch], Hôpital Foch [Suresnes], National Institute of Allergy and Infectious Diseases [Bethesda] (NIAID-NIH), National Institutes of Health [Bethesda] (NIH), Columbia University Irving Medical Center (CUIMC), Center for Chronic Immunodeficiency (CCI), University Medical Center Freiburg, Freiburg, Germany, Centre for Integrative Biological Signaling Studies [Freiburg, Germany], University of Freiburg [Freiburg], Hanover Medical School, Laboratoire de recherche sur les mécanismes moléculaires et pharmacologiques de l’obstruction bronchique (LOBIP), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Université de Versailles Saint-Quentin-en-Yvelines - UFR Sciences de la santé Simone Veil (UVSQ Santé), Department of Pediatrics, Keck School of Medicine, University of Southern California, Los Angeles, Institut de Recherche Saint-Louis - Hématologie Immunologie Oncologie (Département de recherche de l’UFR de médecine, ex- Institut Universitaire Hématologie-IUH) (IRSL), Université de Paris (UP), St. Vincent’s Clinical School [Sydney, Australia], UNSW Faculty of Medicine [Sydney], and University of New South Wales [Sydney] (UNSW)-University of New South Wales [Sydney] (UNSW)
Subjects: Male, Adolescent, Models, Biological, Young Adult, Th2 Cells, Loss of Function Mutation, Cytokine Receptor gp130, Humans, Immunodeficiency, Child, Alleles, Cells, Cultured, Genes, Dominant, Human disease genetics, Cell Membrane, Correction, Fibroblasts, Middle Aged, Pedigree, Up-Regulation, Kinetics, C-Reactive Protein, Genetics, Population, HEK293 Cells, Phenotype, Mutation, Cytokines, [SDV.IMM]Life Sciences [q-bio]/Immunology, Female, Job Syndrome
Abstract: International audience; Autosomal dominant hyper-IgE syndrome (AD-HIES) is typically caused by dominant-negative (DN) STAT3 mutations. Patients suffer from cold staphylococcal lesions and mucocutaneous candidiasis, severe allergy, and skeletal abnormalities. We report 12 patients from 8 unrelated kindreds with AD-HIES due to DN IL6ST mutations. We identified seven different truncating mutations, one of which was recurrent. The mutant alleles encode GP130 receptors bearing the transmembrane domain but lacking both the recycling motif and all four STAT3-recruiting tyrosine residues. Upon overexpression, the mutant proteins accumulate at the cell surface and are loss of function and DN for cellular responses to IL-6, IL-11, LIF, and OSM. Moreover, the patients’ heterozygous leukocytes and fibroblasts respond poorly to IL-6 and IL-11. Consistently, patients with STAT3 and IL6ST mutations display infectious and allergic manifestations of IL-6R deficiency, and some of the skeletal abnormalities of IL-11R deficiency. DN STAT3 and IL6ST mutations thus appear to underlie clinical phenocopies through impairment of the IL-6 and IL-11 response pathways.
Published: 2020

29. Virus-host coexistence in phytoplankton through the genomic lens

Author: Jean-Marc Aury, Marie-Line Escande, Yves Van de Peer, Gwenael Piganeau, Emmelien Vancaester, Sheree Yau, Julie Guy, Mathieu Groussin, Sophie Sanchez-Brosseau, L. Felipe Benites, Nigel Grimsley, Klaas Vandepoele, Sébastien Gourbière, Hervé Moreau, Stephane Rombauts, Evelyne Derelle, Yves Desdevises, Marc Krasovec, Biologie intégrative des organismes marins (BIOM), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Banyuls (OOB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona] (ICM), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Universiteit Gent = Ghent University [Belgium] (UGENT), VIB [Belgium], Massachusetts Institute of Technology (MIT), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), University of Pretoria [South Africa], Laboratoire Génome et développement des plantes (LGDP), Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS), ANR-12-BSV7-0006,REVIREC,Résistance aux prasinovirus analysée par la transcriptomique et la recombinaison(2012), ANR-12-BSV7-0009,DECOVIR,Diversité des prasinovirus et contrôle par les facteurs environnementaux(2012), ANR-13-JSV6-0005,PHYTNESS,Mutation, Recombinaison et Fitness des Eucaryotes, Approches Génomiques sur les Microalgues du Phytoplankton(2013), European Project: 675752,H2020,H2020-MSCA-ITN-2015,SINGEK(2016), Agence Nationale de la Recherche (France), European Commission, Agencia Estatal de Investigación (España), Universiteit Gent = Ghent University (UGENT), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut Universitaire Européen de la Mer (IUEM), and Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)
Subjects: DYNAMICS, [SDV]Life Sciences [q-bio], viruses, Population, DIVERSITY, QUANTITATIVE PCR, Oceanography, Microbiology, SEQUENCE, Virus, Ostreococcus tauri, 03 medical and health sciences, Microalgae, MODE, Symbiosis, education, Research Articles, EUKARYOTE, 030304 developmental biology, Comparative genomics, Evolutionary Biology, 0303 health sciences, education.field_of_study, Experimental evolution, Genome, Multidisciplinary, OSTREOCOCCUS-TAURI, biology, Strain (chemistry), ACQUISITION, 030306 microbiology, ACL, SciAdv r-articles, Biology and Life Sciences, Chromosome, Genomics, Models, Theoretical, biology.organism_classification, Evolutionary biology, Host-Pathogen Interactions, Phytoplankton, Eukaryote, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, MARINE, Algorithms, RESISTANCE, Research Article
Abstract: 11 pages, 5 figures, 1 table, supplementary materials http://advances.sciencemag.org/cgi/content/full/6/14/eaay2587/DC1.-- Data and materials availability: The genome sequence for O. mediterraneus RCC2590 and OmV2 can be found under GenBank accession numbers WMKK00000000 and MN688676, respectively. The complete gene annotations of RCC2590 can be accessed on ORCAE (https://bioinformatics.psb.ugent.be/orcae/). MMETSP sequence data can be accessed from www.imicrobe.us/#/projects/104. The genomes and their GenBank accession numbers used in this study are as follows: B. prasinos (GCA_002220235.1), M. commoda RCC299 (GCA_000090985.2), M. pusilla CCMP1545 (GCA_000151265.1), O. tauri RCC4221 (CAID01000001.2 to CAID01000020.2, CR954200.2, and CR954199.2), O. lucimarinus CCE9901 (GCA_000092065.1), BpV1 (HM004432.1), BpV2 (HM004430.1), MpV1 (HM004429.1), OtV1 (FN386611.1), OtV2 (FN600414.1), OtV5 (EU304328.2), OtV6 (JN225873.1), OlV1 (HM004431.1), OlV2 (KP874736.1), OlV3 (HQ633060.1), OlV4 (JF974316.1), OlV5 (HQ632827.1), OlV6 (HQ633059.1), OlV7 (KP874737.1), and OmV1 (KP874735.1). Ostreococcus sp. RCC809 is available from the JGI Genome Portal under project ID 16233, Virus-microbe interactions in the ocean are commonly described by “boom and bust”dynamics, whereby a numerically dominant microorganism is lysed and replaced by a virus-resistant one. Here, we isolated a microalga strain and its infective dsDNA virus whose dynamics are characterized instead by parallel growth of both the microalga and the virus. Experimental evolution of clonal lines revealed that this viral production originates from the lysis of a minority of virus-susceptible cells, which are regenerated from resistant cells. Whole-genome sequencing demonstrated that this resistant-susceptible switch involved a large deletion on one chromosome. Mathematical modeling explained how the switch maintains stable microalga-virus population dynamics consistent with their observed growth pattern. Comparative genomics confirmed an ancient origin of this “accordion” chromosome despite a lack of sequence conservation. Together, our results show how dynamic genomic rearrangements may account for a previously overlooked coexistence mechanism in microalgae-virus interactions., This research was funded by the ANR grants REVIREC ANR-12-BSV7-0006-01, DECOVIR ANR-12-BSV7-0009, and PHYTNESS ANR-13-JSV6-0005. E.V. is funded by BOF project GOA 01G01715, and L.F.B. is funded by the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement no. H2020-MSCA-ITN-2015-675752, With the funding support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S), of the Spanish Research Agency (AEI)
Published: 2020

30. A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community)

Author: Orengo, Christine, Velankar, Sameer, Wodak, Shoshana, Zoete, Vincent, Bonvin, Alexandre M.J.J., Elofsson, Arne, Feenstra, K. Anton, Gerloff, Dietland L., Hamelryck, Thomas, Hancock, John M., Helmer-Citterich, Manuela, Hospital, Adam, Orozco, Modesto, Perrakis, Anastassis, Rarey, Matthias, Soares, Claudio, Sussman, Joel L., Thornton, Janet M., Tuffery, Pierre, Tusnady, Gabor, Wierenga, Rikkert, Salminen, Tiina, Schneider, Bohdan, Sub NMR Spectroscopy, NMR Spectroscopy, University College of London [London] (UCL), European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, VIB-VUB Center for Structural Biology [Bruxelles], VIB [Belgium], Swiss Institute of Bioinformatics [Lausanne] (SIB), Université de Lausanne (UNIL), Utrecht University [Utrecht], Science for Life Laboratory [Solna], Royal Institute of Technology [Stockholm] (KTH ), Vrije Universiteit Amsterdam [Amsterdam] (VU), IBIVU, Department of Computer Science, Faculty of Sciences (IBIVU,), University of Amsterdam [Amsterdam] (UvA), Luxembourg Centre For Systems Biomedicine (LCSB), University of Luxembourg [Luxembourg], University of Copenhagen = Københavns Universitet (KU), Università degli Studi di Roma Tor Vergata [Roma], Barcelona Institute of Science and Technology (BIST), Netherlands Cancer Institute (NKI), Antoni van Leeuwenhoek Hospital, Universität Hamburg (UHH), Instituto de Tecnologia Química e Biológica António Xavier (ITQB), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA), Weizmann Institute of Science [Rehovot, Israël], Ressource Parisienne en Bioinformatique Structurale, Institute of Enzymology [Budapest], Research Centre for Natural Sciences, Hungarian Academy of Sciences (MTA)-Hungarian Academy of Sciences (MTA), University of Oulu, Åbo Akademi University [Turku], Institute of Biotechnology of the Czech Academy of Sciences (IBT / CAS), Czech Academy of Sciences [Prague] (CAS), Bioinformatics, AIMMS, Integrative Bioinformatics, Sub NMR Spectroscopy, and NMR Spectroscopy
Subjects: 0301 basic medicine, Computer science, [SDV]Life Sciences [q-bio], Genomics, Biological Science Disciplines, ELIXIR, Instruct-ERIC, biomolecular structure, nucleic acids structure, protein structure, structural bioinformatics, General Biochemistry, Genetics and Molecular Biology, Field (computer science), 03 medical and health sciences, Structural bioinformatics, Data sequences, SDG 17 - Partnerships for the Goals, Humans, Settore BIO/10, General Pharmacology, Toxicology and Pharmaceutics, computer.programming_language, 030102 biochemistry & molecular biology, General Immunology and Microbiology, Computational Biology, Proteins, General Medicine, Articles, Opinion Article, Data science, Outreach, Europe, 030104 developmental biology, Elixir (programming language), Benchmark data, computer
Abstract: Structural bioinformatics provides the scientific methods and tools to analyse, archive, validate, and present the biomolecular structure data generated by the structural biology community. It also provides an important link with the genomics community, as structural bioinformaticians also use the extensive sequence data to predict protein structures and their functional sites. A very broad and active community of structural bioinformaticians exists across Europe, and 3D-Bioinfo will establish formal platforms to address their needs and better integrate their activities and initiatives. Our mission will be to strengthen the ties with the structural biology research communities in Europe covering life sciences, as well as chemistry and physics and to bridge the gap between these researchers in order to fully realize the potential of structural bioinformatics. Our Community will also undertake dedicated educational, training and outreach efforts to facilitate this, bringing new insights and thus facilitating the development of much needed innovative applications e.g. for human health, drug and protein design. Our combined efforts will be of critical importance to keep the European research efforts competitive in this respect. Here we highlight the major European contributions to the field of structural bioinformatics, the most pressing challenges remaining and how Europe-wide interactions, enabled by ELIXIR and its platforms, will help in addressing these challenges and in coordinating structural bioinformatics resources across Europe. In particular, we present recent activities and future plans to consolidate an ELIXIR 3D-Bioinfo Community in structural bioinformatics and propose means to develop better links across the community. These include building new consortia, organising workshops to establish data standards and seeking community agreement on benchmark data sets and strategies. We also highlight existing and planned collaborations with other ELIXIR Communities and other European infrastructures, such as the structural biology community supported by Instruct-ERIC, with whom we have synergies and overlapping common interests.
Published: 2020

31. Sustained activation of the Aryl hydrocarbon Receptor transcription factor promotes resistance to BRAF-inhibitors in melanoma

Author: Corre, Sébastien, Tardif, Nina, Mouchet, Nicolas, Leclair, Héloïse M., Boussemart, Lise, Gautron, Arthur, Bachelot, Laura, Perrot, Anthony, Soshilov, Anatoly, Rogiers, Aljosja, Rambow, Florian, Dumontet, Erwan, Tarte, Karin, Bessede, Alban, Guillemin, Gilles J., Marine, Jean-Christophe, Denison, Michael S., Gilot, David, Galibert, Marie-Dominique, Jonchère, Laurent, Institut de Génétique et Développement de Rennes (IGDR), Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), CHU Pontchaillou [Rennes], University of California [Davis] (UC Davis), University of California (UC), Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), VIB [Belgium], Microenvironment, Cell Differentiation, Immunology and Cancer (MICMAC), Université de Rennes (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Macquarie University, AVIESAN plan Cancer [ENV201308, ENV201603], Fondation ARC [PGA1*20160203868], Ligue National Contre le Cancer (LNCC) Departements du Grand-Ouest, Association 'Vaincre le Cancer', FHU CAMIn-CHU Rennes, Region Bretagne, University of Rennes 1, CNRS, Inserm, ministere de la Recherche, Ligue Contre le Cancer (Grand-Ouest), CNRS [UMR6290], Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), University of California, and Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )
Subjects: Skin Neoplasms, endocrine system diseases, Drug Resistance, Mice, SCID, Mice, Oximes, Receptors, 2.1 Biological and endogenous factors, Enzyme Inhibitors, Aetiology, lcsh:Science, Melanoma, Cancer, Tumor, Imidazoles, respiratory system, Tumor Burden, Molecular Docking Simulation, Aryl Hydrocarbon, 5.1 Pharmaceuticals, MCF-7 Cells, [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Development of treatments and therapeutic interventions, Proto-Oncogene Proteins B-raf, Science, [SDV.CAN]Life Sciences [q-bio]/Cancer, SCID, Article, Cell Line, [SDV.CAN] Life Sciences [q-bio]/Cancer, Cell Line, Tumor, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], MD Multidisciplinary, Genetics, Animals, Humans, Protein Kinase Inhibitors, neoplasms, [SDV.MHEP.DERM] Life Sciences [q-bio]/Human health and pathology/Dermatology, Xenograft Model Antitumor Assays, Receptors, Aryl Hydrocarbon, Vemurafenib, Drug Resistance, Neoplasm, Resveratrol, Mutation, Neoplasm, lcsh:Q, [SDV.MHEP.DERM]Life Sciences [q-bio]/Human health and pathology/Dermatology, Transcription Factors
Abstract: BRAF inhibitors target the BRAF-V600E/K mutated kinase, the driver mutation found in 50% of cutaneous melanoma. They give unprecedented anti-tumor responses but acquisition of resistance ultimately limits their clinical benefit. The master regulators driving the expression of resistance-genes remain poorly understood. Here, we demonstrate that the Aryl hydrocarbon Receptor (AhR) transcription factor is constitutively activated in a subset of melanoma cells, promoting the dedifferentiation of melanoma cells and the expression of BRAFi-resistance genes. Typically, under BRAFi pressure, death of BRAFi-sensitive cells leads to an enrichment of a small subpopulation of AhR-activated and BRAFi-persister cells, responsible for relapse. Also, differentiated and BRAFi-sensitive cells can be redirected towards an AhR-dependent resistant program using AhR agonists. We thus identify Resveratrol, a clinically compatible AhR-antagonist that abrogates deleterious AhR sustained-activation. Combined with BRAFi, Resveratrol reduces the number of BRAFi-resistant cells and delays tumor growth. We thus propose AhR-impairment as a strategy to overcome melanoma resistance., Resistance to BRAF inhibitors limits their clinical benefit in melanoma patients. Here, the authors show that the Aryl hydrocarbon Receptor (AhR) is a key mediator of resistant genes and use resveratrol, an AhR antagonist, to revert resistance in melanoma bearing mice.
Published: 2018

32. Chemical shift assignments of the partially deuterated Fyn SH2–SH3 domain

Author: Peter Tompa, Karine Loth, Fabien Kieken, Nico A. J. van Nuland, Tom Lenaerts, Informatics and Applied Informatics, Structural Biology Brussels, Department of Bio-engineering Sciences, Structural Biology Brussels (SBB), Vrije Universiteit Brussel (VUB), VIB-VUB Center for Structural Biology [Bruxelles], VIB [Belgium], Centre de biophysique moléculaire (CBM), Université d'Orléans (UO)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), AI-lab, Vakgroep Computerwetenschappen, Université Libre de Bruxelles, Département d'informatique (MLG), Interuniversity Institute of Bioinformatics in Brussels (IB2), Université libre de Bruxelles (ULB)-Vrije Universiteit Brussel (VUB), Vrije Universiteit [Brussels] (VUB), Université d'Orléans (UO)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), and Université Libre de Bruxelles - Institut de Bioinformatique de Bruxelles
Subjects: 0301 basic medicine, animal structures, Chemistry, Stereochemistry, Kinase, [SDV]Life Sciences [q-bio], Phosphatase, SH3–SH2, Biochemistry, NMR, SH3 domain, Homology (biology), Src family, 03 medical and health sciences, Fyn kinase, Tandem domains, 030104 developmental biology, FYN, Deuterium, Structural Biology, Tyrosine kinase, Proto-oncogene tyrosine-protein kinase Src
Abstract: Src Homology 2 and 3 (SH2 and SH3) are two key protein interaction modules involved in regulating the activity of many proteins such as tyrosine kinases and phosphatases by respective recognition of phosphotyrosine and proline-rich regions. In the Src family kinases, the inactive state of the protein is the direct result of the interaction of the SH2 and the SH3 domain with intra-molecular regions, leading to a closed structure incompetent with substrate modification. Here, we report the 1H, 15N and 13C backbone- and side-chain chemical shift assignments of the partially deuterated Fyn SH3-SH2 domain and structural differences between tandem and single domains. The BMRB accession number is 27165.
Published: 2017

33. Characteristic ERK1/2 signaling dynamics distinguishes necroptosis from apoptosis

Author: Peter Vandenabeele, Wim Declercq, Jolien Bridelance, Laurent Héliot, Pierre Vincent, Franck B. Riquet, François Sipieter, Aymeric Leray, Elke De Schutter, Benjamin Cappe, Guy Van Camp, Paco Hulpiau, Universiteit Gent = Ghent University [Belgium] (UGENT), VIB-UGent Center for Inflammation Research [Gand, Belgique] (IRC), VIB [Belgium], Université de Lille, Laboratoire Interdisciplinaire Carnot de Bourgogne [Dijon] (LICB), Université de Bourgogne (UB)-Université de Technologie de Belfort-Montbeliard (UTBM)-Centre National de la Recherche Scientifique (CNRS), University of Antwerp (UA), VIB Center for Inflammation Research [Ghent, Belgium], Antwerp University Hospital [Edegem] (UZA), Laboratoire de Physique des Lasers, Atomes et Molécules - UMR 8523 (PhLAM), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Adaptation Biologique et Vieillissement = Biological Adaptation and Ageing (B2A), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Paris Seine (IBPS), Sorbonne Université (SU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Universiteit Gent = Ghent University (UGENT), Laboratoire Interdisciplinaire Carnot de Bourgogne (ICB), Université de Technologie de Belfort-Montbeliard (UTBM)-Université de Bourgogne (UB)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Riquet, Franck, Université de Bourgogne (UB), and Leray, Aymeric
Subjects: Cell biology, Programmed cell death, Science, [SDV]Life Sciences [q-bio], Necroptosis, [SDV.BBM.BP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, PROTEIN, MECHANISMS, ESCRT, ACTIVATION, 03 medical and health sciences, 0302 clinical medicine, INFLAMMATION, Gene expression, Medicine and Health Sciences, KINASE, Biology, 030304 developmental biology, 0303 health sciences, Multidisciplinary, IDENTIFICATION, Chemistry, NECROSIS, Dynamics (mechanics), Biology and Life Sciences, Erk1 2 signaling, [SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, [SDV] Life Sciences [q-bio], Biological sciences, Biomolecular engineering, CELL-DEATH, Apoptosis, Cell culture, 030220 oncology & carcinogenesis, Tumor necrosis factor alpha, BIOSENSORS, Human medicine
Abstract: International audience; ERK1/2 involvement in cell death remains unclear, although many studies have demonstrated the importance of ERK1/2 dynamics in determining cellular re- sponses. To untangle how ERK1/2 contributes to two cell death programs, we investigated ERK1/2 signaling dynamics during hFasL-induced apoptosis and TNF-induced necroptosis in L929 cells. We observed that ERK1/2 inhibition sensi- tizes cells to apoptosis while delaying necroptosis. By monitoring ERK1/2 activity by live-cell imaging using an improved ERK1/2 biosensor (EKAR4.0), we reported differential ERK1/2 signaling dynamics between cell survival, apoptosis, and nec- roptosis. We also decrypted a temporally shifted amplitude- and frequency-modu- lated (AM/FM) ERK1/2 activity profile in necroptosis versus apoptosis. ERK1/2 inhibition, which disrupted ERK1/2 signaling dynamics, prevented TNF and IL-6 gene expression increase during TNF-induced necroptosis. Using an inducible cell line for activated MLKL, the final executioner of necroptosis, we showed ERK1/2 and its distinctive necroptotic ERK1/2 activity dynamics to be positioned downstream of MLKL.
Published: 2021

34. Reversion of antibiotic resistance in Mycobacterium tuberculosis by spiroisoxazoline SMARt-420

Author: Alexandre Wohlkonig, David Hot, Sebastien Gagneux, Marc Gitzinger, Julia Feldmann, Mireia Coscolla, Marion Flipo, Nicolas Willand, Martin Moune, Kamel Djaout, Mehdi Kiass, Priscille Brodin, Vincent Delorme, Vanessa Mathys, Rosangela Frita, Karine Soetaert, Benoit Deprez, Ludovic Huot, Nicolas Blondiaux, René Wintjens, Christian Kemmer, Alain R. Baulard, Vincent Trebosc, Camille Locht, Matthieu Desroses, Rudy Antoine, Willand, Nicolas, Appel à projets générique - Reprogrammation de la bioactivation des thioamides comme alternative antituberculeuse - - Tea-4-Two2014 - ANR-14-CE14-0027 - Appel à projets générique - VALID, Equipements d'excellence - Plateau de microscopie de criblage à haut débit et d'analyse à très haute résolution - - Imaginex BioMed2010 - ANR-10-EQPX-0004 - EQPX - VALID, EGID Diabetes Pole - - EGID2010 - ANR-10-LABX-0046 - LABX - VALID, Plate forme Lilloise de séquençage du génome humain pour une médecine personnalisée - - LIGAN PM2010 - ANR-10-EQPX-0007 - EQPX - VALID, A Chemical Genomics Approach of Intracellular Mycobacterium tuberculosis Towards Defining Specific Host Pathogen Interactions - INTRACELLTB - - EC:FP7:ERC2010-12-01 - 2015-11-30 - 260901 - VALID, Compensatory Evolution and Epistasis in Multidrug-resistant Mycobacterium tuberculosis - EVODRTB - - EC:FP7:ERC2013-04-01 - 2018-03-31 - 309540 - VALID, More Medicines for Tuberculosis - MM4TB - - EC:FP7:HEALTH2011-02-01 - 2016-01-31 - 260872 - VALID, Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204 (CIIL), Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Centre National de la Recherche Scientifique (CNRS), Médicaments et molécules pour agir sur les Systèmes Vivants - U 1177 (M2SV), Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille, Karolinska Institutet [Stockholm], Institut Scientifique de Santé Publique [Belgique] - Scientific Institute of Public Health [Belgium] (WIV-ISP), Réseau International des Instituts Pasteur (RIIP), Tuberculosis Lab [Korea], Institut Pasteur Korea - Institut Pasteur de Corée, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Bioversys AG [Basel], University of Basel (Unibas), Université libre de Bruxelles (ULB), VIB-VUB Center for Structural Biology [Bruxelles], VIB [Belgium], Vrije Universiteit Brussel [Bruxelles] (VUB), Swiss Tropical and Public Health Institute [Basel], This work was supported by l’Agence Nationale de la Recherche (ANR), France (Tea-4-Two, ANR-14-CE14-0027-01) (ANR-10-EQPX-04-01), by EU grants ERC-STG INTRACELLTB no 260901, the Feder (12001407 (D-AL), PRIM (NewBio4Tb), European Research Council (grant 309540-EVODRTB), SystemsX.ch, Institut National de la Santé et de la Recherche Médicale, Université de Lille, Institut Pasteur de Lille, Centre National de la Recherche Scientifique, the Région Hauts-de-France (convention no. 12000080), and Société d’Accélération du Transfert de Technologie Nord. R.W. is Research Associate at the National Fund for Scientific Research (FNRS-FRS) (Belgium). M.M. was supported by PRIM (NewBio4Tb), V.D. was supported by EU grant 260872, and V.T. was suppported by the Marie Curie Initial Training Network (ITN-2013-607694-Translocation). The authors also thank the Unité Mixte de Recherche UMR 8199, Lille Integrated Genomics Network for Advanced Personalized Medicine (LIGAN-PM) Genomics platform (Lille, France), which belongs to the Federation de Recherche 3508 Labex EGID (European Genomics Institute for Diabetes, ANR-10-LABX-46) and was supported by the Agence Nationale de la Recherche (ANR) Equipex 2010 session (ANR-10-EQPX-07-01, LIGAN-PM). The LIGAN-PM Genomics platform is supported by the Fonds Européen de Développement Régional and the Region Hauts-de-France., ANR-14-CE14-0027,Tea-4-Two,Reprogrammation de la bioactivation des thioamides comme alternative antituberculeuse(2014), ANR-10-EQPX-0004,Imaginex BioMed,Plateau de microscopie de criblage à haut débit et d'analyse à très haute résolution(2010), ANR-10-LABX-0046,EGID,EGID Diabetes Pole(2010), ANR-10-EQPX-0007,LIGAN PM,Plate forme Lilloise de séquençage du génome humain pour une médecine personnalisée(2010), European Project: 260901,EC:FP7:ERC,ERC-2010-StG_20091118,INTRACELLTB(2010), European Project: 309540,EC:FP7:ERC,ERC-2012-StG_20111109,EVODRTB(2013), European Project: 260872,EC:FP7:HEALTH,FP7-HEALTH-2010-single-stage,MM4TB(2011), and Centre National de la Recherche Scientifique (CNRS)-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Université de Lille-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur de Lille
Subjects: 0301 basic medicine, Tuberculosis, medicine.drug_class, [CHIM.THER] Chemical Sciences/Medicinal Chemistry, 030106 microbiology, Antibiotics, Reversion, [CHIM.THER]Chemical Sciences/Medicinal Chemistry, Microbiology, Mycobacterium tuberculosis, 03 medical and health sciences, Antibiotic resistance, [CHIM] Chemical Sciences, medicine, [CHIM]Chemical Sciences, chemistry.chemical_classification, Multidisciplinary, biology, medicine.disease, biology.organism_classification, 3. Good health, 030104 developmental biology, Enzyme, chemistry, Ethionamide, Bacteria, medicine.drug
Abstract: Countering TB prodrug resistance The arsenal of antibiotics for treating tuberculosis (TB) contains many prodrugs, such as ethionamide, which need activation by normal metabolism to release their toxic effects. Ethionamide is potentiated by small molecules. Blondiaux et al. screened for more potent analogs and identified a lead compound called SMARt-420. This small molecule inactivates a TetR-like repressor, EthR2, and boosts ethionamide activation. SMARt-420 successfully promoted clearance of multidrug-resistant strains of Mycobacterium tuberculosis from the lungs of mice. Science , this issue p. 1206
Published: 2017

35. Allostery in Its Many Disguises: From Theory to Applications

Author: Yassmine Chebaro, Annick Dejaegere, Ruth Nussinov, Rebecca C. Wade, Simone Orioli, Jocelyne Vreede, Riccardo Ravasio, Paraskevi Gkeka, Jing Li, Gerhard Stock, Chung-Jung Tsai, Ivet Bahar, Emanuele Paci, Pietro Faccioli, Joanna Panecka-Hofman, John Karanicolas, Peter G. Bolhuis, Jean-Pierre Changeux, Shoshana J. Wodak, Masha Y. Niv, Antonella Di Pizio, Giulia Palermo, Roland H. Stote, Tom McLeish, Matthieu Wyart, Carolina Brito, Peter Hamm, J. Andrew McCammon, Vincent J. Hilser, Amnon Horovitz, Jerome Eberhardt, Ivan Rivalta, Nikolay V. Dokholyan, Igor N. Berezovsky, Marco Cecchini, Le Yan, Hyunbum Jang, Dima Kozakov, Dzmitry Padhorny, VIB-VUB Center for Structural Biology [Bruxelles], VIB [Belgium], Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA), Institut de Chimie de Strasbourg, Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris], Collège de France (CdF), Physics Department and INFN, University of Trento [Trento], Universidade Federal do Rio Grande do Sul [Porto Alegre] (UFRGS), Ecole Polytechnique Fédérale de Lausanne (EPFL), Laboratoire de Chimie - UMR5182 (LC), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS ), Department of Biomedical Engineering [Boston], Boston University [Boston] (BU), University of Leeds, University of North Carolina at Chapel Hill, University of North Carolina [Chapel Hill] (UNC), University of North Carolina System (UNC)-University of North Carolina System (UNC), National University of Singapore (NUS), Weizmann Institute of Science [Rehovot, Israël], Johns Hopkins University (JHU), University of Pittsburgh (PITT), Pennsylvania Commonwealth System of Higher Education (PCSHE), Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université Louis Pasteur - Strasbourg I-Institut de Chimie du CNRS (INC), Collège de France (CdF (institution)), Institute of Condensed Matter Physics [Lausanne], University of California [Santa Barbara] (UCSB), University of California, Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École normale supérieure - Lyon (ENS Lyon)-Institut de Chimie du CNRS (INC), Cancer and Inflammation Program, Leidos Biomedical Research Inc., Frederick National Laboratory, Frederick National Laboratory for Cancer Research (FNLCR), Stony Brook University [SUNY] (SBU), State University of New York (SUNY), University of York [York, UK], European Union's Horizon 2020 Research and Innovation Program under grant agreement no. 720270 (HBP SGA1)NIH grants R01GM114015, R01GM064803, and R01GM123247, grants P41GM103712 and P30DA035778Marie Curie Reintegration Grant (FP7-PEOPLE-2009-RG, no. 256533), European Project: 720270,H2020 Pilier Excellent Science,H2020-Adhoc-2014-20,HBP SGA1(2016), European Project: 256533,EC:FP7:PEOPLE,FP7-PEOPLE-2009-RG,COMPUT DRUG DESIGN(2010), Simulation of Biomolecular Systems (HIMS, FNWI), Wodak, Shoshana J, Paci, Emanuele, Dokholyan, Nikolay V, Berezovsky, Igor N, Horovitz, Amnon, Li, Jing, Hilser, Vincent J, Bahar, Ivet, Karanicolas, John, Stock, Gerhard, Hamm, Peter, Stote, Roland H, Eberhardt, Jerome, Chebaro, Yassmine, Dejaegere, Annick, Cecchini, Marco, Changeux, Jean-Pierre, Bolhuis, Peter G, Vreede, Jocelyne, Faccioli, Pietro, Orioli, Simone, Ravasio, Riccardo, Yan, Le, Brito, Carolina, Wyart, Matthieu, Gkeka, Paraskevi, Rivalta, Ivan, Palermo, Giulia, McCammon, J Andrew, Panecka-Hofman, Joanna, Wade, Rebecca C, Di Pizio, Antonella, Niv, Masha Y, Nussinov, Ruth, Tsai, Chung-Jung, Jang, Hyunbum, Padhorny, Dzmitry, Kozakov, Dima, McLeish, Tom, Wodak, S, Paci, E, Dokholyan, N, Berezovsky, I, Horovitz, A, Li, J, Hilser, V, Bahar, I, Karanicolas, J, Stock, G, Hamm, P, Stote, R, Eberhardt, J, Chebaro, Y, Dejaegere, A, Cecchini, M, Changeux, J, Bolhuis, P, Vreede, J, Faccioli, P, Orioli, S, Ravasio, R, Yan, L, Brito, C, Wyart, M, Gkeka, P, Rivalta, I, Palermo, G, Mccammon, J, Panecka-Hofman, J, Wade, R, Di Pizio, A, Niv, M, Nussinov, R, Tsai, C, Jang, H, Padhorny, D, Kozakov, D, Mcleish, T, and Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)
Subjects: Transcription, Genetic, Computer science, nuclear receptors, Biosensing Techniques, allosteric switche, Structural Biology, chemical rescue, Allostery, ComputingMilieux_MISCELLANEOUS, Cognitive science, mechanisms, 0303 health sciences, Protein function, ligand-binding, elastic network model, molecular dynamic, dynamic allostery, 030302 biochemistry & molecular biology, regulation, protein function, Biological Sciences, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, modulation, Generic Health Relevance, elastic network models, Thermodynamics, Transcription, Allosteric Site, Metabolic Networks and Pathways, signal transduction, Signal Transduction, 1.1 Normal biological development and functioning, Biophysics, allosteric drug, Molecular Dynamics Simulation, Article, 03 medical and health sciences, protein conformational changes, Genetic, Allosteric Regulation, Underpinning research, conformational-changes, Information and Computing Sciences, Animals, Humans, Molecular Biology, Elastic network models, allosteric material, 030304 developmental biology, pathway, energy landscape, Proteins, allosteric switches, molecular dynamics, protein conformational change, allosteric drugs, Conceptual framework, Gene Expression Regulation, Drug Design, network, Chemical Sciences, protein
Abstract: Allosteric regulation plays an important role in many biological processes, such as signal transduction, transcriptional regulation, and metabolism. Allostery is rooted in the fundamental physical properties of macromo-lecular systems, but its underlying mechanisms are still poorly understood. A collection of contributions to a recent interdisciplinary CECAM (Center Européen de Calcul Atomique et Moléculaire) workshop is used here to provide an overview of the progress and remaining limitations in the understanding of the mechanistic foundations of allostery gained from computational and experimental analyses of real protein systems and model systems. The main conceptual frameworks instrumental in driving the field are discussed. We illustrate the role of these frameworks in illuminating molecular mechanisms and explaining cellular processes, and describe some of their promising practical applications in engineering molecular sensors and informing drug design efforts.
Published: 2019

36. The ubiquitin-editing enzyme A20 controls NK cell homeostasis through regulation of mTOR activity and TNF

Author: Farzaneh Fayazpour, Louis Boon, Manon Vanheerswynghels, Kim Deswarte, Arne Martens, Simon Tavernier, Jessica Vetters, Nozomi Takahashi, Justine Van Moorleghem, Sophie Janssens, Geert van Loo, Sigrid Wahlen, Sofie De Prijck, Peter Vandenabeele, Karl Vergote, Eric Vivier, Bart N. Lambrecht, Mary J. van Helden, Unit of Immunoregulation and Mucosal Immunology [Ghent, Belgium], VIB Inflammation Research Center [Ghent, Belgium], Université de Strasbourg (UNISTRA), Groupe d'études orientales, slaves et néo-helléniques (GEO), Universiteit Gent = Ghent University (UGENT), Bioceros BV, Centre d'Immunologie de Marseille - Luminy (CIML), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), VIB-UGent Center for Inflammation Research [Gand, Belgique] (IRC), VIB [Belgium], Department of Respiratory Medicine, Imperial College London, ER Stress and Inflammation [Ghent, Belgium], VIB Center for Inflammation Research [Ghent, Belgium], Erasmus MC other, Pulmonary Medicine, Universiteit Gent = Ghent University [Belgium] (UGENT), and Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)
Subjects: 0301 basic medicine, PROTECTS CELLS, Programmed cell death, Cell Survival, Immunology, Cell, B-CELL, Regulator, BCL-2, MATURATION, Mice, 03 medical and health sciences, NATURAL-KILLER-CELLS, 0302 clinical medicine, Ubiquitin, immune system diseases, Lymphopenia, hemic and lymphatic diseases, medicine, Medicine and Health Sciences, KINASE, Animals, Homeostasis, Immunology and Allergy, HEMATOPOIETIC STEM-CELLS, Research Articles, Tumor Necrosis Factor alpha-Induced Protein 3, PI3K/AKT/mTOR pathway, biology, Tumor Necrosis Factor-alpha, Chemistry, TOR Serine-Threonine Kinases, Brief Definitive Report, Biology and Life Sciences, Phenotype, 3. Good health, Cell biology, Killer Cells, Natural, 030104 developmental biology, medicine.anatomical_structure, biology.protein, T-CELLS, SURVIVAL, [SDV.IMM]Life Sciences [q-bio]/Immunology, Tumor necrosis factor alpha, OVEREXPRESSION, 030215 immunology
Abstract: The study of Vetters et al. identifies the ubiquitin-modifying enzyme A20 as a critical regulator of mTOR. Loss of A20 unleashes mTOR activity and induces NK cell death, underscoring the need for a tightly controlled mTOR pathway for proper NK cell homeostasis., The ubiquitin-editing enzyme A20 is a well-known regulator of immune cell function and homeostasis. In addition, A20 protects cells from death in an ill-defined manner. While most studies focus on its role in the TNF-receptor complex, we here identify a novel component in the A20-mediated decision between life and death. Loss of A20 in NK cells led to spontaneous NK cell death and severe NK cell lymphopenia. The few remaining NK cells showed an immature, hyperactivated phenotype, hallmarked by the basal release of cytokines and cytotoxic molecules. NK-A20−/− cells were hypersensitive to TNF-induced cell death and could be rescued, at least partially, by a combined deficiency with TNF. Unexpectedly, rapamycin, a well-established inhibitor of mTOR, also strongly protected NK-A20−/− cells from death, and further studies revealed that A20 restricts mTOR activation in NK cells. This study therefore maps A20 as a crucial regulator of mTOR signaling and underscores the need for a tightly balanced mTOR pathway in NK cell homeostasis.
Published: 2019
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37. Endeavors towards transformation of M. tuberculosis thymidylate kinase (MtbTMPK) inhibitors into potential antimycobacterial agents

Author: Fabian Hulpia, Serge Van Calenbergh, He Eun Forbes, Romain Merceron, Steven De Munck, Martijn D. P. Risseeuw, Yanlin Jian, Hélène Munier-Lehmann, Savvas N. Savvides, Kristof Van Hecke, Helena I. Boshoff, Laboratorium voor Medicinale Chemie = Laboratory of Medicinal Chemistry [Ghent], Faculteit Farmaceutische Wetenschappen = Faculty of Pharmaceutical Sciences [Ghent] (FFW), Universiteit Gent = Ghent University (UGENT)-Universiteit Gent = Ghent University (UGENT), VIB-UGent Center for Inflammation Research [Gand, Belgique] (IRC), VIB [Belgium], Universiteit Gent = Ghent University (UGENT), Laboratory of Clinical Immunology and Microbiology [Bethesda, MA, USA] (LCIM), National Institute of Allergy and Infectious Diseases [Bethesda] (NIAID-NIH), National Institutes of Health [Bethesda] (NIH)-National Institutes of Health [Bethesda] (NIH), Chimie et Biocatalyse, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), This work was supported by the China Scholarship Council [grant number 201607060021] and in part by the Intramural Research Program of the National Institute of Allergy and Infectious Diseases (NIAID, NIH, US). KVH thanks the Hercules Foundation (project AUGE/11/029 '3D-SPACE: 3D Structural Platform Aiming for Chemical Excellence', Belgium) and the Special Research Fund (BOF) – UGent (project 01N03217, Belgium) for funding. S.D.M. was supported by a pre-doctoral fellowship from the Flanders Agency for Innovation and Entrepreneurship (VLAIO-Flanders, Belgium). S.N.S. acknowledges research support from the Hercules Foundation (no. AUGE- 11–029, Belgium), Ghent University (BOF17-GOA-028, Belgium) and the VIB., We thank the staff of Proxima 1 at synchrotron SOLEIL (Gif-sur-Yvette, France) for beam time allocation and excellent technical support, Universiteit Gent = Ghent University [Belgium] (UGENT)-Universiteit Gent = Ghent University [Belgium] (UGENT), Universiteit Gent = Ghent University [Belgium] (UGENT), and Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)
Subjects: SIDEROPHORES, [SDV]Life Sciences [q-bio], Antitubercular Agents, Uptake, Antimycobacterial, 0302 clinical medicine, THYMIDINE-5'-O-MONOPHOSPHATE ANALOGS, Siderophore, Drug Discovery, Enzyme Inhibitors, Structural motif, Cytotoxicity, chemistry.chemical_classification, 0303 health sciences, biology, [CHIM.ORGA]Chemical Sciences/Organic chemistry, Chemistry, Drug discovery, Mycobacteria tuberculosis, General Medicine, 3. Good health, Biochemistry, 030220 oncology & carcinogenesis, MYCOBACTERIUM-TUBERCULOSIS, ANTIBIOTICS, NUCLEOSIDES, Thymidine monophosphate kinase (TMPK), medicine.drug_class, Microbial Sensitivity Tests, Thymidylate kinase, Cell Line, Mycobacterium tuberculosis, Structure-Activity Relationship, 03 medical and health sciences, medicine, Humans, 030304 developmental biology, Pharmacology, IDENTIFICATION, THYMIDINE ANALOGS, Organic Chemistry, IN-VITRO, biology.organism_classification, In vitro, Enzyme, PHYSICOCHEMICAL PROPERTIES, DISCOVERY, Drug Design, Nucleoside-Phosphate Kinase
Abstract: International audience; As the last enzyme in nucleotide synthesis as precursors for DNA replication, thymidylate kinase of M. tuberculosis (MtbTMPK) attracts significant interest as a target in the discovery of new anti-tuberculosis agents. Earlier, we discovered potent MtbTMPK inhibitors, but these generally suffered from poor antimycobacterial activity, which we hypothesize is due to poor bacterial uptake. To address this, we herein describe our efforts to equip previously reported MtbTMPK inhibitors with targeting moieties to increase the whole cell activity of the hybrid analogues. Introduction of a simplified Fe-chelating siderophore motif gave rise to analogue 17 that combined favorable enzyme inhibitory activity with significant activity against M. tuberculosis (MIC of 12.5 μM). Conjugation of MtbTMPK inhibitors with an imidazo[1,2-a]pyridine or 3,5-dinitrobenzamide scaffold afforded analogues 26, 27 and 28, with moderate MtbTMPK enzyme inhibitory potency, but sub-micromolar activity against mycobacteria without significant cytotoxicity. These results indicate that conjugation with structural motifs known to favor mycobacterial uptake may be a valid approach for discovering new antimycobacterial agents.
Published: 2020

38. MAVS deficiency induces gut dysbiotic microbiota conferring a proallergic phenotype

Author: Elsa Kress, Mathias Heikenwalder, Gerard Lina, David Bauché, Saskia Lippens, Claire Macari, Marie-Cécile Michallet, Mathias Chamaillard, Sophia Djebali, Emilie Plantamura, Lyvia Moudombi, Jacqueline Marvel, Christophe Caux, Julien C. Marie, Annabelle Cesaro, Lilia Boucinha, Amiran Dzutsev, Jean-Philippe Rasigade, Ulrike Rothermel, Giorgio Trinchieri, Azzak Bentaher-Belaaouaj, Oana Dumitrescu, Morgan Grau, Michelina Plateroti, Clovis Bondu, Immunité et lymphocytes cytotoxiques – Immunity and cytotoxic lymphocytes, Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Cancer Inflammation Program [Frederick], Center for Cancer Research, Leidos Biomedical Research, Inc [Frederick, MD, USA], Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204 (CIIL), Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Centre National de la Recherche Scientifique (CNRS), Centre de Recherche en Cancérologie de Lyon (UNICANCER/CRCL), Centre Léon Bérard [Lyon]-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), German Cancer Research Center - Deutsches Krebsforschungszentrum [Heidelberg] (DKFZ), Hospices Civils de Lyon (HCL), Pathogénie des Staphylocoques – Staphylococcal Pathogenesis (StaPath), VIB-UGent Center for Inflammation Research [Gand, Belgique] (IRC), VIB [Belgium], We acknowledge the contributions of the Structure Fédérative de Recherche BioSciences Gerland-Lyon Sud (UMS3444/US8-Ecole Normale Superieure de Lyon, Universite Claude Bernard de Lyon CNRS, INSERM) facilities, especially AniRA ImmOS. This work was supported by Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche Scientifique, Université de Lyon I, Hospices Civils de Lyon, Association 'ARCHE,' and Agence Nationale de la Recherche Grant ANR-11-RPIB-0019-03 (to J.M.), a grant from the Département du Rhône-Fonds Européen de Développement Régional (PLATINE) (J.M.), and European Commission Grant LSHG-CT-2006-037188, The European Mouse Disease Clinic (to J.M.)., We thank J. Tschopp’s laboratory for Cardif (MAVS-deficient) mice, Martine Tomkowiak, Julien Mafille, and Barbara Gilbert for expert technical assistance, Anca Hennino for confocal images, Christophe Arpin and Mohamad Sobh for statistical data analysis, Bertrand Dubois, Marc Vocanson, and Jean-François Nicolas for helpful discussions on the DTH model, Thierry Walzer, Laurent Genestier, Bertrand Dubois, and Gérard Eberl for critical reading of the manuscript, Bariza Blanquier for help with qPCR analysis (genetic analysis), Thibault Andrieu and Sébastien Dussurgey (AniRA-Cytometry), Olga Azocar and Christophe Chamot from the Plateau Technique Imagerie/Microcopie, and the staff of AniRA-PBES, especially Jean-Louis Thoumas and Céline Angleraux., Centre International de Recherche en Infectiologie - UMR (CIRI), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Centre National de la Recherche Scientifique (CNRS)-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Université de Lille-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), and MICHALLET, MARIE-CECILE
Subjects: 0301 basic medicine, MESH: Signal Transduction, RIG-like receptors, MESH: Intestines/immunology, MESH: Skin Diseases, Bacterial/pathology, Gut flora, MESH: Skin Diseases, Bacterial/metabolism, MESH: Mice, Knockout, [SDV.IMM.II]Life Sciences [q-bio]/Immunology/Innate immunity, Mice, 0302 clinical medicine, MESH: Animals, MESH: Hypersensitivity/metabolism, [SDV.IMM.ALL]Life Sciences [q-bio]/Immunology/Allergology, Sensitization, Mice, Knockout, Multidisciplinary, integumentary system, dysbiosis, Biological Sciences, MAVS, Phenotype, 3. Good health, Intestines, medicine.anatomical_structure, MESH: Intestines/pathology, 030220 oncology & carcinogenesis, [SDV.IMM]Life Sciences [q-bio]/Immunology, Female, [SDV.IMM.ALL] Life Sciences [q-bio]/Immunology/Allergology, Signal Transduction, MESH: Intestines/microbiology, [SDV.IMM] Life Sciences [q-bio]/Immunology, MESH: Dysbiosis/complications, Biology, MESH: Gastrointestinal Microbiome/immunology, MESH: Phenotype, digestive system, 03 medical and health sciences, MESH: Skin Diseases, Bacterial/etiology, MESH: Hypersensitivity/etiology, Immunity, MESH: Mice, Inbred C57BL, MESH: Homeodomain Proteins/metabolism, medicine, Hypersensitivity, allergic skin pathologies, MESH: Hypersensitivity/pathology, Animals, Colitis, Allergic contact dermatitis, [SDV.IMM.II] Life Sciences [q-bio]/Immunology/Innate immunity, MESH: Mice, Adaptor Proteins, Signal Transducing, Homeodomain Proteins, MESH: Adaptor Proteins, Signal Transducing/physiology, Intestinal permeability, Skin Diseases, Bacterial, medicine.disease, biology.organism_classification, Gastrointestinal Microbiome, Mice, Inbred C57BL, Disease Models, Animal, 030104 developmental biology, Immunology, MESH: Homeodomain Proteins/genetics, MESH: Disease Models, Animal, Dysbiosis, MESH: Female
Abstract: International audience; Prominent changes in the gut microbiota (referred to as "dysbiosis") play a key role in the development of allergic disorders, but the underlying mechanisms remain unknown. Study of the delayed-type hypersensitivity (DTH) response in mice contributed to our knowledge of the pathophysiology of human allergic contact dermatitis. Here we report a negative regulatory role of the RIG-I-like receptor adaptor mitochondrial antiviral signaling (MAVS) on DTH by modulating gut bacterial ecology. Cohousing and fecal transplantation experiments revealed that the dysbiotic microbiota of Mavs -/- mice conferred a proallergic phenotype that is communicable to wild-type mice. DTH sensitization coincided with increased intestinal permeability and bacterial translocation within lymphoid organs that enhanced DTH severity. Collectively, we unveiled an unexpected impact of RIG-I-like signaling on the gut microbiota with consequences on allergic skin disease outcome. Primarily, these data indicate that manipulating the gut microbiota may help in the development of therapeutic strategies for the treatment of human allergic skin pathologies.
Published: 2018

39. A comprehensive analysis of the protein-ligand interactions in crystal structures of Mycobacterium tuberculosis EthR

Author: Baptiste Villemagne, Hélène Perée, Alain R. Baulard, René Wintjens, Alexandre Wohlkonig, Sameh H. Soror, Hugues Prevet, Benoit Deprez, Martin Moune, Franck Meyer, Marion Flipo, Abdalkarim Tanina, Nicolas Willand, Faculté de Pharmacie [Bruxelles] (ULB), Université libre de Bruxelles (ULB), VIB-VUB Center for Structural Biology [Bruxelles], VIB [Belgium], Helwan University [Caire], Médicaments et molécules pour agir sur les Systèmes Vivants - U 1177 (M2SV), Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille, Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204 (CIIL), Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Centre National de la Recherche Scientifique (CNRS), We are grateful to the institutions that support our laboratory (Inserm), University of Lille, Institut Pasteur de Lille, CNRS, EU, Région Hauts de France and Pôle de Recherche Interdisciplinaire du Médicament (PRIM). AT thanks to the association ‘les Amis de l'Institut Pasteur à Bruxelles’ for the PhD fellowship. SS thanks the STDF for the support of HSBR (5590). RW is Research Associate at the National Fund for Scientific Research FNRS-FRS (Belgium)., ANR-14-CE14-0027,Tea-4-Two,Reprogrammation de la bioactivation des thioamides comme alternative antituberculeuse(2014), Centre National de la Recherche Scientifique (CNRS)-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Université de Lille-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Willand, Nicolas, Appel à projets générique - Reprogrammation de la bioactivation des thioamides comme alternative antituberculeuse - - Tea-4-Two2014 - ANR-14-CE14-0027 - Appel à projets générique - VALID, Department of Bio-engineering Sciences, and Structural Biology Brussels
Subjects: Protein Folding, Stereochemistry, Protein Conformation, Biochimie, Chimie analytique, Biophysics, Repressor, Biophysique, Ligands, 01 natural sciences, Biochemistry, DNA-binding protein, Drug design, Analytical Chemistry, Mycobacterium tuberculosis, 03 medical and health sciences, chemistry.chemical_compound, Binding interaction, [CHIM.CRIS]Chemical Sciences/Cristallography, Molecule, Tuberculosis, TetR, [CHIM.CRIS] Chemical Sciences/Cristallography, Ethionamide, Molecular Biology, 030304 developmental biology, X-ray crystallography, 0303 health sciences, biology, 010405 organic chemistry, Chemistry, Hydrogen bond, Biologie moléculaire, biology.organism_classification, Small molecule, 0104 chemical sciences, 3. Good health, Repressor Proteins, Protein Multimerization, Protein ligand
Abstract: The Mycobacterium tuberculosis EthR is a member of the TetR family of repressors, controlling the expression of EthA, a mono-oxygenase responsible for the bioactivation of the prodrug ethionamide. This protein was established as a promising therapeutic target against tuberculosis, allowing, when inhibited by a drug-like molecule, to boost the action of ethionamide. Dozens of EthR crystal structures have been solved in complex with ligands. Herein, we disclose EthR structures in complex with 18 different small molecules and then performed in-depth analysis on the complete set of EthR structures that provides insights on EthR-ligand interactions. The 81 molecules solved in complex with EthR show a large diversity of chemical structures that were split up into several chemical clusters. Two of the most striking common points of EthR-ligand interactions are the quasi-omnipresence of a hydrogen bond bridging compounds with Asn179 and the high occurrence of π-π interactions involving Phe110. A systematic analysis of the protein-ligand contacts identified eight hot spot residues that defined the basic structural features governing the binding mode of small molecules to EthR. Implications for the design of new potent inhibitors are discussed., SCOPUS: ar.j, info:eu-repo/semantics/published
Published: 2018

40. Mitochondrial MDM2 regulates respiratory complex i activity independently of p53

Author: Kevin Nay, Romain Riscal, Christelle Bertrand-Gaday, Craig E. Cameron, Christelle Koechlin-Ramonatxo, Madi Y. Cissé, Laurent Le Cam, Béatrice Chabi, Béatrice Orsetti, Laetitia K. Linares, Kerren Murray, Charles Vincent, Hervé Dubouchaud, Laurie Gayte, Markus Kastner, Samuel Pyrdziak, Florence Bernex, Giuseppe Arena, Miria Ricchetti, François Casas, Laurent Chatre, Claire Angebault-Prouteau, Maryse Fuentes, Sandrine Etienne-Manneville, Anne Lombès, Jamie J. Arnold, Jean-Christophe Marine, Institut de Recherche en Cancérologie de Montpellier (IRCM - U1194 Inserm - UM), CRLCC Val d'Aurelle - Paul Lamarque-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), Cellules Souches et Développement / Stem Cells and Development, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Pennsylvania State University (Penn State), Penn State System, Dynamique Musculaire et Métabolisme (DMEM), Institut National de la Recherche Agronomique (INRA)-Université de Montpellier (UM), CHU Montpellier, Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), Polarité cellulaire, Migration et Cancer - Cell Polarity, Migration and Cancer, Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), VIB [Belgium], BioCampus Montpellier (BCM), Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Institut Cochin (IC UM3 (UMR 8104 / U1016)), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratory of Fundamental and Applied Bioenergetics = Laboratoire de bioénergétique fondamentale et appliquée (LBFA), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), This research was supported by grants from the Ligue contre le Cancer (Equipe labelisée 2016), the French National Health Institute for Biomedical Research (INSERM), the French National Cancer Institute (INCa), the General Direction for Care Provision (grant INCa-DGOS-Inserm 6045), and The Laboratory of Excellence EpiGenMed, ANR-10-LABX-0012,EpiGenMed,From Genome and Epigenome to Molecular Medicine: turning new paradigms in biology into the therapeutic strategies of tomorrow(2010), Cellules Souches et Développement, Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA), Polarité cellulaire, Migration et Cancer / Cell Polarity, Migration and Cancer, Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Laboratoire de bioénergétique fondamentale et appliquée (LBFA), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes (UGA), This research was supported by grants from the Ligue contre le Cancer (Equipe labelisée 2016), the French National Health Institute for Biomedical Research (INSERM), the French National Cancer Institute (INCa), the General Direction for Care Provision (grant INCa-DGOS-Inserm 6045), and The Laboratory of Excellence EpiGenMed (grant ANR-10-LABX-12-01), ANR-10-LABX-0012/10-LABX-0012,EpiGenMed,From Genome and Epigenome to Molecular Medicine: turning new paradigms in biology into the therapeutic strategies of tomorrow(2010), ProdInra, Archive Ouverte, Laboratoires d'excellence - From Genome and Epigenome to Molecular Medicine: turning new paradigms in biology into the therapeutic strategies of tomorrow - - EpiGenMed2010 - ANR-10-LABX-0012 - LABX - VALID, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), BioCampus (BCM), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Radiothérapie moléculaire (UMR 1030), Université Paris-Sud - Paris 11 (UP11)-Institut Gustave Roussy (IGR)-Institut National de la Santé et de la Recherche Médicale (INSERM), CRLCC Val d'Aurelle - Paul Lamarque-Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM), Perelman School of Medicine, University of Pennsylvania [Philadelphia], Laboratoire Mouvement Sport Santé (M2S), École normale supérieure - Cachan (ENS Cachan)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Université de Brest (UBO)-Université de Rennes 2 (UR2), Université de Rennes (UNIV-RENNES)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Physiologie & médecine expérimentale du Cœur et des Muscles [U 1046] (PhyMedExp), Perception et Mémoire, Institut national de la recherche agronomique [Montpellier] (INRA Montpellier), Institut de recherche en cancérologie de Montpellier (IRCM - U896 Inserm - UM1), Université Montpellier 1 (UM1)-CRLCC Val d'Aurelle - Paul Lamarque-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), Centre de Génétique Humaine, Université Catholique de Louvain (UCL), Génétique Moléculaire et Cellulaire (UGMC), École nationale vétérinaire d'Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA), Université Grenoble Alpes (UGA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Joseph Fourier - Grenoble 1 (UJF), Génétique Moléculaire des Levures, Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Université Montpellier 1 (UM1), Institut de Génétique Moléculaire de Montpellier (IGMM), and Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Mitochondrial ROS, Lung Neoplasms, Transcription, Genetic, [SDV]Life Sciences [q-bio], translocation, Biochemistry, biophysics & molecular biology [F05] [Life sciences], Mitochondrion, dna, migration, medicine.disease_cause, Adenocarcinoma/genetics/metabolism/pathology, Mice, Cell Movement, Carcinoma, Non-Small-Cell Lung, Tumor Cells, Cultured, Carcinoma, Non-Small-Cell Lung/genetics/metabolism/pathology, Biochimie, biophysique & biologie moléculaire [F05] [Sciences du vivant], ComputingMilieux_MISCELLANEOUS, Mice, Knockout, biology, Proto-Oncogene Proteins c-mdm2/genetics/metabolism, apoptosis, Proto-Oncogene Proteins c-mdm2, Cell biology, Mitochondria, Electron Transport Complex I/genetics/metabolism, mitochondria, [SDV] Life Sciences [q-bio], Gene Expression Regulation, Neoplastic, medicine.anatomical_structure, Cell Transformation, Neoplastic, Mdm2, MT-ND6, transcription, Signal Transduction, respiratory complex I, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Adenocarcinoma, Cell Transformation, Neoplastic/genetics/metabolism/pathology, Article, Mitochondria/genetics/metabolism/pathology, 03 medical and health sciences, MDM2, medicine, Animals, Humans, metastasis, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Neoplasm Invasiveness, skeletal muscle, Molecular Biology, Lung Neoplasms/genetics/metabolism/pathology, Electron Transport Complex I, hypoxia, Skeletal muscle, Cell Biology, Xenograft Model Antitumor Assays, initiation, Mice, Inbred C57BL, Oxidative Stress, 030104 developmental biology, Apoptosis, Tumor progression, Tumor Suppressor Protein p53/genetics/metabolism, Genome, Mitochondrial, biology.protein, activation, Tumor Suppressor Protein p53, protein import, Carcinogenesis
Abstract: International audience; Accumulating evidence indicates that the MDM2 oncoprotein promotes tumorigenesis beyond its canonical negative effects on the p53 tumor suppressor, but these p53-independent functions remain poorly understood. Here, we show that a fraction of endogenous MDM2 is actively imported in mitochondria to control respiration and mitochondrial dynamics independently of p53. Mitochondrial MDM2 represses the transcription of NADH-dehydrogenase 6 (MT-ND6) in vitro and in vivo, impinging on respiratory complex I activity and enhancing mitochondrial ROS production. Recruitment of MDM2 to mitochondria increases during oxidative stress and hypoxia. Accordingly, mice lacking MDM2 in skeletal muscles exhibit higher MT-ND6 levels, enhanced complex I activity, and increased muscular endurance in mild hypoxic conditions. Furthermore, increased mitochondrial MDM2 levels enhance the migratory and invasive properties of cancer cells. Collectively, these data uncover a previously unsuspected function of the MDM2 oncoprotein in mitochondria that play critical roles in skeletal muscle physiology and may contribute to tumor progression.
Published: 2018

41. The Transcription Factor ZEB2 Is Required to Maintain the Tissue-Specific Identities of Macrophages

Author: Wendy Toussaint, Clare Pridans, Sandrine Henri, Helena Todorov, Bernard Malissen, Pieter De Bleser, Patrick De Baetselier, Johnny Bonnardel, Peter Vandenabeele, David A. Hume, Martin Guilliams, Bavo Vanneste, Niels Vandamme, Jo A. Van Ginderachter, Bart N. Lambrecht, Alain Beschin, Yvan Saeys, Robrecht Cannoodt, Liesbet Martens, Charlotte L. Scott, Dorine Sichien, Simon Milling, Wouter Saelens, Sofie De Prijck, Geert Berx, Wouter T’Jonck, Nozomi Takahashi, Bieke Soen, Cell Biology and Histology, Medical Biochemistry, Vriendenkring VUB, Cellular and Molecular Immunology, Department of Bio-engineering Sciences, Faculty of Sciences and Bioengineering Sciences, VIB-UGent Center for Inflammation Research [Gand, Belgique] (IRC), VIB [Belgium], Department of Biomedical Molecular Biology [Ghent], Universiteit Gent = Ghent University [Belgium] (UGENT), College of Medical, Veterinary and Life Sciences [UK], University of Glasgow, Data Mining and Modelling for Biomedicine [Ghent, Belgium], VIB Center for Inflammation Research [Ghent, Belgium], Unit of Immunoregulation and Mucosal Immunology [Ghent, Belgium], VIB Inflammation Research Center [Ghent, Belgium], Molecular and Cellular Oncology Lab, Inflammation Research Center, VIB, Department of Biomedical Molecular Biology, Cancer Research Institute Ghent (CRIG), Ghent University Hospital, Department of Cell Biology and Genetics, Erasmus University Medical Center [Rotterdam] (Erasmus MC), Centre d'Immunologie de Marseille - Luminy (CIML), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU), The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Department of Respiratory Medicine, Imperial College London, Vrije Universiteit Brussel - Myeloid Cell immunology Laboratory, Vrije Universiteit Brussel (VUB), Laboratory of cellular & Molecular Immunology [Vrije Universiteit Brussel], Department of Applied Mathematics, Computer Science and Statistics [Ghent, Belgium], Universiteit Gent = Ghent University (UGENT), and Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Male, 0301 basic medicine, HOMEOSTASIS, LXRα, Macrophage, Clec4f-cre, MOUSE, infectious diseases, Mice, 0302 clinical medicine, Medicine and Health Sciences, Immunology and Allergy, TRANSCRIPTION FACTOR, Lung, IN-VIVO, Liver X Receptors, ZEB2, Kupffer cell, COLONY-STIMULATING FACTOR, Cell biology, Gene Expression Regulation, Neoplastic, DIFFERENTIATION, medicine.anatomical_structure, Liver, MONOCYTES, 030220 oncology & carcinogenesis, [SDV.IMM]Life Sciences [q-bio]/Immunology, Female, EXPRESSION, Epithelial-Mesenchymal Transition, Lineage (genetic), Kupffer Cells, Immunology, Mice, Transgenic, Biology, DENDRITIC CELLS, Article, 03 medical and health sciences, Immune system, RESIDENT MACROPHAGES, Identity, medicine, Animals, Cell Lineage, Epithelial–mesenchymal transition, Transcription factor, Zinc Finger E-box Binding Homeobox 2, Biology and Life Sciences, Colony-stimulating factor, Mice, Inbred C57BL, MICE, 030104 developmental biology, Fcgr1-cre, Homeostasis
Abstract: Summary Heterogeneity between different macrophage populations has become a defining feature of this lineage. However, the conserved factors defining macrophages remain largely unknown. The transcription factor ZEB2 is best described for its role in epithelial to mesenchymal transition; however, its role within the immune system is only now being elucidated. We show here that Zeb2 expression is a conserved feature of macrophages. Using Clec4f-cre, Itgax-cre, and Fcgr1-cre mice to target five different macrophage populations, we found that loss of ZEB2 resulted in macrophage disappearance from the tissues, coupled with their subsequent replenishment from bone-marrow precursors in open niches. Mechanistically, we found that ZEB2 functioned to maintain the tissue-specific identities of macrophages. In Kupffer cells, ZEB2 achieved this by regulating expression of the transcription factor LXRα, removal of which recapitulated the loss of Kupffer cell identity and disappearance. Thus, ZEB2 expression is required in macrophages to preserve their tissue-specific identities., Graphical Abstract, Highlights • ZEB2 is highly expressed across the macrophage lineage • ZEB2 preserves the tissue-specific identities of macrophages across tissues • ZEB2 deficient macrophages are outcompeted by WT counterparts • LXRα is crucial for Kupffer cell identity and is maintained by ZEB2, Scott et al. demonstrate that ZEB2 is critical for maintaining the tissue identities of macrophages. Loss of ZEB2 results in tissue-specific changes in different macrophage populations and their subsequent disappearance. In Kupffer cells, ZEB2 maintains LXRα expression, loss of which reproduces the change in Kupffer cell identity and their disappearance.
Published: 2018
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42. Nonselective Chemical Inhibition of Sec7 Domain-Containing ARF GTPase Exchange Factors

Author: Steven De Munck, Riet De Rycke, Bram Denoo, Sacco C. de Vries, Jan Hullaert, Wim Annaert, Isha Sharma, Kaija Goodman, Wim Dejonghe, Johan M. Winne, Marisa S. Otegui, François Peurois, Wim Nerinckx, Andrzej Drozdzecki, Annemieke Madder, Jacqueline Cherfils, Marine Bretou, Qing Lu, Sara Martins, Sjef Boeren, Grégory Vert, Kamila Kalinowska, Veronique Storme, Long Nguyen, Dominique Audenaert, Erika Isono, Kiril Mishev, Savvas N. Savvides, Eugenia Russinova, Laboratoire de Biologie et de Pharmacologie Appliquée (LBPA), École normale supérieure - Cachan (ENS Cachan)-Centre National de la Recherche Scientifique (CNRS), Department of Plant Systems Biology, Flanders Institute for Biotechnology, Ghent University Hospital, Laboratory of Biochemistry, Wageningen University and Research [Wageningen] (WUR), Immunité et cancer (U932), Université Paris Descartes - Paris 5 (UPD5)-Institut Curie [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratory for Protein Biochemistry and Biomolecular Engineering, Department of Biochemistry, Physiology and Microbiology, Universiteit Gent = Ghent University [Belgium] (UGENT), Department of Plant Biotechnology and Bioinformatics, Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Ghent University, Compound Screening Facility, VIB, Signalisation Cellulaire et Ubiquitination chez les plantes (UBINET), Département Biologie Cellulaire (BioCell), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Organic and Biomimetic Chemistry Research Group, VIB-UGent Center for Inflammation Research [Gand, Belgique] (IRC), VIB [Belgium], Laboratory for Protein Biochemistry and Biomolecular Engineering, Department of Biochemistry and Microbiology, Laboratory of Membrane Trafficking and VIB11, Center for Human Genetics, Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Polymer Research Group, State Univ Ghent, Department of Systems Biology, Institut d’Électronique, de Microélectronique et de Nanotechnologie (IEMN) - UMR 8520 (IEMN), Ecole Centrale de Lille-Institut supérieur de l'électronique et du numérique (ISEN)-Université de Valenciennes et du Hainaut-Cambrésis (UVHC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université Polytechnique Hauts-de-France (UPHF), Ghent University [Belgium] (UGENT), Laboratoire de dynamique membranaire et maladies neurologiques (UMR 8192), Université Paris Descartes - Paris 5 (UPD5)-Centre National de la Recherche Scientifique (CNRS), VIB Inflammation Research Center, Laboratoire d'enzymologie et biochimie structurales (LEBS), Centre National de la Recherche Scientifique (CNRS), Universiteit Gent = Ghent University (UGENT), Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Curie [Paris]-Université Paris Descartes - Paris 5 (UPD5), Universiteit Gent [Ghent], Centre National de la Recherche Scientifique (CNRS)-Université de Lille-Université Polytechnique Hauts-de-France (UPHF)-Ecole Centrale de Lille-Université Polytechnique Hauts-de-France (UPHF)-Institut supérieur de l'électronique et du numérique (ISEN), Wageningen University and Research Centre [Wageningen] (WUR), Centre National de la Recherche Scientifique (CNRS)-Université Paris Descartes - Paris 5 (UPD5), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay, Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay-Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay-Institut de Biologie Intégrative de la Cellule (I2BC), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay-Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay, Université Paris Descartes - Paris 5 (UPD5)-Institut Curie-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), and Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, ADP ribosylation factor, Endosome, [SDV]Life Sciences [q-bio], Arabidopsis, Biochemie, Endosomes, Plant Science, arabidopsis-thaliana, Biology, receptor kinase bri1, Endocytosis, Biochemistry, UBINET, Piperazines, 03 medical and health sciences, symbols.namesake, chemistry.chemical_compound, golgi network/early endosome, BIOCELL, Guanine Nucleotide Exchange Factors, Life Science, Endomembrane system, endomembrane trafficking, Research Articles, brefeldin-a, Brefeldin A, protein complexes, Arabidopsis Proteins, plasma-membrane, plant-cells, Cell Biology, Golgi apparatus, Plants, Genetically Modified, Transport protein, Cell biology, wide analysis, Protein Transport, small molecules, 030104 developmental biology, chemistry, Vacuoles, symbols, Phthalazines, Guanine nucleotide exchange factor, Protein Kinases
Abstract: International audience; Small GTP-binding proteins from the ADP-ribosylation factor (ARF) family are important regulators of vesicle formation and cellular trafficking in all eukaryotes. ARF activation is accomplished by a protein family of guanine nucleotide exchange factors (GEFs) that contain a conserved catalytic Sec7 domain. Here, we identified and characterized Secdin, a small-molecule inhibitor of Arabidopsis thaliana ARF-GEFs. Secdin application caused aberrant retention of plasma membrane (PM) proteins in late endosomal compartments, enhanced vacuolar degradation, impaired protein recycling, and delayed secretion and endocytosis. Combined treatments with Secdin and the known ARF-GEF inhibitor Brefeldin A (BFA) prevented the BFA-induced PM stabilization of the ARF-GEF GNOM, impaired its translocation from the Golgi to the trans-Golgi network/early endosomes, and led to the formation of hybrid endomembrane compartments reminiscent of those in ARF-GEF-deficient mutants. Drug affinity-responsive target stability assays revealed that Secdin, unlike BFA, targeted all examined Arabidopsis ARF-GEFs, but that the interaction was probably not mediated by the Sec7 domain because Secdin did not interfere with the Sec7 domain-mediated ARF activation. These results show that Secdin and BFA affect their protein targets through distinct mechanisms, in turn showing the usefulness of Secdin in studies in which ARF-GEF-dependent endomembrane transport cannot be manipulated with BFA.
Published: 2018

43. Nanoscopic X-ray fluorescence imaging and quantification of intracellular key-elements in cryofrozen Friedreich’s ataxia fibroblasts

Author: Rudy Van Coster, Eline Meul, Brecht Laforce, Björn De Samber, Peter Cloetens, Peter Vandenabeele, Michiel De Bruyne, Riet De Rycke, Sylvain Bohic, Joél Smet, Boel De Paepe, Tom Vanden Berghe, Universiteit Gent = Ghent University [Belgium] (UGENT), VIB-UGent Center for Inflammation Research [Gand, Belgique] (IRC), VIB [Belgium], Grenoble Institut des Neurosciences (GIN), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Santé et de la Recherche Médicale (INSERM), European Synchrotron Radiation Facility (ESRF), ORANGE, Colette, and Universiteit Gent = Ghent University (UGENT)
Subjects: 0301 basic medicine, Cytoplasm, Luminescence, Glaciology, [SDV]Life Sciences [q-bio], Synchrotron radiation, lcsh:Medicine, PROTEIN, COPPER, Negative Staining, YEAST FRATAXIN, ZINC, 0302 clinical medicine, Limit of Detection, Animal Cells, Ice Cores, Medicine and Health Sciences, Group-Specific Staining, Nanotechnology, OXIDATIVE STRESS, lcsh:Science, Chemical composition, Connective Tissue Cells, Staining, Multidisciplinary, Chemistry, IRON, Physics, Electromagnetic Radiation, Reference Standards, Fluorescence, [SDV] Life Sciences [q-bio], DEFICIENCY, Zinc, medicine.anatomical_structure, Connective Tissue, Physical Sciences, LIBRARY, Prussian Blue Staining, Cellular Types, Anatomy, Cellular Structures and Organelles, Elementary Particles, Research Article, Chemical Elements, Iron, chemistry.chemical_element, X-ray fluorescence, Research and Analysis Methods, 03 medical and health sciences, REDISTRIBUTION, medicine, Humans, Fibroblast, Particle Physics, Nanoscopic scale, Cryopreservation, Photons, CARDIOMYOPATHY, lcsh:R, Spectrometry, X-Ray Emission, Correction, Biology and Life Sciences, Cell Biology, Fibroblasts, 030104 developmental biology, Biological Tissue, Friedreich Ataxia, Specimen Preparation and Treatment, Biophysics, Earth Sciences, lcsh:Q, 030217 neurology & neurosurgery
Abstract: International audience; Synchrotron radiation based nanoscopic X-ray fluorescence (SR nano-XRF) analysis can visualize trace level elemental distribution in a fully quantitative manner within single cells. However, in-air XRF analysis requires chemical fixation modifying the cell's chemical composition. Here, we describe first nanoscopic XRF analysis upon cryogenically frozen (-150 degrees C) fibroblasts at the ID16A-NI 'Nano-imaging' end-station located at the European Synchrotron Radiation Facility (ESRF) in Grenoble (France). Fibroblast cells were obtained from skin biopsies from control and Friedreich's ataxia (FRDA) patients. FRDA is an autosomal recessive disorder with dysregulation of iron metabolism as a key feature. By means of the X-ray Fundamental Parameter (FP) method, including absorption correction of the ice layer deposited onto the fibroblasts, background-corrected mass fraction elemental maps of P, S, Cl, K, Ca, Fe and Zn of entire cryofrozen human fibroblasts were obtained. Despite the presence of diffracting microcrystals in the vitreous ice matrix and minor sample radiation damage effects, clusters of iron-rich hot-spots with similar mass fractions were found in the cytoplasm of both control and FRDA fibroblasts. Interestingly, no significant difference in the mean iron concentration was found in the cytoplasm of FRDA fibroblasts, but a significant decrease in zinc concentration. This finding might underscore metal dysregulation, beyond iron, in cells derived from FRDA patients. In conclusion, although currently having slightly increased limits of detection (LODs) compared to non-cryogenic mode, SR based nanoscopic XRF under cryogenic sample conditions largely obliterates the debate on chemical sample preservation and provides a unique tool for trace level elemental imaging in single cells close to their native state with a superior spatial resolution of 20 nm.
Published: 2018

44. Rational Design of Nanobody80 Loop Peptidomimetics

Author: Cecilia Betti, Els Pardon, Daniel Sejer Pedersen, May C. Morris, Samuel L. C. Moors, Krisztina Fehér, Jesper Mosolff Mathiesen, Jan Steyaert, Mia Danielsen, Frank De Proft, Cecilia Fabris, Nick Devoogdt, Marion Peyressatre, Vicky Caveliers, Charlotte Martin, Steven Ballet, José C. Martins, Chemistry, WE Academic Unit, Department of Bio-engineering Sciences, Faculty of Sciences and Bioengineering Sciences, Structural Biology Brussels, Translational Imaging Research Alliance, Medical Imaging, Supporting clinical sciences, General Chemistry, Vrije Universiteit Brussel (VUB), University of Copenhagen = Københavns Universitet (KU), Department of Drug Design and Pharmacology [Copenhagen] (ILF), Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), VIB-VUB Center for Structural Biology [Bruxelles], VIB [Belgium], Institut des Biomolécules Max Mousseron [Pôle Chimie Balard] (IBMM), Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université de Montpellier (UM)-Ecole Nationale Supérieure de Chimie de Montpellier (ENSCM), Department of Organic and Macromolecular Chemistry, Universiteit Gent = Ghent University [Belgium] (UGENT), NMR and Structure Analysis Unit, In vivo Cellular and Molecular Imaging Laboratory, and Eenheid Algemene Chemie
Subjects: 0301 basic medicine, Protein-protein interactions, Stereochemistry, G protein, Peptidomimetic, receptors, Plasma protein binding, protein–protein interactions, 01 natural sciences, Catalysis, Protein–protein interaction, 03 medical and health sciences, MESH: Receptors, Adrenergic, Beta-2 / metabolism, Protein structure, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Binding site, G protein-coupled receptor, MESH: Optical Imaging, MESH: Peptidomimetics / chemical synthesis, 010405 organic chemistry, Chemistry, Organic Chemistry, Rational design, MESH: Single-Domain Antibodies / chemistry, General Chemistry, nanobodies, 0104 chemical sciences, 030104 developmental biology, MESH: HEK293 Cells, peptidomimetics, protein structures, [SDV.IB]Life Sciences [q-bio]/Bioengineering
Abstract: International audience; G protein-coupled receptors (GPCRs) play an important role in many cellular responses; as such, their mechanism of action is of utmost interest. To gain insight into the active conformation of GPCRs, the X-ray crystal structures of nanobody (Nb)-stabilized β2 -adrenergic receptor (β2 AR) have been reported. Nb80, in particular, is able to bind the intracellular G protein binding site of β2 AR and stabilize the receptor in an active conformation. Within Nb80, the complementarity-determining region 3 (CDR3) is responsible for most of the binding interactions. Hence, we hypothesized that peptidomimetics of the CDR3 loop might be sufficient for binding to the receptor, inhibiting the interaction of β2 AR with intracellular GPCR interacting proteins (e.g., G proteins). Based on previous crystallographic data, a set of peptidomimetics were synthesized that, similar to the Nb80 CDR3 loop, adopt a β-hairpin conformation. Syntheses, conformational analysis, binding and functional in vitro assays, as well as internalization experiments, were performed. We demonstrate that peptidomimetics can structurally mimic the CDR3 loop of a nanobody and its function by inhibiting G protein coupling as measured by partial inhibition of cAMP production.
Published: 2017

45. Neutrophilic NLRP3 inflammasome-dependent IL-1β secretion regulates the γδT17 cell response in respiratory bacterial infections

Author: Lance E. Keller, Mohamed Lamkanfi, J-C Sirard, Christophe Paget, EC Patin, Daphnée Soulard, Dieter Demon, Aras Kadioglu, Christelle Faveeuw, Immo Prinz, J-W Veening, Josette Fontaine, Rémi Porte, Maya Hassane, François Trottein, Bernhard Ryffel, Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204 (CIIL), Centre National de la Recherche Scientifique (CNRS)-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Université de Lille-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Faculté des Sciences, Université Libanaise, Universiteit Gent = Ghent University [Belgium] (UGENT), VIB-UGent Center for Inflammation Research [Gand, Belgique] (IRC), VIB [Belgium], Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen [Groningen], Hannover Medical School [Hannover] (MHH), Immunologie et Neurogénétique Expérimentales et Moléculaires (INEM), Centre National de la Recherche Scientifique (CNRS)-Université d'Orléans (UO), University of Cape Town, Institute of Infection and Global Health [University of Liverpool, UK], University of Liverpool, C.P., J.-C.S., and C.F. were supported by INSERM. B.R. and F.T. were supported by CNRS. Work in M.L.’s laboratory is supported by VIB, Ghent University (BOF 01N02313, BOF 01J11113, BOF14/GOA/013), the Fund for Scientific Research-Flanders (grants G030212N and G011315N), and the European Research Council (grant 281600). M.H. was the recipient of a doctoral fellowship from the AZM foundation. E.C.P. was supported by a post-doctoral fellowship from the French Institute of cancer (INCa)., Dr Isabelle Wolowczuk (CIIL, Institut Pasteur, Lille) is acknowledged for critical reading of this manuscript. We thank Nathalie Messéant and Bruno Couvreur for mouse husbanding. We also thank Aurélie Maillard, Pauline Chenuet, and the BICeL flow cytometry core facility for technical assistance., Sirard, Jean-Claude, Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Centre National de la Recherche Scientifique (CNRS), Universiteit Gent = Ghent University (UGENT), Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS), Centre d’Etude des Pathologies Respiratoires (CEPR), UMR 1100 (CEPR), Université de Tours-Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Tours (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM), and Molecular Genetics
Subjects: 0301 basic medicine, Male, Inflammasomes, Neutrophils, [SDV]Life Sciences [q-bio], Interleukin-1beta, MESH: Interleukin-1beta/metabolism, MESH: Mice, Knockout, MESH: Th17 Cells/immunology, Mice, 0302 clinical medicine, MESH: Bacterial Proteins/immunology, Immunology and Allergy, MESH: Animals, Respiratory Tract Infections, ComputingMilieux_MISCELLANEOUS, Cells, Cultured, Mice, Knockout, MESH: Interleukin-17/metabolism, Interleukin-17, MESH: Streptococcus pneumoniae/immunology, Inflammasome, Receptors, Antigen, T-Cell, gamma-delta, 3. Good health, medicine.anatomical_structure, Streptococcus pneumoniae, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Streptolysins, [SDV.IMM]Life Sciences [q-bio]/Immunology, Tumor necrosis factor alpha, medicine.symptom, Cell activation, medicine.drug, MESH: Cells, Cultured, MESH: Streptolysins/immunology, MESH: Macrophages, Alveolar/immunology, [SDV.IMM] Life Sciences [q-bio]/Immunology, T cell, Immunology, MESH: NLR Family, Pyrin Domain-Containing 3 Protein/genetics, MESH: Tumor Necrosis Factor-alpha/metabolism, Inflammation, Biology, MESH: Respiratory Tract Infections/immunology, Pneumococcal Infections, Microbiology, 03 medical and health sciences, Immune system, Bacterial Proteins, MESH: Mice, Inbred C57BL, Macrophages, Alveolar, NLR Family, Pyrin Domain-Containing 3 Protein, medicine, Animals, Humans, Secretion, [SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology, MESH: Mice, MESH: Receptors, Antigen, T-Cell, gamma-delta/genetics, Innate immune system, MESH: Humans, Tumor Necrosis Factor-alpha, MESH: Inflammasomes/metabolism, MESH: Receptors, Antigen, T-Cell, gamma-delta/metabolism, MESH: Neutrophils/immunology, MESH: Interleukin-17/genetics, MESH: Male, Mice, Inbred C57BL, Disease Models, Animal, 030104 developmental biology, Th17 Cells, MESH: Pneumococcal Infections/immunology, MESH: Disease Models, Animal, MESH: NLR Family, Pyrin Domain-Containing 3 Protein/metabolism, 030215 immunology
Abstract: Traditionally regarded as simple foot soldiers of the innate immune response limited to the eradication of pathogens, neutrophils recently emerged as more complex cells endowed with a set of immunoregulatory functions. Using a model of invasive pneumococcal disease, we highlighted an unexpected key role for neutrophils as accessory cells in innate interleukin (IL)-17A production by lung resident Vγ6Vδ1(+) T cells via nucleotide-binding oligomerization domain receptor, pyrin-containing 3 (NLRP3) inflammasome-dependent IL-1β secretion. In vivo activation of the NLRP3 inflammasome in neutrophils required both host-derived and bacterial-derived signals. Elaborately, it relies on (i) alveolar macrophage-secreted TNF-α for priming and (ii) subsequent exposure to bacterial pneumolysin for activation. Interestingly, this mechanism can be translated to human neutrophils. Our work revealed the cellular and molecular dynamic events leading to γδT17 cell activation, and highlighted for the first time the existence of a fully functional NLRP3 inflammasome in lung neutrophils. This immune axis thus regulates the development of a protective host response to respiratory bacterial infections.Mucosal Immunology advance online publication, 4 January 2017; doi:10.1038/mi.2016.113.
Published: 2017

46. Helicobacter pylori Adapts to Chronic Infection and Gastric Disease via pH-Responsive BabA-Mediated Adherence

Author: Verena Königer, D. Scott Merrell, Roman Andriiovych Moskalenko, Rainer Haas, Thomas Borén, Sara Henriksson, Jafar Mahdavi, Abhijit Chowdhury, Johan Ögren, Anders Hofer, Jay V. Solnick, Dan Danielsson, Sara K. Lindén, Dag Ilver, Konstantinos S. Papadakos, Susanne Vikström, Jörgen Ådén, Jan Holgersson, Gerhard Gröbner, Alexej Schmidt, Jeanna Bugaytsova, Oscar Björnham, Göran O. Bylund, Rolf Sjöström, Stefan Oscarson, Dionyssios N. Sgouras, Lori M. Hansen, Yevgen A Chernov, Anders Esberg, Kristof Moonens, Christopher Aisenbrey, Charles Kelly, Ludmilla A. Morozova-Roche, Jeannette M. Whitmire, Beatriz Martinez-Gonzalez, Asish K. Mukhopadhyay, Angela Eldridge, Nicklas Strömberg, Robert H. Gilman, Andre Dubois, Lars Engstrand, Staffan Schedin, Brett A. Chromy, Justine Younson, Matthew Goldman, Anna Shevtsova, Macarena P. Quintana-Hayashi, Hui Liu, Magnus Unemo, Lena Rakhimova, Anna Åberg, Sebastian Suerbaum, Anna Arnqvist, Pär Gideonsson, Maréne Landström, Douglas E. Berg, Kristoffer Brännström, Anders Olofsson, Melissa Mendez, G. Balakrish Nair, Han Remaut, Umeå University, School of Life Sciences, University of Nottingham, UK (UON), Sahlgrenska Academy at University of Gothenburg [Göteborg], Université libre de Bruxelles (ULB), VIB-VUB Center for Structural Biology [Bruxelles], VIB [Belgium], Sumy State University, Max Von Pettenkofer Institute (MVP), Ludwig-Maximilians-Universität München (LMU), Uniformed Services University of the Health Sciences (USUHS), King‘s College London, Johns Hopkins Bloomberg School of Public Health [Baltimore], Johns Hopkins University (JHU), School of Digestive and Liver Diseases [Kolkata] (SDLD), National Institute of Cholera and Enteric Diseases, Translational Health Science and Technology Institute [Faridabad] (THSTI), Institut Pasteur Hellénique, Réseau International des Instituts Pasteur (RIIP), Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Karolinska Institutet [Stockholm], Örebro University Hospital [Örebro, Sweden], Hannover Medical School [Hannover] (MHH), German Center for Infection Research - partner site Hannover-Braunschweig (DZIF), School of Chemistry and Chemical Biology (UCD), University College Dublin [Dublin] (UCD), University of California [Davis] (UC Davis), University of California, German Center for Infection Research, Partnersite Munich (DZIF), Département d'Informatique [Bruxelles] (ULB), Faculté des Sciences [Bruxelles] (ULB), Université libre de Bruxelles (ULB)-Université libre de Bruxelles (ULB), University of California [San Diego] (UC San Diego), This work was supported by grants from Vetenskapsrådet (VR/M) to T.B. and S.K.L., Cancerfonden to T.B. and A.A., VR/NT to A.A. and S. Schedin, Formas to S.K.L., the J.C. Kempe and Seth M. Kempe Memorial Foundation, the Knut and Alice Wallenberg Foundation (2012.0090) to T.B. and M.L., European Union Seventh Framework Program GastricGlycoExplorer ITN grant number 316929 to T.B. and Y.A.C., Magn. Bergvall’s Foundation to S. Schedin, DFG (SFB 900/A1) to S. Suerbaum, DFG (HA2697/16-1) to R.H., FP6 ANR-06-PATHO-00701 ERA-NET and Actions Concertées Inter-Pasteuriennes (ACIP) (2006) to D.N.S., NIH R01DK063041 to D.E.B., NIH CA082312 to D.S.M., NIH AI070803 and AI081037 to J.V.S., CSIR project, India (No. 37(1640)/14/EMR –II) to A.K.M., and VIB and FWO (grants: G033717N and 12H8416N) to K.M. and H.R., This paper is dedicated to the memory of our friend, collaborator, and co-author Dr. Andre Dubois, a great scientist who contributed importantly both intellectually and materially to this project. We thank S. Michopoulos and G. Mantzaris for H. pylori clinical isolates and Ö. Furberg (NoPolo.se), N. Ulander (softplanbangkok.com), S. Lindström, and M. Borén for the digital movie, tech, art, and figure work, respectively., Vrije Universiteit Brussel, Basic (bio-) Medical Sciences, Structural Biology Brussels, and Department of Bio-engineering Sciences
Subjects: 0301 basic medicine, MESH: Hydrogen-Ion Concentration, Gastric acidity, MESH: Helicobacter Infections/pathology, MESH: Helicobacter pylori/physiology, Disease, adaptation, Bacterial Adhesion, polymorphism, acid responsiveness, MESH: Bacterial Adhesion, Bacterial, Hydrogen-Ion Concentration, gastric acidity, Adhesins, 3. Good health, Cell and molecular biology, medicine.anatomical_structure, Infectious Diseases, MESH: Gastric Mucosa/microbiology, Medical Microbiology, 030106 microbiology, Immunology, Digestive Diseases - (Peptic Ulcer), Biology, blood group antigen-binding adhesion, Microbiology, Helicobacter Infections, diversity, Vaccine Related, 03 medical and health sciences, Virology, ABO blood group system, Biodefense, Gastric mucosa, medicine, MESH: Helicobacter Infections/microbiology, multimerization, Adhesins, Bacterial, subpopulations, Helicobacter pylori, Prevention, gastric cancer, MESH: Adhesins, Bacterial/metabolism, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, MESH: Gastric Mucosa/pathology, Bacterial adhesin, Chronic infection, 030104 developmental biology, Emerging Infectious Diseases, Gastric Mucosa, Parasitology, Digestive Diseases
Abstract: The BabA adhesin mediates high-affinity binding of Helicobacter pylori to the ABO blood group antigen-glycosylated gastric mucosa. Here we show that BabA is acid responsive-binding is reduced at low pH and restored by acid neutralization. Acid responsiveness differs among strains; often correlates with different intragastric regions and evolves during chronic infection and disease progression; and depends on pH sensor sequences in BabA and on pH reversible formation of high-affinity binding BabA multimers. We propose that BabA's extraordinary reversible acid responsiveness enables tight mucosal bacterial adherence while also allowing an effective escape from epithelial cells and mucus that are shed into the acidic bactericidal lumen andthat bio-selection and changes in BabA bindingproperties through mutation and recombination with babA-related genes are selected by differencesamong individuals and by changes in gastric acidity over time. These processes generate diverse H.pylori subpopulations, in which BabA's adaptive evolution contributes to H.pylori persistence and overt gastric disease.
Published: 2017

47. Modeling protein-protein and protein-peptide complexes: CAPRI 6th edition

Author: Lensink, Marc, Velankar, Sameer, Wodak, Shoshana J., Unité de Glycobiologie Structurale et Fonctionnelle UMR 8576 (UGSF), Université de Lille-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, VIB-VUB Center for Structural Biology [Bruxelles], VIB [Belgium], and Université de Lille-Centre National de la Recherche Scientifique (CNRS)
Subjects: Binding Sites, Protein Conformation, protein-peptide interation, Proteins, Computational Biology, Water, Capri, water modeling, protein docking, Nucleosomes, Molecular Docking Simulation, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, Benchmarking, Research Design, Multiprotein Complexes, Protein Interaction Mapping, Humans, Blind prediction, Peptides, Algorithms, Software, Protein Binding
Abstract: International audience; We present the sixth report evaluating the performance of methods for predicting the atomic resolution structures of protein complexes offered as targets to the community-wide initiative on the Critical Assessment of Predicted Interactions (CAPRI). The evaluation is based on a total of 20,670 predicted models for 8 protein-peptide complexes, a novel category of targets in CAPRI, and 12 protein-protein targets in CAPRI prediction Rounds held during the years 2013-2016. For two of the protein-protein targets, the focus was on the prediction of side-chain conformation and positions of interfacial water molecules. Seven of the protein-protein targets were particularly challenging owing to their multicomponent nature, to conformational changes at the binding site, or to a combination of both. Encouragingly, the very large multiprotein complex with the nucleosome was correctly predicted, and correct models were submitted for the protein-peptide targets, but not for some of the challenging protein-protein targets. Models of acceptable quality or better were obtained for 14 of the 20 targets, including medium quality models for 13 targets and high quality models for 8 targets, indicating tangible progress of present-day computational methods in modeling protein complexes with increased accuracy. Our evaluation suggests that the progress stems from better integration of different modeling tools with docking procedures, as well as the use of more sophisticated evolutionary information to score models. Nonetheless, adequate modeling of conformational flexibility in interacting proteins remains an important area with a crucial need for improvement. Proteins 2017; 85:359-377. © 2016 Wiley Periodicals, Inc.
Published: 2017

48. Epicutaneous sensitization to house dust mite allergen requires interferon regulatory factor 4-dependent dermal dendritic cells

Author: Manon Vanheerswynghels, Hamida Hammad, Maud Plantinga, Bernard Malissen, Dorine Sichien, Julie Deckers, David Dombrowicz, Bart N. Lambrecht, Justine Van Moorleghem, Martin Guilliams, Esther Hoste, Karolien De Bosscher, Pulmonary Medicine, Unit of Immunoregulation and Mucosal Immunology [Ghent, Belgium], VIB Inflammation Research Center [Ghent, Belgium], Department of Biomedical Molecular Biology [Ghent], Universiteit Gent = Ghent University (UGENT), Centre d'Immunologie de Marseille - Luminy (CIML), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre d'Immunophénomique (CIPHE), Récepteurs nucléaires, maladies cardiovasculaires et diabète - U 1011 (RNMCD), Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), VIB-UGent Center for Inflammation Research [Gand, Belgique] (IRC), VIB [Belgium], Department of Respiratory Medicine, Imperial College London, VIB Inflammation Research Center, Universiteit Gent = Ghent University [Belgium] (UGENT), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU), and Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Institut National de la Santé et de la Recherche Médicale (INSERM)
Subjects: 0301 basic medicine, Adoptive cell transfer, Allergy, Langerhans cell, Immunology, Antigen presentation, Receptors, Antigen, T-Cell, Mice, Transgenic, Arthropod Proteins, Allergic inflammation, Mice, 03 medical and health sciences, Th2 Cells, Hypersensitivity, Animals, Immunology and Allergy, Medicine, Antigens, Dermatophagoides, Cells, Cultured, Sensitization, Skin, House dust mite, Antigen Presentation, integumentary system, biology, business.industry, Pyroglyphidae, Dendritic Cells, Dendritic cell, biology.organism_classification, medicine.disease, 3. Good health, Mice, Inbred C57BL, Cysteine Endopeptidases, 030104 developmental biology, medicine.anatomical_structure, Langerhans Cells, Interferon Regulatory Factors, [SDV.IMM]Life Sciences [q-bio]/Immunology, business
Abstract: International audience; Background: Exposure to allergens, such as house dust mite (HDM), through the skin often precedes allergic inflammation in the lung. It was proposed that T(H)2 sensitization through the skin occurs when skin barrier function is disrupted by, for example, genetic predisposition, mechanical damage, or the enzymatic activity of allergens. Objective: We sought to study how HDM applied to unmanipulated skin leads to T(H)2 sensitization and to study which antigen-presenting cells mediate this process. Methods: HDM was applied epicutaneously by painting HDM on unmanipulated ear skin or under an occlusive tape. HDM challenge was through the nose. Mouse strains lacking different dendritic cell (DC) populations were used, and 1-DER T cells carrying a transgenic T-cell receptor reactive to Der p 1 allergen were used as a readout for antigen presentation. The T(H)2-inducing capacity of sorted skin-derived DC subsets was determined by means of adoptive transfer to naive mice. Results: Epicutaneous HDM application led to T(H)2 sensitization and eosinophilic airway inflammation upon intranasal HDM challenge. Skin sensitization did not require prior skin damage or enzymatic activity within HDM extract, yet was facilitated by applying the allergen under an occlusive tape. Primary proliferation of 1-DER T cells occurred only in the regional skin-draining lymph nodes. Epicutaneous sensitization was found to be driven by 2 variants of interferon regulatory factor 4-dependent dermal type 2 conventional DC subsets and not by epidermal Langerhans cells. Conclusion: These findings identify skin type 2 conventional DCs as crucial players in T(H)2 sensitization to common inhaled allergens that enter the body through the skin and can provoke features of allergic asthma.
Published: 2017

49. The function of Fcγ receptors in dendritic cells and macrophages

Author: Hamida Hammad, Pierre Bruhns, Martin Guilliams, Bart N. Lambrecht, Yvan Saeys, VIB-UGent Center for Inflammation Research [Gand, Belgique] (IRC), VIB [Belgium], Universiteit Gent = Ghent University [Belgium] (UGENT), Anticorps en Thérapie et Pathologie, Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Department of Pulmonary Medicine, Erasmus University Medical Center [Rotterdam] (Erasmus MC), Pulmonary Medicine, Universiteit Gent = Ghent University (UGENT), and Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)
Subjects: History, Antigen presentation, chemical and pharmacologic phenomena, Receptors, Fc, Immune receptor, MESH: Receptors, IgG, Biology, MESH: Phagocytes, Education, 03 medical and health sciences, 0302 clinical medicine, Immune system, Animals, Humans, MESH: Animals, Antibody-dependent enhancement, RNA, Messenger, Antigen-presenting cell, Receptor, MESH: RNA, Messenger, 030304 developmental biology, Antigen Presentation, Phagocytes, 0303 health sciences, MESH: Humans, Innate immune system, MESH: Dendritic Cells, Macrophages, Receptors, IgG, MESH: Macrophages, Cross-presentation, hemic and immune systems, Dendritic Cells, 3. Good health, Computer Science Applications, MESH: Antigen Presentation, Immunology, [SDV.IMM]Life Sciences [q-bio]/Immunology, MESH: Receptors, Fc, 030215 immunology
Abstract: An Erratum to this article was published on 07 April 2014; International audience; Dendritic cells (DCs) and macrophages use various receptors to recognize foreign antigens and to receive feedback control from adaptive immune cells. Although it was long believed that all immunoglobulin Fc receptors are universally expressed by phagocytes, recent findings indicate that only monocyte-derived DCs and macrophages express high levels of activating Fc receptors for IgG (FcγRs), whereas conventional and plasmacytoid DCs express the inhibitory FcγR. In this Review, we discuss how the uptake, processing and presentation of antigens by DCs and macrophages is influenced by FcγR recognition of immunoglobulins and immune complexes in the steady state and during inflammation.
Published: 2014

50. Prediction of homo- and hetero-protein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment

Author: Eichiro Ichiishi, Dmitri Beglov, Bernard Maigret, Gyu Rie Lee, Artem B. Mamonov, Shoshana J. Wodak, Jonathan C. Fuller, Dima Kozakov, Jong Young Joung, Petr Popov, Xiaofeng Yu, Keehyoung Joo, João P. G. L. M. Rodrigues, Anna Vangone, Koen M. Visscher, Xiaoqin Zou, Paul A. Bates, Andriy Kryshtafovych, Shourya S. Roy Burman, Daisuke Kihara, Romina Oliva, Efrat Ben-Zeev, Jeffrey J. Gray, Yang Shen, Li C. Xue, Sameer Velankar, Emilie Neveu, Shruthi Viswanath, Dina Schneidman-Duhovny, Juan Esquivel-Rodríguez, Mieczyslaw Torchala, Amit Roy, Alexandre M. J. J. Bonvin, David R. Hall, Tanggis Bohnuud, Xusi Han, David W. Ritchie, Ron Elber, Daisuke Kuroda, Zhiwei Ma, Joan Segura, Carlos A. Del Carpio, Nicholas A. Marze, Jong Yun Kim, Andrej Sali, Petras J. Kundrotas, Ezgi Karaca, Neil J. Bruce, Chaok Seok, Panagiotis L. Kastritis, Shen You Huang, Ilya A. Vakser, Lim Heo, Sanbo Qin, Raphael A. G. Chaleil, Adrien S. J. Melquiond, Miguel Romero-Durana, Anisah W. Ghoorah, Surendra S. Negi, Andrey Tovchigrechko, Françoise Ochsenbein, Narcis Fernandez-Fuentes, Liming Qiu, Miriam Eisenstein, Mehdi Nellen, Marie-Dominique Devignes, Lenna X. Peterson, Jinchao Yu, Minkyung Baek, Brian G. Pierce, Hasup Lee, Toshiyuki Oda, Rebecca C. Wade, Raphael Guerois, Juan Fernández-Recio, Iain H. Moal, Edrisse Chermak, Sergei Grudinin, Sangwoo Park, Ivan Anishchenko, Chengfei Yan, Thom Vreven, Kentaro Tomii, Bing Xia, Hyung Rae Kim, Chiara Pallara, Jooyoung Lee, Kazunori D. Yamada, Xianjin Xu, Kenichiro Imai, Zhiping Weng, Luigi Cavallo, Tyler M. Borrman, Jianlin Cheng, Marc F. Lensink, Huan-Xiang Zhou, Jilong Li, Gydo C. P. van Zundert, Brian Jiménez-García, Tsukasa Nakamura, Scott E. Mottarella, Sandor Vajda, Institut de Recherche Interdisciplinaire [Villeneuve d'Ascq] ( IRI ), Université de Lille, Sciences et Technologies-Université de Lille, Droit et Santé-Centre National de la Recherche Scientifique ( CNRS ), European Molecular Biology Laboratory, European Bioinformatics Institute, Genome Center [UC Davis], University of California at Davis, Research Support Computing [Columbia], University of Missouri-Columbia, Bioinformatics Consortium and Department of Computer Science [Columbia], Department of Bioengineering and Therapeutic Sciences, University of California [San Francisco] ( UCSF ), Department of Pharmaceutical Chemistry, Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, University of California [San Francisco] ( UCSF ) -California Institute for Quantitative Biosciences, GN7 of the National Institute for Bioinformatics (INB) and Biocomputing Unit, Centro Nacional de Biotecnología (CSIC), Institute of Biological, Environmental and Rural Sciences ( IBERS ), Institute for Computational Engineering and Sciences [Austin] ( ICES ), University of Texas at Austin [Austin], Department of Computer Science, Department of Chemistry, Algorithms for Modeling and Simulation of Nanosystems ( NANO-D ), Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique ( Inria ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -Laboratoire Jean Kuntzmann ( LJK ), Université Pierre Mendès France - Grenoble 2 ( UPMF ) -Université Joseph Fourier - Grenoble 1 ( UJF ) -Institut Polytechnique de Grenoble - Grenoble Institute of Technology-Centre National de la Recherche Scientifique ( CNRS ) -Université Grenoble Alpes ( UGA ) -Université Pierre Mendès France - Grenoble 2 ( UPMF ) -Université Joseph Fourier - Grenoble 1 ( UJF ) -Institut Polytechnique de Grenoble - Grenoble Institute of Technology-Centre National de la Recherche Scientifique ( CNRS ) -Université Grenoble Alpes ( UGA ) -Institut National Polytechnique de Grenoble ( INPG ), Moscow Institute of Physics and Technology [Moscow] ( MIPT ), Seoul National University [Seoul], Florida State University [Tallahassee] ( FSU ), Computational Algorithms for Protein Structures and Interactions ( CAPSID ), Inria Nancy - Grand Est, Institut National de Recherche en Informatique et en Automatique ( Inria ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -Department of Complex Systems, Artificial Intelligence & Robotics ( LORIA - AIS ), Laboratoire Lorrain de Recherche en Informatique et ses Applications ( LORIA ), Institut National de Recherche en Informatique et en Automatique ( Inria ) -Université de Lorraine ( UL ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -Université de Lorraine ( UL ) -Centre National de la Recherche Scientifique ( CNRS ) -Laboratoire Lorrain de Recherche en Informatique et ses Applications ( LORIA ), Institut National de Recherche en Informatique et en Automatique ( Inria ) -Université de Lorraine ( UL ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Lorraine ( UL ) -Centre National de la Recherche Scientifique ( CNRS ), University of Mauritius, Biomolecular Modelling Laboratory, The Francis Crick Institute, Lincoln's Inn Fields Laboratory, G-INCPM, Weizmann Institute of Science, Chemical Research Support [Rehovot], Sealy Center for Structural Biology and Molecular Biophysics, The University of Texas Medical Branch ( UTMB ), Program in Bioinformatics and Integrative Biology [Worcester], University of Massachusetts Medical School [Worcester] ( UMASS ), Institut de Biologie Intégrative de la Cellule ( I2BC ), Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Sud - Paris 11 ( UP11 ), Bijvoet Center for Biomolecular Research [Utrecht], Utrecht University [Utrecht], Dalton Cardiovascular Research Center [Columbia], Department of Computer Science [Columbia], Informatics Intitute, Department of Biochemistry, University of Missouri, UNIVERSITY OF MISSOURI, Toyota Technological Institute at Chicago [Chicago] ( TTIC ), Department of Biological Sciences, Purdue University, Purdue University [West Lafayette], Department of Computer Science [Purdue], Bioinformatics and Computational Biosciences Branch, Rocky Mountain Laboratories, Molecular and Cellular Modeling Group, Heidelberg Institute of Theoretical Studies, Center for Molecular Biology ( ZMBH ), Universität Heidelberg [Heidelberg], Interdisciplinary Center for Scientiﬁc Computing ( IWR ), Department of Molecular Biosciences [Lawrence], University of Kansas [Lawrence] ( KU ), Computational Biology Research Center ( CBRC ), National Institute of Advanced Industrial Science and Technology ( AIST ), Graduate School of Frontier Sciences, The University of Tokyo, Joint BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center - Centro Nacional de Supercomputacion ( BSC - CNS ), Center for In-Silico Protein Science, Korea Institute for Advanced Study ( KIAS ), Center for Advanced Computation, Department of Biomedical Engineering [Boston], Boston University [Boston] ( BU ), Institute of Biological Diversity, International Pacific Institute of Indiana, Drosophila Genetic Resource Center, Kyoto Institute of Technology, International University of Health and Welfare Hospital ( IUHW Hospital ), International University of Health and Welfare Hospital, Department of Chemical and Biomolecular Engineering [Baltimore], Johns Hopkins University ( JHU ), Program in Molecular Biophysics [Baltimore], King Abdullah University of Science and Technology ( KAUST ), University of Naples, J Craig Venter Institute, Structural Biology Research Center, VIB, 1050 Brussels, Belgium, Institut de Recherche Interdisciplinaire [Villeneuve d'Ascq] (IRI), Université de Lille, Sciences et Technologies-Université de Lille, Droit et Santé-Centre National de la Recherche Scientifique (CNRS), European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, University of California [Davis] (UC Davis), University of California (UC)-University of California (UC), University of Missouri [Columbia] (Mizzou), University of Missouri System, University of California [San Francisco] (UC San Francisco), Centro Nacional de Biotecnología [Madrid] (CNB-CSIC), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC)-Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Institute of Biological, Environmental and Rural Sciences (IBERS), Institute for Computational Engineering and Sciences [Austin] (ICES), Algorithms for Modeling and Simulation of Nanosystems (NANO-D), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Laboratoire Jean Kuntzmann (LJK ), Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Moscow Institute of Physics and Technology [Moscow] (MIPT), Seoul National University [Seoul] (SNU), Florida State University [Tallahassee] (FSU), Computational Algorithms for Protein Structures and Interactions (CAPSID), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Department of Complex Systems, Artificial Intelligence & Robotics (LORIA - AIS), Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Biomolecular Modelling Laboratory [London], The Francis Crick Institute [London], Weizmann Institute of Science [Rehovot, Israël], The University of Texas Medical Branch (UTMB), University of Massachusetts Medical School [Worcester] (UMASS), University of Massachusetts System (UMASS)-University of Massachusetts System (UMASS), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Assemblage moléculaire et intégrité du génome (AMIG), Département Biochimie, Biophysique et Biologie Structurale (B3S), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), University of Missouri System-University of Missouri System, Toyota Technological Institute at Chicago [Chicago] (TTIC), Department of Biological Sciences [Lafayette IN], Heidelberg Institute for Theoretical Studies (HITS ), Center for Molecular Biology (ZMBH), Universität Heidelberg [Heidelberg] = Heidelberg University, Interdisciplinary Center for Scientiﬁc Computing (IWR), University of Kansas [Lawrence] (KU), Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), The University of Tokyo (UTokyo), Barcelona Supercomputing Center - Centro Nacional de Supercomputacion (BSC - CNS), Korea Institute for Advanced Study (KIAS), Boston University [Boston] (BU), International University of Health and Welfare Hospital (IUHW Hospital), Johns Hopkins University (JHU), King Abdullah University of Science and Technology (KAUST), University of Naples Federico II = Università degli studi di Napoli Federico II, J. Craig Venter Institute, VIB-VUB Center for Structural Biology [Bruxelles], VIB [Belgium], Centre National de la Recherche Scientifique (CNRS)-Université de Lille, Droit et Santé-Université de Lille, Sciences et Technologies, University of California-University of California, University of California [San Francisco] (UCSF), Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL), University of Naples Federico II, Barcelona Supercomputing Center, NMR Spectroscopy, and Sub NMR Spectroscopy
Subjects: 0301 basic medicine, Protein Conformation, alpha-Helical, Protein Folding, Computer science, International Cooperation, Amino Acid Motifs, Oligomer state, Homoprotein, DATA-BANK, computer.software_genre, Molecular Docking Simulation, Biochemistry, CAPRI Round 30, DESIGN, Structural Biology, ALIGN, Blind prediction, AFFINITY, Protein interaction, Enginyeria biomèdica [Àrees temàtiques de la UPC], ZDOCK, Oligomer State, computer.file_format, Articles, Protein structure prediction, Proteïnes--Investigació, 3. Good health, WEB SERVER, CASP, Thermodynamics, Data mining, CAPRI, Protein docking, Molecular Biology, Algorithms, INTERFACES, Protein Binding, [ INFO.INFO-MO ] Computer Science [cs]/Modeling and Simulation, Bioinformatics, STRUCTURAL BIOLOGY, Computational biology, Molecular Dynamics Simulation, Article, 03 medical and health sciences, [ INFO.INFO-BI ] Computer Science [cs]/Bioinformatics [q-bio.QM], Heteroprotein, Humans, Protein binding, Macromolecular docking, Protein Interaction Domains and Motifs, Homology modeling, ALGORITHM, Protein-protein docking, Internet, Binding Sites, Models, Statistical, 030102 biochemistry & molecular biology, Bacteria, Sequence Homology, Amino Acid, Computational Biology, Proteins, Protein Data Bank, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, Protein Structure, Tertiary, 030104 developmental biology, Structural biology, Docking (molecular), Protein structure, Protein Conformation, beta-Strand, Protein Multimerization, oligomer state, blind prediction, protein interaction, protein docking, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], computer, Software
Abstract: We present the results for CAPRI Round 30, the first joint CASP-CAPRI experiment, which brought together experts from the protein structure prediction and protein–protein docking communities. The Round comprised 25 targets from amongst those submitted for the CASP11 prediction experiment of 2014. The targets included mostly homodimers, a few homotetramers, and two heterodimers, and comprised protein chains that could readily be modeled using templates from the Protein Data Bank. On average 24 CAPRI groups and 7 CASP groups submitted docking predictions for each target, and 12 CAPRI groups per target participated in the CAPRI scoring experiment. In total more than 9500 models were assessed against the 3D structures of the corresponding target complexes. Results show that the prediction of homodimer assemblies by homology modeling techniques and docking calculations is quite successful for targets featuring large enough subunit interfaces to represent stable associations. Targets with ambiguous or inaccurate oligomeric state assignments, often featuring crystal contact-sized interfaces, represented a confounding factor. For those, a much poorer prediction performance was achieved, while nonetheless often providing helpful clues on the correct oligomeric state of the protein. The prediction performance was very poor for genuine tetrameric targets, where the inaccuracy of the homology-built subunit models and the smaller pair-wise interfaces severely limited the ability to derive the correct assembly mode. Our analysis also shows that docking procedures tend to perform better than standard homology modeling techniques and that highly accurate models of the protein components are not always required to identify their association modes with acceptable accuracy. We are most grateful to the PDBe at the European Bioinformatics Institute in Hinxton, UK, for hosting the CAPRI website. Our deepest thanks go to all the structural biologists and to the following structural genomics initiatives: Northeast Structural Genomics Consortium, Joint Center for Structural Genomics, NatPro PSI:Biology, New York Structural Genomics Research Center, Midwest Center for Structural Genomics, Structural Genomics Consortium, for contributing the targets for this joint CASP-CAPRI experiment. MFL acknowledges support from the FRABio FR3688 Research Federation “Structural & Functional Biochemistry of Biomolecular Assemblies.”
Published: 2016

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