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In vivo cell biology of organ morphogenesis

Applicant Affolter Markus
Number 156838
Funding scheme Project funding (Div. I-III)
Research institution Abteilung Zellbiologie Biozentrum Universität Basel
Institution of higher education University of Basel - BS
Main discipline Embryology, Developmental Biology
Start/End 01.12.2014 - 30.11.2017
Approved amount 1'045'589.10
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Keywords (1)

drosophila, zebrafish, cell biology, nanobodies

Lay Summary (German)

Lead
Blutgefässe sind zentrale Bestandteile aller Organe, und doch ist deren Bildung wenig untersucht worden. Unsere Studien mit dem Zebrafisch sollen ein besseres Verständnis für die Blutgefässbildung ergeben.
Lay summary

Wie sich Organe bilden; eine in vivo Studie mit dem Zebrafisch

Die Bildung von Organen im sich entwickelnden Embryo blieb bis anhin wenig erforscht, da es nicht möglich war, vertiefte Einblicke in das Innenleben des Embryos zu erlangen. Mit Hilfe der Fluoreszenzmikroskope und transgene Fischen, die fluoreszierende Proteine in den Blutgefässen exprimieren, ist es heute möglich, die komplexe Entwicklung der Blutgefässe im Detail und zum ersten Mal im lebendigen Tier zu verfolgen. Unsere Studien zielen darauf ab, ein besseres Verständnis der Blutgefässbildung zu erhalten, und dies auf zellulärer und molekularer Ebene. Unsere Studien sollen dazu beitragen, die Blutgefässbildung besser beeinflussen zu können, um eventuell die vielen Krankheiten, die mit abnormalen Gefässen einhergehen oder durch Letztere verursacht werden, besser behandeln zu können.

Direct link to Lay Summary Last update: 28.10.2014

Responsible applicant and co-applicants

Employees

Publications

Publication
Live imaging molecular changes in junctional tension upon VE-cadherin in zebrafish.
Lagendijk Anne Karine, Gomez Guillermo A, Baek Sungmin, Hesselson Daniel, Hughes William E, Paterson Scott, Conway Daniel E, Belting Heinz-Georg, Affolter Markus, Smith Kelly A, Schwartz Martin A, Yap Alpha S, Hogan Benjamin M (2017), Live imaging molecular changes in junctional tension upon VE-cadherin in zebrafish., in Nature communications, 8(1), 1402-1402.
Spatio-temporally separated cortical flows and spindle geometry establish physical asymmetry in fly neural stem cells.
Roubinet Chantal, Tsankova Anna, Pham Tri Thanh, Monnard Arnaud, Caussinus Emmanuel, Affolter Markus, Cabernard Clemens (2017), Spatio-temporally separated cortical flows and spindle geometry establish physical asymmetry in fly neural stem cells., in Nature communications, 8(1), 1383-1383.
Myosin II is not required for Drosophila tracheal branch elongation and cell intercalation.
Ochoa-Espinosa Amanda, Harmansa Stefan, Caussinus Emmanuel, Affolter Markus (2017), Myosin II is not required for Drosophila tracheal branch elongation and cell intercalation., in Development (Cambridge, England), 144(16), 2961-2968.
Dpp from the anterior stripe of cells is crucial for the growth of the Drosophila wing disc.
Matsuda Shinya, Affolter Markus (2017), Dpp from the anterior stripe of cells is crucial for the growth of the Drosophila wing disc., in eLife, 6, 1-13.
Distinct and redundant functions of Esama and VE-cadherin during vascular morphogenesis.
Sauteur Loïc, Affolter Markus, Belting Heinz-Georg (2017), Distinct and redundant functions of Esama and VE-cadherin during vascular morphogenesis., in Development (Cambridge, England), 144(8), 1554-1565.
A nanobody-based toolset to investigate the role of protein localization and dispersal in Drosophila.
Harmansa Stefan, Alborelli Ilaria, Bieli Dimitri, Caussinus Emmanuel, Affolter Markus (2017), A nanobody-based toolset to investigate the role of protein localization and dispersal in Drosophila., in eLife, 6, 1-22.
Flow-Dependent Endothelial YAP Regulation Contributes to Vessel Maintenance.
Nakajima Hiroyuki, Yamamoto Kimiko, Agarwala Sobhika, Terai Kenta, Fukui Hajime, Fukuhara Shigetomo, Ando Koji, Miyazaki Takahiro, Yokota Yasuhiro, Schmelzer Etienne, Belting Heinz-Georg, Affolter Markus, Lecaudey Virginie, Mochizuki Naoki (2017), Flow-Dependent Endothelial YAP Regulation Contributes to Vessel Maintenance., in Developmental cell, 40(6), 523-536.
Absence of 11-keto reduction of cortisone and 11-ketotestosterone in the model organism zebrafish.
Tsachaki Maria, Meyer Arne, Weger Benjamin, Kratschmar Denise V, Tokarz Janina, Adamski Jerzy, Belting Heinz-Georg, Affolter Markus, Dickmeis Thomas, Odermatt Alex (2017), Absence of 11-keto reduction of cortisone and 11-ketotestosterone in the model organism zebrafish., in The Journal of endocrinology, 232(2), 323-335.
deGradFP: A System to Knockdown GFP-Tagged Proteins.
Caussinus Emmanuel, Affolter Markus (2016), deGradFP: A System to Knockdown GFP-Tagged Proteins., in Methods in molecular biology (Clifton, N.J.), 1478, 177-187.
Development and Application of Functionalized Protein Binders in Multicellular Organisms.
Bieli D, Alborelli I, Harmansa S, Matsuda S, Caussinus E, Affolter M (2016), Development and Application of Functionalized Protein Binders in Multicellular Organisms., in International review of cell and molecular biology, 325, 181-213.
Seeing is Believing, or How GFP Changed My Approach to Science.
Affolter Markus (2016), Seeing is Believing, or How GFP Changed My Approach to Science., in Current topics in developmental biology, 116, 1-16.
Amnioserosa cell constriction but not epidermal actin cable tension autonomously drives dorsal closure.
Pasakarnis Laurynas, Frei Erich, Caussinus Emmanuel, Affolter Markus, Brunner Damian (2016), Amnioserosa cell constriction but not epidermal actin cable tension autonomously drives dorsal closure., in Nature cell biology, 18(11), 1161-1172.
Cell behaviors and dynamics during angiogenesis.
Betz Charles, Lenard Anna, Belting Heinz-Georg, Affolter Markus (2016), Cell behaviors and dynamics during angiogenesis., in Development (Cambridge, England), 143(13), 2249-60.
Homeodomain proteins: an update.
Bürglin Thomas R, Affolter Markus (2016), Homeodomain proteins: an update., in Chromosoma, 125(3), 497-521.
Mapping the molecular steps of secretory-lysosome-driven tracheal tube fusion.
Aydogan Vahap, Belting Heinz-Georg, Affolter Markus (2016), Mapping the molecular steps of secretory-lysosome-driven tracheal tube fusion., in Nature cell biology, 18(7), 720-2.
BMP morphogen gradients in flies.
Matsuda Shinya, Harmansa Stefan, Affolter Markus (2016), BMP morphogen gradients in flies., in Cytokine & growth factor reviews, 27, 119-27.
A bacterial type III secretion-based protein delivery tool for broad applications in cell biology.
Ittig Simon J, Schmutz Christoph, Kasper Christoph A, Amstutz Marlise, Schmidt Alexander, Sauteur Loïc, Vigano M Alessandra, Low Shyan Huey, Affolter Markus, Cornelis Guy R, Nigg Erich A, Arrieumerlou Cécile (2015), A bacterial type III secretion-based protein delivery tool for broad applications in cell biology., in The Journal of cell biology, 211(4), 913-31.
Dpp spreading is required for medial but not for lateral wing disc growth.
Harmansa Stefan, Hamaratoglu Fisun, Affolter Markus, Caussinus Emmanuel (2015), Dpp spreading is required for medial but not for lateral wing disc growth., in Nature, 527(7578), 317-22.
Establishment of a Developmental Compartment Requires Interactions between Three Synergistic Cis-regulatory Modules.
Bieli Dimitri, Kanca Oguz, Requena David, Hamaratoglu Fisun, Gohl Daryl, Schedl Paul, Affolter Markus, Slattery Matthew, Müller Martin, Estella Carlos (2015), Establishment of a Developmental Compartment Requires Interactions between Three Synergistic Cis-regulatory Modules., in PLoS genetics, 11(10), 1005376-1005376.
In memoriam--Walter J. Gehring.
Affolter Markus, Nigg Erich A (2015), In memoriam--Walter J. Gehring., in Chromosoma, 124(3), 291-291.
Endothelial cell division in angiogenic sprouts of differing cellular architecture.
Aydogan Vahap, Lenard Anna, Denes Alexandru Stefan, Sauteur Loic, Belting Heinz-Georg, Affolter Markus (2015), Endothelial cell division in angiogenic sprouts of differing cellular architecture., in Biology open, 4(10), 1259-69.
A cellular process that includes asymmetric cytokinesis remodels the dorsal tracheal branches in Drosophila larvae.
Denes Alexandru Stefan, Kanca Oguz, Affolter Markus (2015), A cellular process that includes asymmetric cytokinesis remodels the dorsal tracheal branches in Drosophila larvae., in Development (Cambridge, England), 142(10), 1794-805.
Endothelial cell self-fusion during vascular pruning.
Lenard Anna, Daetwyler Stephan, Betz Charles, Ellertsdottir Elin, Belting Heinz-Georg, Huisken Jan, Affolter Markus (2015), Endothelial cell self-fusion during vascular pruning., in PLoS biology, 13(4), 1002126-1002126.
The Drosophila melanogaster Mutants apblot and apXasta Affect an Essential apterous Wing Enhancer.
Bieli Dimitri, Kanca Oguz, Gohl Daryl, Denes Alexandru, Schedl Paul, Affolter Markus, Müller Martin (2015), The Drosophila melanogaster Mutants apblot and apXasta Affect an Essential apterous Wing Enhancer., in G3 (Bethesda, Md.), 5(6), 1129-43.
Formin-mediated actin polymerization at endothelial junctions is required for vessel lumen formation and stabilization.
Phng Li-Kun, Gebala Véronique, Bentley Katie, Philippides Andrew, Wacker Andrin, Mathivet Thomas, Sauteur Loïc, Stanchi Fabio, Belting Heinz-Georg, Affolter Markus, Gerhardt Holger (2015), Formin-mediated actin polymerization at endothelial junctions is required for vessel lumen formation and stabilization., in Developmental cell, 32(1), 123-32.
Protein interference applications in cellular and developmental biology using DARPins that recognize GFP and mCherry.
Brauchle Michael, Hansen Simon, Caussinus Emmanuel, Lenard Anna, Ochoa-Espinosa Amanda, Scholz Oliver, Sprecher Simon G, Plückthun Andreas, Affolter Markus (2014), Protein interference applications in cellular and developmental biology using DARPins that recognize GFP and mCherry., in Biology open, 3(12), 1252-61.
Cdh5/VE-cadherin promotes endothelial cell interface elongation via cortical actin polymerization during angiogenic sprouting.
Sauteur Loïc, Krudewig Alice, Herwig Lukas, Ehrenfeuchter Nikolaus, Lenard Anna, Affolter Markus, Belting Heinz-Georg (2014), Cdh5/VE-cadherin promotes endothelial cell interface elongation via cortical actin polymerization during angiogenic sprouting., in Cell reports, 9(2), 504-13.
Fibroblast growth factor signaling affects vascular outgrowth and is required for the maintenance of blood vessel integrity.
De Smet Frederik, Tembuyser Bieke, Lenard Anna, Claes Filip, Zhang Jie, Michielsen Christof, Van Schepdael Ann, Herbert Jean-Marc, Bono Françoise, Affolter Markus, Dewerchin Mieke, Carmeliet Peter (2014), Fibroblast growth factor signaling affects vascular outgrowth and is required for the maintenance of blood vessel integrity., in Chemistry & biology, 21(10), 1310-1317.
The evolution of cichlid fish egg-spots is linked with a cis-regulatory change.
Santos M Emília, Braasch Ingo, Boileau Nicolas, Meyer Britta S, Sauteur Loïc, Böhne Astrid, Belting Heinz-Georg, Affolter Markus, Salzburger Walter (2014), The evolution of cichlid fish egg-spots is linked with a cis-regulatory change., in Nature communications, 5, 5149-5149.
Walter Jakob Gehring: A master of developmental biology.
Affolter Markus, Wüthrich Kurt (2014), Walter Jakob Gehring: A master of developmental biology., in Proceedings of the National Academy of Sciences of the United States of America, 111(35), 12574-5.
Dpp/BMP signaling in flies: from molecules to biology.
Hamaratoglu Fisun, Affolter Markus, Pyrowolakis George (2014), Dpp/BMP signaling in flies: from molecules to biology., in Seminars in cell & developmental biology, 32, 128-36.
IV. Tools and methods for studying cell migration and cell rearrangement in tissue and organ development.
Kanca Oguz, Ochoa-Espinosa Amanda, Affolter Markus (2014), IV. Tools and methods for studying cell migration and cell rearrangement in tissue and organ development., in Methods (San Diego, Calif.), 68(1), 228-32.
AmotL2 links VE-cadherin to contractile actin fibres necessary for aortic lumen expansion.
Hultin Sara, Zheng Yujuan, Mojallal Mahdi, Vertuani Simona, Gentili Christian, Balland Martial, Milloud Rachel, Belting Heinz-Georg, Affolter Markus, Helker Christian S M, Adams Ralf H, Herzog Wiebke, Uhlen Per, Majumdar Arindam, Holmgren Lars (2014), AmotL2 links VE-cadherin to contractile actin fibres necessary for aortic lumen expansion., in Nature communications, 5, 3743-3743.
Raeppli: a whole-tissue labeling tool for live imaging of Drosophila development.
Kanca Oguz, Caussinus Emmanuel, Denes Alexandru S, Percival-Smith Anthony, Affolter Markus (2014), Raeppli: a whole-tissue labeling tool for live imaging of Drosophila development., in Development (Cambridge, England), 141(2), 472-80.

Collaboration

Group / person Country
Types of collaboration
Jan Huisken, Max Planck Institute of Molecular Cell Biology and Genetics Germany (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Research Infrastructure
- Exchange of personnel
Andreas Plückthun, Dept. of Biochemistry, University of Zürich Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Aurelien Olichon, Centre de Recherche en Cancerologie de Toulouse, University of Toulouse France (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Research Infrastructure
- Exchange of personnel
Ben Hogan, Institute for Molecular Bioscience, University of Queensland Australia (Oceania)
- in-depth/constructive exchanges on approaches, methods or results
- Publication

Scientific events

Active participation

Title Type of contribution Title of article or contribution Date Place Persons involved
Keynote Lecture 18. Unionstagung der Schweizerischen Gesellschaft für Gefässkrankheiten Talk given at a conference Imaging the Developing Vasculature Uncovers Interesting Endothelial Cell Behavior 02.11.2017 Montreux, Switzerland Affolter Markus;
Lifecourse Biology: from Development to Disease and the Clinic Talk given at a conference Angiogenesis in the Zebrafish Embryo: Novel Mechanisms & Novel Tools 14.09.2017 The Bateson Centre, Sheffield, Great Britain and Northern Ireland Affolter Markus;
International Cells in Motion Symposium 2017 Talk given at a conference Angiogenesis Live: New Insights & New Tools 04.09.2017 Münster, Germany Affolter Markus;
GRC Developmental Biology Talk given at a conference Protein Binders as New Tools to Study Tissue Patterning & Growth 25.06.2017 Mount Holyoke College, South Hadley MA, United States of America Affolter Markus;
ESM-EVBO 2017 - 2nd Joint Meeting Talk given at a conference Vascular Morphogenesis: Novel Mechanisms & Novel Tools 30.05.2017 Geneva, Switzerland Affolter Markus;
The 4th International Workshop on Mammalian Synthetic Biology Talk given at a conference Novel Protein Binder-based Tools for Functional Studies in Developing Organisms 06.05.2017 Boston MA, United States of America Affolter Markus;
9th Kloster Seeon Angiogenesis Molecular Mechanisms & Functional Interactions Talk given at a conference From Cells to Networks: Cell Behavior in Angiogenesis 17.09.2016 Kloster Seeon, Germany Affolter Markus;
EMBO Molecular & Developmental Biology of Drosophila Talk given at a conference Protein binder-mediated morphogen trapping: growth & patterning in the absence of Dpp 21.06.2016 Crete, Greece Affolter Markus;
International FishMed Conference Talk given at a conference Dynamic Imaging in Angiogenesis Research: Cell Behavior in Vascular Remodelling 18.03.2016 Warsaw, Poland Affolter Markus;
Gulbenkian IGC Cell Biology Talk given at a conference Dynamic Imaging in Angiogenesis Research: Cell Behavior in Vascular Remodeling 26.02.2016 Lisbon, Portugal Affolter Markus;
Seminars on Developmental & Stem Cell Biology Talk given at a conference Vascular Morphogenesis in Living Embryos: Novel Mechanisms & Novel Tools 18.12.2015 Pasteur Institute, Paris, France Affolter Markus;
Gordon Research Conference - New Mechanisms in Vascular Patterning & Specialization: From Cells to Functional Networks Talk given at a conference Building Tubular Networks - Morphogenic Principles: An Introduction to Tubulogenesis 03.08.2015 Salve Regina University, Newport RI, United States of America Affolter Markus;
INSERM Workshop: Methodologies & Experimental Strategies in Angiogenesis Research Talk given at a conference Dynamic Imaging in Angiogenesis Research 09.04.2015 Bordeaux, France Affolter Markus;
Frances Crick Institute Talk given at a conference From Genes to Proteins: Live Imaging of the Developing Vasculature in the Zebrafish Embryo 20.02.2015 London, Great Britain and Northern Ireland Affolter Markus;
VIB Faculty of Medicine, KU Leuven Talk given at a conference From Live Imaging to Acute Protein Modification: Novel Approaches to Investigate Protein Function in Living Organisms 12.02.2015 Leuven, Belgium Affolter Markus;


Communication with the public

Communication Title Media Place Year
Talks/events/exhibitions Biologische Vorgänge live erfolgen: Wie sich Blutgefässe bilden und vernetzen German-speaking Switzerland 2016
Talks/events/exhibitions CRISP in der Grundlagenforschung: Eröffnung neuer Horizonte German-speaking Switzerland 2016
Other activities Preparation & provision of zebrafish embryos for external parties e.g. Roche. Ongoing basis. International 2014
Other activities Preparation of Drosophila embryos for school biology classes. Ongoing basis. German-speaking Switzerland 2014

Associated projects

Number Title Start Funding scheme
138651 Zell Zell Interaktionen in der Morphogenese 01.12.2011 Project funding (Div. I-III)
176400 In vivo cell biology of organ morphogenesis 01.12.2017 Project funding (Div. I-III)
164085 Subcellular targeting microscopy - Signaling in Development and Oncology 01.06.2016 R'EQUIP
138651 Zell Zell Interaktionen in der Morphogenese 01.12.2011 Project funding (Div. I-III)
157700 Lightsheet microscopy 01.12.2014 R'EQUIP

Abstract

Project: In vivo cell biology of organ morphogenesis1 .Summary of the research planOrgans and tissues acquire particular three-dimensional shapes during development, which are intimately linked to the particular function(s) an organ has to fulfil. Organ shape is to a large extent determined by cell behaviour, and cell behaviour is to a large extent regulated by cell-cell signalling and cell mechanics. A major interest of my laboratory over the last few years has been to determine how branching morphogenesis restructures epithelial tissues to generate such fascinating structures as the trachea or the vasculature. While we have initially put much effort in understanding this process in vivo in an invertebrate system (tracheal development in Drosophila melanogaster) using state of the art genetics in combination with high resolution live imaging, we have recently moved much of our research efforts to vertebrates, in particular to zebrafish (Danio rerio). Using high resolution in vivo imaging, we have described the cellular activities during angiogenesis, in particular during sprouting, vessel fusion and vessel pruning. To our surprise, we find that the plasticity of developing vessels is accompanied by unexpected cell behaviour; endothelial cells can fission and self-fuse during anastomosis and pruning, respectively. With the advent of the recently introduced genome manipulation tools (TALEN, CRISPR/Cas9), a genetic dissection of the different steps in angiogenesis is now possible at unprecedented level, and proteins can be tagged at endogenous loci and used as marker for high resolution live imaging. We have recently applied intracellular nanobodies for the first time in developing drosophila embryos to directly manipulate protein function, in particular for protein degradation. We used an anti-GFP nanobody fused to an F-box in degrade GFP-fusion proteins (we called the method “deGradFP” for degrading GFP). In the meantime, we have functionalized the anti-GFP nanobody manifold, so that it can be used for in vivo protein trapping, protein localisation and for post-translation modification of proteins of interest. During the next granting period, we will introduce the use of intracellular nanobodies (and other protein binders) for studying the zebrafish vascular system, in particular to answer the following questions:Q1: How is the dynamic cell behaviour during sprouting controlled?Q2: How do endothelial cells recognize each other in order to connect?Q3: Which molecular processes are involved in luminal membrane expansion?Q4: Which molecular processes are involved in membrane fusion and membrane fission?In order to answer these questions, we propose to undertake the following experimental strategies:1) Investigate the role of VE-cad in the dynamic rearrangements of endothelial cells.2) Generate and use cutting edge in vivo live imaging tools to characterize molecular aspects of cell behaviour during angiogenesis processes.3) Generate and analyse mutations in candidate genes affecting distinct cellular activities.4) Generate and use novel tools to manipulate protein function in vivo - a step closer to a synthetic biology approach to organ formation.
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