Project

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engineering gastruloids to study the impact of mechanical constraints upon mammalian development

Applicant Duboule Denis
Number 189956
Funding scheme Sinergia
Research institution Département de Génétique et Evolution Faculté des Sciences Université de Genève
Institution of higher education EPF Lausanne - EPFL
Main discipline Interdisciplinary
Start/End 01.02.2020 - 31.01.2024
Approved amount 3'181'822.00
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All Disciplines (7)

Discipline
Interdisciplinary
Material Sciences
Genetics
Information Technology
Molecular Biology
Mechanical Engineering
Embryology, Developmental Biology

Keywords (9)

Pseudo-embryos; 3R principle; Micro-chambers; Stem ES cells; High-content imaging; Cell tracking system; Mechanical constraints; Gastruloids; Light-sheet microscopy

Lay Summary (French)

Lead
Le développement des embryons mammifères se déroule à l’intérieur des tissus maternels. De ce fait, l’influence potentielle des contacts physiques qui existent entre ces tissus et l’embryon sur son développement est encore mystérieuse et peu étudiée. Ce projet de recherche vise à mieux comprendre les effets de contraintes mécaniques sur le développement des embryons.
Lay summary

Contenu et objectifs du travail de recherche

 

Depuis quelques années, des progrès appréciables ont été réalisés dans la production de pseudo-embryons (embryoïdes) en culture in vitro, à partir de cultures de cellules souches embryonnaire. Ces embryoïdes se développement en absence complète de milieu cellulaire extra-embryonnaire et donc sans pression mécanique particulière de leur environnement.

 

Nous proposons d’utiliser des gastruloïdes, à savoir des pseudo-embryons in vitro représentant la partie la plus postérieure de l’embryon mammifère, pour analyser les effets de contraintes mécaniques sur les réseaux cellulaires et génétiques qui conduisent à la formation du fœtus. 

 

Le projet de recherche consiste à définir, à automatiser et à construire des conditions de culture de gastruloïdes permettant d’appliquer pendant leur développement des forces mécaniques soit globales, soit partielles. Une nouvelle approche microscopique sera développée pour suivre les effets cellulaires de ces différentes contraintes. Cette approche sera complétée par une approche génétique permettant de rechercher les réseaux de gènes modifiés par ces forces. Ces réseaux pourront alors être modifiés génétiquement, en cellules souche, et des gastruloïdes mutants seront produits pour vérifier les hypothèses émises par un processus réitératif, les gastruloïdes mutants étant ré-analysés en utilisant les mêmes conditions.

 

L’objectif central de ce projet collaboratif est de déterminer l’importance des contraintes mécaniques sur les comportements cellulaires et sur la régulation des gènes, pendant le développement embryonnaire in vitro.

 

Contexte scientifique et social du projet de recherche

 

Le projet relève de la recherche fondamentale. Pour mieux comprendre l’importance du milieu extérieur sur le développement embryonnaire, il est important de sortir l’embryon de son contexte et de lui appliquer des forces contrôlées pour en voir les effets. Ce projet s’inscrit également dans le principe des 3R qui consiste à essayer de réduire, raffiner et remplacer, à terme, l’utilisation d’animaux dans la recherche biomédicale.

Direct link to Lay Summary Last update: 04.12.2019

Responsible applicant and co-applicants

Employees

Publications

Publication
Bioengineered embryoids mimic post-implantation development in vitro
Girgin Mehmet U., Broguiere Nicolas, Hoehnel Sylke, Brandenberg Nathalie, Mercier Bastien, Arias Alfonso Martinez, Lutolf Matthias P. (2021), Bioengineered embryoids mimic post-implantation development in vitro, in Nature Communications, 12(1), 5140-5140.
Bioengineering in vitro models of embryonic development
Gupta Ananya, Lutolf Matthias P., Hughes Alex J., Sonnen Katharina F. (2021), Bioengineering in vitro models of embryonic development, in Stem Cell Reports, 16(5), 1104-1116.
Stem-cell-based embryo models for fundamental research and translation
Fu Jianping, Warmflash Aryeh, Lutolf Matthias P. (2021), Stem-cell-based embryo models for fundamental research and translation, in Nature Materials, 20(2), 132-144.
Capturing Cardiogenesis in Gastruloids
Rossi Giuliana, Broguiere Nicolas, Miyamoto Matthew, Boni Andrea, Guiet Romain, Girgin Mehmet, Kelly Robert G., Kwon Chulan, Lutolf Matthias P. (2021), Capturing Cardiogenesis in Gastruloids, in Cell Stem Cell, 28(2), 230-240.e6.

Scientific events

Active participation

Title Type of contribution Title of article or contribution Date Place Persons involved
SY-stem Symposium 2022 Poster Gastruloids as a model to study complex developmental gene regulation – case study of Mesp1 and Mesp2 23.03.2022 Vienne, Austria Kolly Dominique;
SY-stem Symposium 2022 Poster CTCF-driven insulation at the HoxB locus using gastruloids at a model system 23.03.2022 Vienne, Austria Bochaton Célia;
Systems Biology: Global Regulation of Gene Expression Talk given at a conference Symmetry breaking in gastruloid development 09.03.2022 Cold Spring Harbour, United States of America Liberali Prisca;
Till & McCulloch Meetings (TMM) conference Talk given at a conference Symmetry breaking in gastruloids development 15.11.2021 Toronto, Canada Liberali Prisca;
Chromatin and Epigenetics: From Mechanisms to Execution Talk given at a conference Symmetry breaking in gastruloids development 14.04.2021 Munich, Germany Liberali Prisca;


Associated projects

Number Title Start Funding scheme
155863 Collinear regulation of HoxD genes during development and evolution 01.11.2014 Project funding (Div. I-III)
157531 An image-based systems biology approach to symmetry breaking in collective cell behavior 01.07.2015 SNSF Professorships
179447 Bioengineering intestinal organoids 01.10.2018 Project funding (Div. I-III)

Abstract

The impact of the physical environment upon the development of the mammalian embryo has been difficult to evaluate, due to the challenge to access and perturb these embryos in their native niches, at the precise time when the major decisions are taken regarding the general body architecture and the onset of cellular differentiation. In the past five years, several systems have been developed, which can recapitulate some aspects of mammalian development under in vitro conditions, amongst which gastruloids i.e. ‘pseudo-embryos’ lacking a head produced out of embryonic stem (ES) cell aggregates that can self-organize into the three major body axes. The overarching goal of our research programme is to use such gastruloids to study the potential impacts of external mechanical stresses and geometrical constraints on their symmetry breaking, self-organization and axial extension. To achieve this goal, we want to set up novel analytical tools and platforms such that both normal and genetically modified gastruloids can be grown and monitored live under a variety of mechano-geometrical environmental conditions. The effects of these extrinsic physical cues upon the implementation of developmental pathways will be analysed at the single cell level both by using fluorescent marker genes and by detailed epigenetic and transcriptomics analyses of the affected gastruloids. The results obtained will identify candidate genes or pathways potentially involved in the response of mammalian embryos to their physical environment, which will be further studied in an iterative manner, after genetic modifications, using the same approaches.This research programme absolutely requires the tight collaboration between three laboratories coming from different fields and with complementary expertise, in terms of both technological know-how and conceptual frameworks. The laboratory of Denis Duboule, a mammalian geneticist at the Swiss Cancer Institute of EPFL will produce the different types of modified gastruloids and implement their molecular analyses once experimentally challenged. The laboratory of Matthias Lutolf, a bio-engineer at EPFL’s Bioengineering Institute will launch a new high-throughput in vitro platform composed of micro-chamber arrays moulded in bioartificial hydrogels, where gastruloids can be grown in the required statistical number and exposed to defined mechano-geometrical perturbations, in micro-engineered niches. The laboratory of Prisca Liberali, a quantitative biologist at the Friedrich Miescher Institute in Basel will develop a new imaging platform for in-toto imaging of gastruloid development at single cell resolution, based on light-sheet microscopy technology and computational frameworks for inference of trajectories from time-course experiments. The pooling of forces amongst these three laboratories will build a unique pipeline whereby labelled and/or modified gastruloids, for example with various gene markers of the different axes, will be grown under particular mechanical stimuli and their reactions followed live by using in-toto microscopy. Because of both their high derivation efficiency (above 75%) and their easiness to produce under laboratory conditions, gastruloids are the only type of ‘pseudo-embryos’ that can reasonably be used in such a high-throughput experimental design. Consequently, we believe that this complementary programme is truly original and will deliver critical results and information regarding an aspect of mammalian development that is only starting to emerge now. We also believe that the conclusions obtained by studying the effects of physical effectors on the developing embryo will likely reflect fundamental ways that the organism implements to deal with its immediate environment and thus be applicable to a wide variety of situations occurring either in later stages of development or in homeostatic and pathological conditions. These insights should be useful even outside the fields of developmental and stem cell biology, for example in the implementation of biology inspired approaches for tissue engineering and regenerative medicine.
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