2023. Towards a theoretical model of human |
A. Baffet (team leader, UMR144), P. Sens (team leader UMR168)
- The human neocortex has undergone an important size expansion during evolution, reflected by
a high diversity of cell types. Recent advances in genomic methods have shed light on this cellular
diversity, but how it arises during development is unclear. Cell diversity is a consequence of cell fate
decisions that occur upon division of radial glial (RG) cells, the progenitors of all neuronal and most
glial subtypes. RG cells can indeed undertake several different fate choices (amplification, neuronal
subtype generation, gliogenic switch) which may vary in time, but also in space depending on their
position within the tissue. These cell fate decision hubs are likely to underlie evolutionary differences
in neocortex size and composition, and to be affected in pathological contexts. Identifying them,
especially in the human neocortex, is however a major challenge with the current approaches.
We have developed a semi-automated live/fixed correlative imaging method enabling to
identify the fate of RG daughter cells, following live imaging in human fetal tissue and cerebral
organoids. Using this method, we are revealing how cell fate decisions vary during the course of human neocortex development, along the temporal and spatial axes. By comparing human fetal tissue and organoids, we aim to generate a reference point for the use of these 3D models. The ultimate goal of this project is developing a predictive mathematical model of human neurogenesis. In collaboration with Pierre Sens, we are establishing this model, integrating the probability of each type of cell fate decisions in space and time, as well as the migratory properties of stem cells. The funding requested here will be used to generate the quantitative data that feed into the model, which is the current bottleneck. Altogether, our project will unravel critical insights on the mechanisms governing human neocortex development and evolution.
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2023. Mesodermal morphogenesis and somite generation in chicken embryo: a mechano-chemical stud |
K. Guevorkian (team Hersen, UMR168), B. Sorre (team Hersen UMR168), C. Blanch Mercader (team Sens UMR168)
- A prime example of patterning and shape generation during embryonic development is observed
during the development of the lower body of the vertebrate embryos, where epithelial segments
of well-defined size and shape, called somites emerge from the posterior mesoderm, and detach
periodically, reminiscent of droplets formed from a water jet. Somites are multi-cellular transient
structures that later give rise to our musculoskeletal structures. To generate these compact structures, under the action of morphogen gradients, cells switch from loosely bound highly motile
mesenchymal phenotype to more sessile and tightly interconnected epithelial state, undergo
cellular reorganization, and rearrange into tissue segments. Our goal is to understand the
underlying physical mechanisms involved in this process in a well-defined, controlled conditions.
The contribution of mechanical processes such as cell contractility, geometrical constraints, and
the feedback between mechanics and biochemical signaling remains an under-explored domain in
somitogenesis. Here, we will develop a novel microfluidics assay to study somitogenesis ex vivo in
controlled morphogen concentrations. By studying the dynamics of somite formation in various
morphogen conditions, and evaluation of the mechanical properties of the mesoderm, we aim at
proposing a theoretical model of somitogenesis in the framework of active matter physics. Besides
its importance in vertebrate development, somitogenesis is a perfect example of tissue patterning
and shaping. Therefore, the findings of our project could also be relevant to other morphogenetic
events and in disease such as tumor formation.
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2022. SpineOnChip : a microfluidic platform to recapitulate the cellular diversity and the spatial organisation of the spinal cord |
B. Sorre (team Hersen UMR168)
- We want to use microfluidics to generate, from Embryonic Stem Cells, spinal cord tissues in vitro with the correct cellular composition and organization. Doing so, helped by modelling and simulations, we expect to learn how the spinal cord is made in the embryo and how to generate functional spinal tissue from Stem Cells.
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2022. Deciphering functional role of Vap-B Microtubules interaction using in vitro Cryo-electron tomography and in cellulo studies |
M. Dezi (team Lévy UMR168), Carsten Janke (team leader UMR13348)
- One of the most promising next-generation cancer treatments is living bacterial therapeutics (LBTs). The basic idea of LBTs is that treatment can be provided with a “smart”, highly controllable therapeutic delivery system, capable of dynamic behavior long sought by pharmacology such as an “adaptive” drug delivery, where drug release changes according to the behavior of the target. A crucial bottleneck of these is however the lack of control over the LBT growth, which can be both drained by the immune system or increase to dangerous levels. LBTs are part of the more general emerging technology of engineered biomaterials, which is beginning to focus on such adaptive character through the implementation homeostasis into their design. Although present in bioproduction applications and in natural cell systems, population-abundance homeostasis (or cell stoichiometry) has, to our knowledge, been absent from the design of most biomaterials and LBTs. Here we present a strategy to create a proof-of-principle, yet functional ratiostatic living therapeutic, namely one that keeps the LBT:tumor ratio, constant. Here we aim to modify available therapeutic microbes by endowing them with the capacity to maintain their relative mass respect to that of a tumor-mimicking spheroid. We will use a circuit containing the key feature of antagonistic (or
antithetic) regulation of growth, allowing LBTs to stimulate their proliferation when detecting molecules produced by the tumor, and slowing growth when detecting a different molecule type, produced by themselves. We will address this challenge by using interdisciplinary state-of-the-art methodologies combining modular cloning and gene synthesis with a light-controlled spheroid experimental tumor model, high-throughput assays, and mathematical modelling to construct circuits with, crucially, enough genetic sequence variability and sufficient screening power to maximize the chance of success. This proof-of-principle approach is instrumental for designing a clinical therapeutic which will reliably maintain the bacteria-tumor mass ratio. In the future, once taken from the cell culture to living tissue, this approach will allow for precise tumor targeting and drug deposition, while minimizing the harmful side effects which are untamable with current methods.
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2022. Project Engineering bacteria-tumor population homeostasis: a proof of principle for therapeutic applications |
M. Kramar (team Coppey UMR168), Alvaro Banderas (team Hersen UMR168)
- One of the most promising next-generation cancer treatments is living bacterial therapeutics (LBTs). The basic idea of LBTs is that treatment can be provided with a “smart”, highly controllable therapeutic delivery system, capable of dynamic behavior long sought by pharmacology such as an “adaptive” drug delivery, where drug release changes according to the behavior of the target. A crucial bottleneck of these is however the lack of control over the LBT growth, which can be both drained by the immune system or increase to dangerous levels. LBTs are part of the more general emerging technology of engineered biomaterials, which is beginning to focus on such adaptive character through the implementation homeostasis into their design. Although present in bioproduction applications and in natural cell systems, population-abundance homeostasis (or cell stoichiometry) has, to our knowledge, been absent from the design of most biomaterials and LBTs. Here we present a strategy to create a proof-of-principle, yet functional ratiostatic living therapeutic, namely one that keeps the LBT:tumor ratio, constant. Here we aim to modify available therapeutic microbes by endowing them with the capacity to maintain their relative mass respect to that of a tumor-mimicking spheroid. We will use a circuit containing the key feature of antagonistic (or
antithetic) regulation of growth, allowing LBTs to stimulate their proliferation when detecting molecules produced by the tumor, and slowing growth when detecting a different molecule type, produced by themselves. We will address this challenge by using interdisciplinary state-of-the-art methodologies combining modular cloning and gene synthesis with a light-controlled spheroid experimental tumor model, high-throughput assays, and mathematical modelling to construct circuits with, crucially, enough genetic sequence variability and sufficient screening power to maximize the chance of success. This proof-of-principle approach is instrumental for designing a clinical therapeutic which will reliably maintain the bacteria-tumor mass ratio. In the future, once taken from the cell culture to living tissue, this approach will allow for precise tumor targeting and drug deposition, while minimizing the harmful side effects which are untamable with current methods.
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2022. Combination of microfabrication by two-photon polymerization and Lattice Light Sheet Microscopy to get insight into endothelial dynamics in controlled 3D fiber networks |
S. Coscoy (team Silberzan UMR168), Jean Salamero (team leader UMR144)
- The aim of this project is to decipher the dynamics of endothelial cells in fiber networks with perfectly controllable 3D geometry, local chemistry and stiffness. The work of Team1 in recent years has enabled us to reach a point of technological maturity on the use of two-photon polymerization to produce versatile 3D microstructures and to develop associated tools for the local control of chemical properties (collab. Vincent Semetey). After a first work on endothelial dynamics and the generation of filopodia triggered by 3D microtopographies (collab. Catherine Monnot), we are now developing more complex, fiber-based 3D microstructures, principally tunnel-like, in order to study the multicellular engagement of endothelial cells dictated by the controlled microenvironment, in relation with the dynamics of actin-rich protrusions and the measurement of 3D forces. The recent years have shown the potential of Lattice Light Sheet Microscopy (LLSM) to unveil new aspects of actin and membrane organization in living cells, and a collaboration between the two teams involved in this project has been initiated in the past months in order to use full 3D fast live acquisition to study the detailed dynamics of protrusions in the 3D microfabricated fiber networks. This subcellular information will be coupled to the global multicellular reaction to 3D cues like gradients of fiber densities or structure chirality. In addition to expertises in imaging (Team2) and microfabrication (Team1), this project involves important data processing and image analysis, which will centrally need the experience of Team2 in term of processing, visualization and data management, and will be coupled to a joined specific image analysis work. In addition, this new inter-Labex collaboration benefits from the dynamics of ongoing projects (including within the Labex) about fluorescence polarization microscopy led by Jean Salamero, and will put the first milestone to study dynamically actin orientation in link with the deformations of the fibers in contact with cell protrusions. In a competitive context where LLSM has not yet been applied to microstructures generated by two-photon polymerization, the idea of this project is to develop together at a short time scale (typically less than 1 year), as a proof of concept, an original method combining 3D microfabrication and LLSM.
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2022. Role of PIEZO mechanotransduction channels in cancer stem cells and tumorigenesis |
M. Baghdadi (team Vignjevic UMR144)
- Tissue turnover and regeneration are orchestrated by stem cells that both differentiate and self-renew. The balance of self-renewal, proliferation, and commitment depends on the stem cell microenvironment, or “niche”. Importantly, stem cells are not simply passive responders to their niches; instead, they play an integral role in building and communicating with their immediate microenvironment1–3. Although multiple studies have described the molecular and cellular composition of the niche to date, it is still unclear if and how the mechanical properties of the microenvironment regulate stem cell maintenance. Importantly, it has been shown that all tumor cells have the capacity to become cancer stem cells (CSCs) when positioned in the right microenvironment4. Thus, the niche is critical for the emergence of CSC and tumorigenesis.
Here, we use mouse colorectal cancer as a model to study how CSCs sense the mechanical properties of their niche and if this triggers downstream signaling events leading to cell fate decisions. This research proposal aims to understand if CSCs can sense their physical microenvironment through mechanosensitive PIEZO channels and if this mechanotransduction process can modulate CSC proliferation, self-renewal, and differentiation.
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2021. Shaping of biological tissues by topological defects |
I. Bonnet (team Silberzan UMR168), C. Blanch Mercader (team Sens UMR168)
- Tissues exhibit characteristics of liquid crystals, such as long-range orientational order and topological defects: regions where orientational order is ill-defined. During the development of organisms, topological defects are at the core of morphogenetic events and biological processes, such as protrusion formation or cell extrusion. However, the linkage between morphogenesis and topological defects remains to be discovered. Two main limitations can be identified: the lack of well-controlled biological model systems, and the lack of a theoretical
mapping between morphologies and topological defects in active liquid crystals. To address the former, we propose to create a suspended composite bilayer made of a cell monolayer attached to a deformable gel layer: such in vitro device will allow us to study correlations between orientational order of cells and deformations on the gel layer.
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2021. Flow and single protein motion in the way out from the Endoplasmic Reticulum |
A. Joaquina Jimenez (team Perez UMR144), M. Cannata Serio (team Perez UMR144) and C. Guedj (PICT Burg, UMR144)
- Newly synthesized proteins travel through the ER network and find their way out within few minutes. Yet, it is unknown how the cell ensures this highly efficient process. To unravel this enigma, we propose a multidisciplinary approach combining leading edge and highly quantitative microscopy and image analysis, with strategies for traffic synchronization. Using SPT-PALM we will image and track hundreds of thousands overlapping single protein trajectories of different biochemical classes (eg. soluble, transmembrane). We will model the proteins motion to extract the physical parameters throughout their journey inside the ER network, from their release to their packaging into the ER-exit sites. We will screen for biological variables affecting these biophysical parameters, like ER structural proteins or cell contractility, to understand how different genetic mutations can affect protein traffic and sorting, and cellular homeostasis.
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2021. Deciphering the mechanisms of nuclear size scaling |
S. Gemble (team Basto UMR144), P. Sens (team leader UMR168) and R. Rollin (team Sens UMR168)
- Establish theoretical models that help us to characterize cellular architecture remodeling in response to modifications in cell size and to experimentally test the model in order to clearly define the functional and structural relationship between intracellular architecture and cell size, with implications in developmental biology and in various diseases.
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2020. Spatial regulation of exocytosis |
S. Miserey-Lenkei (team Goud UMR144), G. Boncompain (Perez UMR144), S. Descroix (team leader UMR168), P. Sens (team leader UMR168)
- Understand the mechanical influence of the cell microenvironment on the regulation and dynamics of secretion hotspots and monitor the organization and dynamics of secretion events in 3D and in polarized models.
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2019. Nucleus deformation of triple negative cancer cells and mechanism of cell migration. |
C. Sykes (team leader UMR168), M. Piel (team leader UMR168)
- Characterize the nucleus mechanics of tumor and metastatic Triple negative breast cancer (TNBC) cell lines, their link to the cytoskeleton and cell contractility using microfluidic and biophysical approaches; investigate the effect on their migratory characteristics.
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2019. Mechanisms of actin-driven membrane fission mediated by curved membrane proteins. |
F-C. Tsai (team Bassereau UMR168), A. Bertin (team Lévy UMR168), P. Sens (team leader UMR168), C. Delevoye (team Raposo UMR144)
- Study how actin polymerization and architecture are coupled to membrane shape dynamics to generate sufficient forces to power membrane fission.
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2018. Magnetic targeting and ultrasonic release of the inhibitors of the mice colon mechanotransductive tumorigenic pathways in vivo. |
I. Farge (team leader UMR168)
- Establish in mice a new optimized and patentable treatment of colorectal cancer, based on specific magnetic targeting and ultrasonic progressive release of the colon tumour mechanical induction inhibitor.
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2018. Dynamic, super-resolution, volumetric imaging of cellular organization using reversible cryo-arrest technology. |
B. Hajj (team Dahan UMR168), M. Dahan (team leader UMR168)
- Develop an instrument that combines state of the art 3D single molecule microscopy with low temperature reversible cell arrest to follow the evolution of molecular organization at different stages of the cell cycle.
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2017. Integrin and aPKCi interplay in mammary epithelial cells during early steps of tumorigenesis. |
C. Rosse (team Chavrier UMR144), M. Romagnoli (team Glukhova UMR144)
- Decipher the interplay between aPKCi and alpha6-integrin during the loss of polarity and cell extrusion induced by aPKCi-overexpression in mammary luminal cells leading to a deeper understanding of the early stages of mammary tumorigenesis.
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2017. Explore the architecture of human centromeres and its influence on the maintenance of genome stability. |
D. Fachinetti (team leader UMR144), Lumicks
- Investigate the chromosomal architecture of human centromeres and the components that are required for its maintenance in physiological conditions, and ascertain how genetic or physical manipulation of the centromere architecture affects chromosome integrity.
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2016. Selective volumetric illuminaton microscopy (soSPIM-MFM). |
B. Hajj (team Dahan UMR168), M. Dahan (team leader UMR168)
- Develop and combine cutting edge technologies in 3D imaging to reach an effective way for live imaging single molecules in the volume of a cell by combining volumetric detection using multifocus microscopy (MFM) with selective plane illumination.
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2016. Influence of matrix stiffening on tumor cell invasion. |
M. Verhulsel (team Viovy UMR168), Y. Attieh (team Vignjevic UMR144)
- Analyze the relative importance of ECM stiffness in cancer cell invasion using 3D in vitro culture models that offer the ability to decouple all parameters at play in cancer cell invasion; identify whether stroma gets activated prior or post-invasion.
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2016. Auxin-based conditional protein-protein interaction. |
D. Fachinetti (team leader UMR144), G. Van Niel (team Raposo UMR144), F. Verweij (team Raposo UMR144)
- Develop a system to reversibly induce conditional protein-protein dimerization in living cells with rapid kinetics and adaptability to in vivo systems by adapting the Auxin Inducible Degron (AID) system. This will enable the simulation of protein-protein interaction in any phase of the cell cycle and within any compartment of the cell.
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2015. Revealing the physiology of exosome secretion in vivo by a 4D-imaging approach. |
F. Verweij (team Raposo UMR144)
- Develop a unique transgenic-zebrafish model that expresses a recently developed fluorescent reporter that visualizes exosome secretion from living cells in vitro to study the release dynamics of exosomes in detail.
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2015. Formation and propagation of renal cysts: study in biomimetic tubular systems. |
S. Coscoy (team Silberzan UMR168), S. Descroix (team Viovy UMR168)
- Investigate the dynamic multicellular organization of the renal epithelium involved in cyst generation in autosomal dominant polycystic kidney disease (ADPKD), proliferation and planar polarity, in response to inherent geometrical constraints, acquired geometrical changes, and/or laminar flow disturbances.
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2015. Combining theory of membrane deformations and force measurements to study the effects of local mechanical perturbations on plasma membrane organization. |
C. Lamaze (team leader UMR3666/U1143), P. Sens (team Joanny/Prost UMR168), D. Köster (NCBS Bangalore)
- Study how caveolae affect the behavior of the plasma membrane on short time and length scales during a local change in cell membrane shape.
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2015. Architecture of membrane associated machineries at sub-nanometer resolution. |
D. Levy (team leader UMR168), A. Bertin (team Levy UMR168), P. Bassereau (UMR168), S. Mangenot (team leader UMR168), C. Delevoye (team Raposo UMR144)
- Build 3D models of proteins at sub-nanometer resolutions to understand how these proteins interacts, form specific assemblies and remodel membranes at the molecular level.
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2013. Optogenetics to study interactions between normal and transformed cells.
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I. Bonnet (team Silberzan/Buguin UMR168)
- Investigate the crosstalk of mechanical and genetics factors on the tissue cohesion during early tumorigenesis, studying the dynamics at the interface between normal and precancerous cells in relation with mechanical state and oncogene activity.
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2013. Mechanical modification of collagen gels by single cells and spheroids. |
T. Betz (U. Münster), D. Vignjevic (team leader UMR144)
- Combine cell biological and physics approaches to study if cancer cells modify the mechanical properties of their environment (collagen elasticity) during invasion, and if this facilitates the conditions for invasion.
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2013. Magnetogenetic control of cell migration. |
D. Lisse, M. Dahan (UMR168)
- Development of magnetogenetics towards precisely controlling the migration of cells in 2D and 3D in vitro assays.
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2013. Analysis of centrosomes in ovarian cancer. |
R. Basto (UMR144), O. Goundiam (team Sastre, Hospital), X. Sastre (Hospital), JF. Joanny (UMR168), E. Barillot (U900), P. Hupé (U900)
- Analysis of centrosome structural abnormalities
- Identification and validation of key molecules (centrosomal proteins and/or regulators)
- Link between centrosome amplification and DNA repair
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2012. In vitro reconstitution of Myosin IIA-driven membrane fission. |
P. Bassereau (UMR 168), B. Goud (UMR144)
- Development of an in vitro system to mimic the MyoIIA–driven fission process. Membrane nanotubes will be pulled from giant unilamellar vesicles (GUVs) using optical tweezers and we will monitor tube stability in the presence of Rab6, MyoIIA, actin and ATP.
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2012. Development of a minimal in vitro system of lipid membrane based amyloidogenesis |
G. Raposo (UMR144), G. Van Niel (team Raposo UMR144), D. Levy (UMR168)
- Study the molecular mechanisms involved in the formation of amyloid fibers in exosomes through the establishment of a minimal in vitro model of amyloidogenesis that can be further exploited to understand pathological situations.
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