Project acronym ACE-OF-SPACE
Project Analysis, control, and engineering of spatiotemporal pattern formation
Researcher (PI) Patrick MÜLLER
Host Institution (HI) MAX-PLANCK-GESELLSCHAFT ZUR FORDERUNG DER WISSENSCHAFTEN EV
Call Details Consolidator Grant (CoG), LS3, ERC-2019-COG
Summary A central problem in developmental biology is to understand how tissues are patterned in time and space - how do identical cells differentiate to form the adult body plan? Patterns often arise from prior asymmetries in developing embryos, but there is also increasing evidence for self-organizing mechanisms that can break the symmetry of an initially homogeneous cell population. These patterning processes are mediated by a small number of signaling molecules, including the TGF-β superfamily members BMP and Nodal. While we have begun to analyze how biophysical properties such as signal diffusion and stability contribute to axis formation and tissue allocation during vertebrate embryogenesis, three key questions remain. First, how does signaling cross-talk control robust patterning in developing tissues? Opposing sources of Nodal and BMP are sufficient to produce secondary zebrafish axes, but it is unclear how the signals interact to orchestrate this mysterious process. Second, how do signaling systems self-organize to pattern tissues in the absence of prior asymmetries? Recent evidence indicates that axis formation in mammalian embryos is independent of maternal and extra-embryonic tissues, but the mechanism underlying this self-organized patterning is unknown. Third, what are the minimal requirements to engineer synthetic self-organizing systems? Our theoretical analyses suggest that self-organizing reaction-diffusion systems are more common and robust than previously thought, but this has so far not been experimentally demonstrated. We will address these questions in zebrafish embryos, mouse embryonic stem cells, and bacterial colonies using a combination of quantitative imaging, optogenetics, mathematical modeling, and synthetic biology. In addition to providing insights into signaling and development, this high-risk/high-gain approach opens exciting new strategies for tissue engineering by providing asymmetric or temporally regulated signaling in organ precursors.
Summary
A central problem in developmental biology is to understand how tissues are patterned in time and space - how do identical cells differentiate to form the adult body plan? Patterns often arise from prior asymmetries in developing embryos, but there is also increasing evidence for self-organizing mechanisms that can break the symmetry of an initially homogeneous cell population. These patterning processes are mediated by a small number of signaling molecules, including the TGF-β superfamily members BMP and Nodal. While we have begun to analyze how biophysical properties such as signal diffusion and stability contribute to axis formation and tissue allocation during vertebrate embryogenesis, three key questions remain. First, how does signaling cross-talk control robust patterning in developing tissues? Opposing sources of Nodal and BMP are sufficient to produce secondary zebrafish axes, but it is unclear how the signals interact to orchestrate this mysterious process. Second, how do signaling systems self-organize to pattern tissues in the absence of prior asymmetries? Recent evidence indicates that axis formation in mammalian embryos is independent of maternal and extra-embryonic tissues, but the mechanism underlying this self-organized patterning is unknown. Third, what are the minimal requirements to engineer synthetic self-organizing systems? Our theoretical analyses suggest that self-organizing reaction-diffusion systems are more common and robust than previously thought, but this has so far not been experimentally demonstrated. We will address these questions in zebrafish embryos, mouse embryonic stem cells, and bacterial colonies using a combination of quantitative imaging, optogenetics, mathematical modeling, and synthetic biology. In addition to providing insights into signaling and development, this high-risk/high-gain approach opens exciting new strategies for tissue engineering by providing asymmetric or temporally regulated signaling in organ precursors.
Max ERC Funding
1 997 750 €
Duration
Start date: 2020-07-01, End date: 2025-06-30
Project acronym BacForce
Project Quantifying minute forces: How mechanoregulation determines the behavior of pathogenic bacteria
Researcher (PI) Benedikt SABASS
Host Institution (HI) LUDWIG-MAXIMILIANS-UNIVERSITAET MUENCHEN
Call Details Starting Grant (StG), LS3, ERC-2019-STG
Summary Bacteria can generate mechanical forces that are important for the colonization of surfaces, formation of biofilms, and infection of host cells. This proposal addresses the fundamental question of how bacteria can control their force generation to robustly respond to chemo-mechanical cues on complex surfaces. Currently, a knowledge gap exists between the molecular regulation pathways on the one hand and the mechanical behavior on the other hand. One major impediment for understanding of how behavior is connected to control is, to date, the impossibility of studying bacterial force directly in unconstrained situations. Based on an initial study, I propose employing new methods for the unperturbed, high-resolution measurement of bacterial traction forces on wide spatiotemporal scales. Thus, the force-generation linking behavior to control can be investigated directly.
The objectives are to (A) gain access to nanoscopic mechanical phenomena through the development of cutting-edge super-resolution traction force microscopy, (B) employ the methods to characterize how Pseudomonas aeruginosa controls pilus-generated forces while responding to chemical cues, and (C) establish how surface rigidity affects force generation by P. aeruginosa during biofilm formation. In an interdisciplinary approach, I will combine traction measurements with genetic perturbations, molecule labeling, and computer simulations to produce functional models of the mechanocontrol strategies.
Altogether, I will establish a novel technique, opening up the possibility of studying nanoscopic force generation in many types of cells. Through these advances, I will characterize a set of mechanoregulation strategies in P. aeruginosa that are paradigmatic for diverse Gram-negative pathogens employing the same type of pili. Broadly, I expect that the studied bacterial control strategies have a generic, minimal nature and can appear as basic motives throughout development, homeostasis, and disease.
Summary
Bacteria can generate mechanical forces that are important for the colonization of surfaces, formation of biofilms, and infection of host cells. This proposal addresses the fundamental question of how bacteria can control their force generation to robustly respond to chemo-mechanical cues on complex surfaces. Currently, a knowledge gap exists between the molecular regulation pathways on the one hand and the mechanical behavior on the other hand. One major impediment for understanding of how behavior is connected to control is, to date, the impossibility of studying bacterial force directly in unconstrained situations. Based on an initial study, I propose employing new methods for the unperturbed, high-resolution measurement of bacterial traction forces on wide spatiotemporal scales. Thus, the force-generation linking behavior to control can be investigated directly.
The objectives are to (A) gain access to nanoscopic mechanical phenomena through the development of cutting-edge super-resolution traction force microscopy, (B) employ the methods to characterize how Pseudomonas aeruginosa controls pilus-generated forces while responding to chemical cues, and (C) establish how surface rigidity affects force generation by P. aeruginosa during biofilm formation. In an interdisciplinary approach, I will combine traction measurements with genetic perturbations, molecule labeling, and computer simulations to produce functional models of the mechanocontrol strategies.
Altogether, I will establish a novel technique, opening up the possibility of studying nanoscopic force generation in many types of cells. Through these advances, I will characterize a set of mechanoregulation strategies in P. aeruginosa that are paradigmatic for diverse Gram-negative pathogens employing the same type of pili. Broadly, I expect that the studied bacterial control strategies have a generic, minimal nature and can appear as basic motives throughout development, homeostasis, and disease.
Max ERC Funding
1 498 864 €
Duration
Start date: 2020-08-01, End date: 2025-07-31
Project acronym CellSex
Project The importance of cellular sex in physiology and the underlying mechanisms
Researcher (PI) BRUNO HUDRY
Host Institution (HI) CENTRE NATIONAL DE LA RECHERCHE SCIENTIFIQUE CNRS
Call Details Starting Grant (StG), LS3, ERC-2019-STG
Summary The difference between males and females constitutes the largest phenotypic dimorphism in most species. In humans, this variation accounts for differences seen in the risk, incidence and response to treatment for a plethora of diseases; and much of these striking differences are not explained at this time. While sex organ-derived hormones play key roles in sculpting and maintaining sex differences, my recent work highlighted the importance of cell-intrinsic mechanisms involving the sex chromosomes. In fact, using fly models I demonstrated that the sex of intestinal stem cells plays a key role in the adult gut, both for the organ size and for the sex-specific pre-disposition to tumours. While these findings establish the proof-of-principle of the influence of sex chromosomes in adult cells, essential gaps remain to be filled. Indeed, the full range of phenotypic consequences of the presence of sex chromosomes in somatic cells, the genes, the mechanisms involved and their sites of action remain entirely elusive. My research proposal aims to understand how cellular sex impacts physiology across the body using Drosophila as an in vivo model. This question has been poorly investigated in part due to the difficulties of studying sex chromosome effects. Flies will offer the remarkable possibility of generating mosaic animals in which sex chromosomes will be genetically manipulated in defined organs.
Here I will combine classical fly genetics, novel genetic methods and cutting-edge genomic techniques to: 1. characterise new cellular sex pathways driving sex differences in body size and in behaviours, 2. study the role of sex determinant coding changes in sex trait evolution, 3. achieve, for the first time, organ-specific Y chromosome deletion, and use this new method to study how the Y chromosome controls sex gap in longevity.
Thus, results from this research should have major impact on our understanding of the importance of cellular sex in physiology and disease.
Summary
The difference between males and females constitutes the largest phenotypic dimorphism in most species. In humans, this variation accounts for differences seen in the risk, incidence and response to treatment for a plethora of diseases; and much of these striking differences are not explained at this time. While sex organ-derived hormones play key roles in sculpting and maintaining sex differences, my recent work highlighted the importance of cell-intrinsic mechanisms involving the sex chromosomes. In fact, using fly models I demonstrated that the sex of intestinal stem cells plays a key role in the adult gut, both for the organ size and for the sex-specific pre-disposition to tumours. While these findings establish the proof-of-principle of the influence of sex chromosomes in adult cells, essential gaps remain to be filled. Indeed, the full range of phenotypic consequences of the presence of sex chromosomes in somatic cells, the genes, the mechanisms involved and their sites of action remain entirely elusive. My research proposal aims to understand how cellular sex impacts physiology across the body using Drosophila as an in vivo model. This question has been poorly investigated in part due to the difficulties of studying sex chromosome effects. Flies will offer the remarkable possibility of generating mosaic animals in which sex chromosomes will be genetically manipulated in defined organs.
Here I will combine classical fly genetics, novel genetic methods and cutting-edge genomic techniques to: 1. characterise new cellular sex pathways driving sex differences in body size and in behaviours, 2. study the role of sex determinant coding changes in sex trait evolution, 3. achieve, for the first time, organ-specific Y chromosome deletion, and use this new method to study how the Y chromosome controls sex gap in longevity.
Thus, results from this research should have major impact on our understanding of the importance of cellular sex in physiology and disease.
Max ERC Funding
1 498 365 €
Duration
Start date: 2020-05-01, End date: 2025-04-30
Project acronym CiliaCircuits
Project Molecular Principles of Mammalian Axonemal Dynein Assembly
Researcher (PI) Pleasantine Mill
Host Institution (HI) THE UNIVERSITY OF EDINBURGH
Call Details Consolidator Grant (CoG), LS3, ERC-2019-COG
Summary Motile cilia are tiny microtubule-based projections which create fluid flow and are essential to human health. Cilia movement is powered by coordinated action of complex macromolecular motors, the axonemal dyneins. During differentiation, as cells produce hundreds of motile cilia, millions of dynein subunits must be pre-assembled in the cytoplasm into very large complexes in the correct stoichiometry which are then trafficked into growing cilia. This poses a sizeable challenge for the cell in terms of allocation of a significant fraction of the global translational machinery for streamlined assembly of dyneins within a crowded cellular space.
The key question remains: How does the cell know how much is enough? This is an extreme example of a common problem in cell biology. Responsive and adaptive mechanisms must exist to prevent futile expenditure of cellular resources in making a surplus of large molecules like dyneins that may also pose a risk of toxic aggregation. While a well-defined transcriptional code for induction of cilia motility genes exists, the translational dynamics and subsequent feedback circuitry coordinating dynein pre-assembly with ciliogenesis remain unexplored.
The molecular logic underlying the construction of motile cilia assembly are still not fully understood. The ambitious nature of CiliaCircuits proposes to use super-resolution and systems approaches to elucidate key mechanisms regulating this process in health and disease.
Human genetics tells us that making cilia motile is a complex process. To date, almost 40 genes have been implicated in primary ciliary dyskinesia (PCD), the disease of motile cilia, for which there is no cure. The long-term vision is to understand this dynamic control operating over a specialized proteome in time and space in order to develop effective PCD therapeutics and identify additional candidate genes involved in this translation regulation.
Summary
Motile cilia are tiny microtubule-based projections which create fluid flow and are essential to human health. Cilia movement is powered by coordinated action of complex macromolecular motors, the axonemal dyneins. During differentiation, as cells produce hundreds of motile cilia, millions of dynein subunits must be pre-assembled in the cytoplasm into very large complexes in the correct stoichiometry which are then trafficked into growing cilia. This poses a sizeable challenge for the cell in terms of allocation of a significant fraction of the global translational machinery for streamlined assembly of dyneins within a crowded cellular space.
The key question remains: How does the cell know how much is enough? This is an extreme example of a common problem in cell biology. Responsive and adaptive mechanisms must exist to prevent futile expenditure of cellular resources in making a surplus of large molecules like dyneins that may also pose a risk of toxic aggregation. While a well-defined transcriptional code for induction of cilia motility genes exists, the translational dynamics and subsequent feedback circuitry coordinating dynein pre-assembly with ciliogenesis remain unexplored.
The molecular logic underlying the construction of motile cilia assembly are still not fully understood. The ambitious nature of CiliaCircuits proposes to use super-resolution and systems approaches to elucidate key mechanisms regulating this process in health and disease.
Human genetics tells us that making cilia motile is a complex process. To date, almost 40 genes have been implicated in primary ciliary dyskinesia (PCD), the disease of motile cilia, for which there is no cure. The long-term vision is to understand this dynamic control operating over a specialized proteome in time and space in order to develop effective PCD therapeutics and identify additional candidate genes involved in this translation regulation.
Max ERC Funding
1 965 460 €
Duration
Start date: 2020-08-01, End date: 2025-07-31
Project acronym CollectiveDynamics
Project Collective signaling oscillations in embryonic patterning – revealing underlying principles
Researcher (PI) Alexander Aulehla
Host Institution (HI) EUROPEAN MOLECULAR BIOLOGY LABORATORY
Call Details Consolidator Grant (CoG), LS3, ERC-2019-COG
Summary In this proposal, we study collective signaling oscillations during embryonic patterning. Signaling oscillations during vertebrate embryo segmentation are governed by a molecular oscillatory machinery referred to as segmentation clock (Palmeirim et al., 1997). The segmentation clock is linked to periodic activity of the Notch, Wnt and Fgf pathway in presomitic mesoderm (PSM) cells (period~2 hours in mouse embryos). Importantly, PSM cells display complex, collective synchronization and, as a result, wave-like activity patterns (phase waves) sweep periodically along the embryonic axis. We have previously shown that phase waves are an emergent and collective phenomenon in PSM cells (Tsiairis and Aulehla, 2016).
Conceptually, this proposal builds on our previous discovery that the relative timing between Wnt/Notch oscillations is critical for proper mesoderm patterning (Sonnen et al., 2018). What are the principles underlying the emergence of collective synchronization and how do PSM cells decode relative timing of signalling oscillations?
As outlined in this proposal, we are now in a unique position to address these fundamental questions in novel ways. Importantly, we have established an entrainment strategy that enables, for the first time, precise experimental control of oscillation dynamics (Sonnen et al., 2018). Our strategy is to further expand the entrainment approach, including the future use of optogenetics, and also combine it with our expertise in quantitative, multi-scale analysis of signalling dynamics and functional, genetic perturbations.
A central aim of this ERC proposal is to build on discoveries made in versatile in vitro assays that we developed and to address their significance in vivo. To this end, we propose a novel line of research using the medaka fish model. We will entrain and challenge collective synchronization in vivo to address how signalling oscillations are integrated with growth dynamics to yield robust embryonic patterning.
Summary
In this proposal, we study collective signaling oscillations during embryonic patterning. Signaling oscillations during vertebrate embryo segmentation are governed by a molecular oscillatory machinery referred to as segmentation clock (Palmeirim et al., 1997). The segmentation clock is linked to periodic activity of the Notch, Wnt and Fgf pathway in presomitic mesoderm (PSM) cells (period~2 hours in mouse embryos). Importantly, PSM cells display complex, collective synchronization and, as a result, wave-like activity patterns (phase waves) sweep periodically along the embryonic axis. We have previously shown that phase waves are an emergent and collective phenomenon in PSM cells (Tsiairis and Aulehla, 2016).
Conceptually, this proposal builds on our previous discovery that the relative timing between Wnt/Notch oscillations is critical for proper mesoderm patterning (Sonnen et al., 2018). What are the principles underlying the emergence of collective synchronization and how do PSM cells decode relative timing of signalling oscillations?
As outlined in this proposal, we are now in a unique position to address these fundamental questions in novel ways. Importantly, we have established an entrainment strategy that enables, for the first time, precise experimental control of oscillation dynamics (Sonnen et al., 2018). Our strategy is to further expand the entrainment approach, including the future use of optogenetics, and also combine it with our expertise in quantitative, multi-scale analysis of signalling dynamics and functional, genetic perturbations.
A central aim of this ERC proposal is to build on discoveries made in versatile in vitro assays that we developed and to address their significance in vivo. To this end, we propose a novel line of research using the medaka fish model. We will entrain and challenge collective synchronization in vivo to address how signalling oscillations are integrated with growth dynamics to yield robust embryonic patterning.
Max ERC Funding
2 153 310 €
Duration
Start date: 2020-09-01, End date: 2025-08-31
Project acronym EXECUT.ER
Project Dissecting the molecular mechanisms that execute developmental programmed cell death in plants
Researcher (PI) Moritz NOWACK
Host Institution (HI) VIB VZW
Call Details Consolidator Grant (CoG), LS3, ERC-2019-COG
Summary Programmed Cell Death (PCD) is fundamental to the development and health of multicellular organisms. However, our knowledge on developmentally controlled PCD in plants remains fragmentary, despite its undoubted significance for plant growth and reproduction.
My team has established the Arabidopsis root cap as a novel model system for developmental PCD in plants. This model has enabled us to identify a gene regulatory network controlling the preparation of PCD. However, the molecular processes that terminate the vital functions of a plant cell during the final steps of PCD execution remain unknown.
Exploiting the accessibility of the root cap for live-cell analysis of PCD execution, we obtained preliminary data revealing an unexpected succession of distinct membrane permeabilization events in which the endoplasmic reticulum breaks up before the central vacuole. I hypothesize that this sequential de-compartmentalization is the mechanism underlying the irreversible and orderly execution of PCD.
Recent advances in several key technologies provide unprecedented opportunities to test this hypothesis and make a quantum leap in our understanding of the mechanisms carrying out PCD execution.
I will employ correlative super-resolution light and electron microscopy to analyse PCD execution in unparalleled spatial and temporal resolution. RNA sequencing of single cells at the onset of PCD execution will provide information on the genes that are required for this rapid process. Advanced proteomics techniques will provide a direct route to identify proteins acting on membrane permeabilization during PCD execution. Lastly, multiplex and tissue-specific mutagenesis via innovative CRISPR screens will enable me to overcome genetic redundancy and lethality in the PCD context.
The detailed understanding of plant PCD execution generated by this research program will shed light on a fundamental principle of plant development and open new avenues for crop improvement and protection.
Summary
Programmed Cell Death (PCD) is fundamental to the development and health of multicellular organisms. However, our knowledge on developmentally controlled PCD in plants remains fragmentary, despite its undoubted significance for plant growth and reproduction.
My team has established the Arabidopsis root cap as a novel model system for developmental PCD in plants. This model has enabled us to identify a gene regulatory network controlling the preparation of PCD. However, the molecular processes that terminate the vital functions of a plant cell during the final steps of PCD execution remain unknown.
Exploiting the accessibility of the root cap for live-cell analysis of PCD execution, we obtained preliminary data revealing an unexpected succession of distinct membrane permeabilization events in which the endoplasmic reticulum breaks up before the central vacuole. I hypothesize that this sequential de-compartmentalization is the mechanism underlying the irreversible and orderly execution of PCD.
Recent advances in several key technologies provide unprecedented opportunities to test this hypothesis and make a quantum leap in our understanding of the mechanisms carrying out PCD execution.
I will employ correlative super-resolution light and electron microscopy to analyse PCD execution in unparalleled spatial and temporal resolution. RNA sequencing of single cells at the onset of PCD execution will provide information on the genes that are required for this rapid process. Advanced proteomics techniques will provide a direct route to identify proteins acting on membrane permeabilization during PCD execution. Lastly, multiplex and tissue-specific mutagenesis via innovative CRISPR screens will enable me to overcome genetic redundancy and lethality in the PCD context.
The detailed understanding of plant PCD execution generated by this research program will shed light on a fundamental principle of plant development and open new avenues for crop improvement and protection.
Max ERC Funding
1 999 963 €
Duration
Start date: 2020-06-01, End date: 2025-05-31
Project acronym GHOSTS
Project Genetically enhanced, optically superior tissues (GHOSTS)
Researcher (PI) Moritz Kreysing
Host Institution (HI) MAX-PLANCK-GESELLSCHAFT ZUR FORDERUNG DER WISSENSCHAFTEN EV
Call Details Starting Grant (StG), LS3, ERC-2019-STG
Summary Most biological tissues are optically opaque, largely precluding access by light microscopy. In stark contrast, some living tissues and organisms are highly transparent. Examples include many deep-sea fish, your retina, and cells that we exposed to directed evolution.
Here we propose to uncover the genetic basis of tissue transparency, such that living cells and tissue cultures can be optically cleared by precision genetics. For this we will combine insights into origins of retina transparency, and a set of unique methods, to answer the question how genetically cells become more transparent during directed evolution.
Specifically, we will use a three-fold approach to find transparency genes that do not compromise cellular integrity. For this we will use i) directed evolution towards transparency while co-selecting for cell fitness, ii) extensive phenotyping of transparent cells, both optically and functionally, and iii) use of transcriptomics to rule out stressed cells, and those that deviate too much from wildtype gene expression profiles.
Knowing about physiological transparency genes will allow unprecedented insights into living tissues. If model tissues in the lab were just 1% as transparent as some glass-like fish found in the deep sea, optical microscopes could unleash their full potential, and enable high resolution views into developmental processes in their native environment. We see further transformative potential especially in the fields of organotypic tissue models, functional brain imaging, as well as pharmaceutical screens in 3D tissue cultures.
Summary
Most biological tissues are optically opaque, largely precluding access by light microscopy. In stark contrast, some living tissues and organisms are highly transparent. Examples include many deep-sea fish, your retina, and cells that we exposed to directed evolution.
Here we propose to uncover the genetic basis of tissue transparency, such that living cells and tissue cultures can be optically cleared by precision genetics. For this we will combine insights into origins of retina transparency, and a set of unique methods, to answer the question how genetically cells become more transparent during directed evolution.
Specifically, we will use a three-fold approach to find transparency genes that do not compromise cellular integrity. For this we will use i) directed evolution towards transparency while co-selecting for cell fitness, ii) extensive phenotyping of transparent cells, both optically and functionally, and iii) use of transcriptomics to rule out stressed cells, and those that deviate too much from wildtype gene expression profiles.
Knowing about physiological transparency genes will allow unprecedented insights into living tissues. If model tissues in the lab were just 1% as transparent as some glass-like fish found in the deep sea, optical microscopes could unleash their full potential, and enable high resolution views into developmental processes in their native environment. We see further transformative potential especially in the fields of organotypic tissue models, functional brain imaging, as well as pharmaceutical screens in 3D tissue cultures.
Max ERC Funding
1 496 994 €
Duration
Start date: 2019-12-01, End date: 2024-11-30
Project acronym IC-CCD-qHSC
Project Intrapopulation communication and collective cell decisions of hematopoietic stem cells
Researcher (PI) Cesar NOMBELA
Host Institution (HI) UNIVERSITAT ZURICH
Call Details Consolidator Grant (CoG), LS3, ERC-2019-COG
Summary Hematopoietic stem cells (HSCs) contribute to blood cell production throughout life and are found at rare, yet tightly regulated frequencies in adult bone marrow (BM). During embryonic and postnatal development, HSCs expand through continuous self-renewing proliferation. Upon entry into adulthood the vast majority of HSCs synchronously convert to a quiescent state. From then on, at any given moment very few HSCs are found in active stages of cell cycle, which suffices to compensate basal HSC loss due to differentiation or cell death. Since proliferation rates of individual HSCs are heterogeneous, entry and exit from cell cycle need to be coordinated at the level of the HSC pool. To date, the mechanisms that orchestrate this collective proliferative behavior and effectively control the maintenance of homeostatic HSC numbers remain unknown. In preliminary work for this project we have customized a pipeline that combines 3D microscopy, deep learning-based image analysis and spatial statistics. Using these tools, we observed that despite showing broad spatial heterogeneity, HSCs tend to cluster and accumulate in relatively large regions of the BM. We now postulate that molecular crosstalk between proximal HSCs enables them to perceive their local densities and triggers collective regulation of HSC function to preserve homeostasis. Through a multidisciplinary approach involving high-level microscopy, spatial analyses, comprehensive metabolomic profiling and single-cell transcriptomics we aim to 1) characterize the basic anatomical and functional features of spatial dependencies between HSCs 2) study the potential role of quorum-sensing mechanisms in HSC crosstalk and 3) investigate if competition for molecular resources in local neighborhoods contributes to maintenance of HSC homeostasis. Our research has the potential to unravel novel complex forms of cellular interplay and substantially advance our understanding of hematopoietic tissue organization.
Summary
Hematopoietic stem cells (HSCs) contribute to blood cell production throughout life and are found at rare, yet tightly regulated frequencies in adult bone marrow (BM). During embryonic and postnatal development, HSCs expand through continuous self-renewing proliferation. Upon entry into adulthood the vast majority of HSCs synchronously convert to a quiescent state. From then on, at any given moment very few HSCs are found in active stages of cell cycle, which suffices to compensate basal HSC loss due to differentiation or cell death. Since proliferation rates of individual HSCs are heterogeneous, entry and exit from cell cycle need to be coordinated at the level of the HSC pool. To date, the mechanisms that orchestrate this collective proliferative behavior and effectively control the maintenance of homeostatic HSC numbers remain unknown. In preliminary work for this project we have customized a pipeline that combines 3D microscopy, deep learning-based image analysis and spatial statistics. Using these tools, we observed that despite showing broad spatial heterogeneity, HSCs tend to cluster and accumulate in relatively large regions of the BM. We now postulate that molecular crosstalk between proximal HSCs enables them to perceive their local densities and triggers collective regulation of HSC function to preserve homeostasis. Through a multidisciplinary approach involving high-level microscopy, spatial analyses, comprehensive metabolomic profiling and single-cell transcriptomics we aim to 1) characterize the basic anatomical and functional features of spatial dependencies between HSCs 2) study the potential role of quorum-sensing mechanisms in HSC crosstalk and 3) investigate if competition for molecular resources in local neighborhoods contributes to maintenance of HSC homeostasis. Our research has the potential to unravel novel complex forms of cellular interplay and substantially advance our understanding of hematopoietic tissue organization.
Max ERC Funding
2 312 500 €
Duration
Start date: 2020-10-01, End date: 2025-09-30
Project acronym LIP-ATG
Project The missing link: how do membrane lipids interplay with ATG proteins to instruct plant autophagy
Researcher (PI) Amelie BERNARD
Host Institution (HI) CENTRE NATIONAL DE LA RECHERCHE SCIENTIFIQUE CNRS
Call Details Starting Grant (StG), LS3, ERC-2019-STG
Summary Autophagy is an intracellular catabolic process critical to eukaryotic life and indispensable for plant survival to drought, nutrient scarcity or pathogen attacks. Autophagy relies on the formation of specialized vesicles called autophagosomes (AP) which engulf and deliver cell components to the lytic vacuole. AP biogenesis is carried out by a group of dedicated proteins (named ATG) and hinges on intense remodelling events and on the remarkable capacity of an initial membrane, the phagophore, to assemble de novo, shape like a cup, expand while maintaining structure and function and re-shape to a complete vesicle. To date the molecular mechanisms underlying these events remain elusive. Research has focused on the role of autophagy proteins but, despite AP biogenesis being a membrane-based process, the fundamental contributions of lipids to AP membrane formation, identity and activities have been largely unexplored; in other words, when it comes to AP formation we are only looking at half of the picture.
I propose to address the fundamental question of how APs form and shape from a novel angle: by exploring how lipids’ nature, dynamics and lateral heterogeneity instruct the phagophore structure, its protein composition and its functions. The project builds on our recent results and expands on strategies that we have developed, integrating proteomic/bioinformatic approaches, lipidomics and high-resolution 3D imaging. We will tackle 3 complementary objectives: 1) Reveal the dynamic lipid signature of the phagophore, 2) Elucidate the implication of lipids nature and repartition in the phagophore ultrastructure, 3) Decrypt the molecular mechanisms by which lipids interplay with ATG proteins to control autophagy activity and plant physiology. Overall the project will articulate an integrated vision of the molecular processes controlling autophagy and provide fundamental knowledge in our understanding of plant adaptive programs.
Summary
Autophagy is an intracellular catabolic process critical to eukaryotic life and indispensable for plant survival to drought, nutrient scarcity or pathogen attacks. Autophagy relies on the formation of specialized vesicles called autophagosomes (AP) which engulf and deliver cell components to the lytic vacuole. AP biogenesis is carried out by a group of dedicated proteins (named ATG) and hinges on intense remodelling events and on the remarkable capacity of an initial membrane, the phagophore, to assemble de novo, shape like a cup, expand while maintaining structure and function and re-shape to a complete vesicle. To date the molecular mechanisms underlying these events remain elusive. Research has focused on the role of autophagy proteins but, despite AP biogenesis being a membrane-based process, the fundamental contributions of lipids to AP membrane formation, identity and activities have been largely unexplored; in other words, when it comes to AP formation we are only looking at half of the picture.
I propose to address the fundamental question of how APs form and shape from a novel angle: by exploring how lipids’ nature, dynamics and lateral heterogeneity instruct the phagophore structure, its protein composition and its functions. The project builds on our recent results and expands on strategies that we have developed, integrating proteomic/bioinformatic approaches, lipidomics and high-resolution 3D imaging. We will tackle 3 complementary objectives: 1) Reveal the dynamic lipid signature of the phagophore, 2) Elucidate the implication of lipids nature and repartition in the phagophore ultrastructure, 3) Decrypt the molecular mechanisms by which lipids interplay with ATG proteins to control autophagy activity and plant physiology. Overall the project will articulate an integrated vision of the molecular processes controlling autophagy and provide fundamental knowledge in our understanding of plant adaptive programs.
Max ERC Funding
1 499 880 €
Duration
Start date: 2020-02-01, End date: 2025-01-31
Project acronym MechanoSelfFate
Project Role of Tissue Mechanics in Embryonic Self-Organization and Cell Fate Plasticity
Researcher (PI) Jérôme GROS
Host Institution (HI) INSTITUT PASTEUR
Call Details Consolidator Grant (CoG), LS3, ERC-2019-COG
Summary How molecular and mechanical cues interplay to coordinate the morphogenesis and patterning of embryonic structures is an open question in developmental biology. The early avian embryo is an ideal model for the study of such interplay as it exhibits highly regulative development, is greatly amenable to live imaging approaches and can be readily mechanically challenged. Whereas avian embryos have long been known to remarkably adapt and readjust cell fate upon surgical perturbations, such regulative potential has been investigated solely from a molecular standpoint, leaving the role for mechanical forces unexplored. This proposal builds on our recent results and methods characterizing the mechanical control of gastrulation to investigate the role of mechanical forces in embryonic regulation and in cell fate plasticity. Specifically, we propose 1) to develop innovative tools allowing to perturb the mechanical state of early embryos in order characterize the role of forces during development; 2) to test whether a mechanical self-organizing system underlies the remarkable regulative potential avian embryos; 3) to investigate the role of mechanical forces in mesoderm, embryonic and extra-embryonic regional fate allocation. To this end, we will use an interdisciplinary approach combining novel transgenic quail lines, live imaging, and pharmacological/molecular/optogenetic/mechanical perturbations along with theoretical frameworks and modeling approaches. These studies will decipher the interplay between cellular, molecular and mechanical cues that ensures the robust, yet plastic allocation of cell fate in amniote embryos (i.e. reptiles, birds and mammals, including humans).
Summary
How molecular and mechanical cues interplay to coordinate the morphogenesis and patterning of embryonic structures is an open question in developmental biology. The early avian embryo is an ideal model for the study of such interplay as it exhibits highly regulative development, is greatly amenable to live imaging approaches and can be readily mechanically challenged. Whereas avian embryos have long been known to remarkably adapt and readjust cell fate upon surgical perturbations, such regulative potential has been investigated solely from a molecular standpoint, leaving the role for mechanical forces unexplored. This proposal builds on our recent results and methods characterizing the mechanical control of gastrulation to investigate the role of mechanical forces in embryonic regulation and in cell fate plasticity. Specifically, we propose 1) to develop innovative tools allowing to perturb the mechanical state of early embryos in order characterize the role of forces during development; 2) to test whether a mechanical self-organizing system underlies the remarkable regulative potential avian embryos; 3) to investigate the role of mechanical forces in mesoderm, embryonic and extra-embryonic regional fate allocation. To this end, we will use an interdisciplinary approach combining novel transgenic quail lines, live imaging, and pharmacological/molecular/optogenetic/mechanical perturbations along with theoretical frameworks and modeling approaches. These studies will decipher the interplay between cellular, molecular and mechanical cues that ensures the robust, yet plastic allocation of cell fate in amniote embryos (i.e. reptiles, birds and mammals, including humans).
Max ERC Funding
1 995 334 €
Duration
Start date: 2020-09-01, End date: 2025-08-31
