Project acronym ANTHROPOID
Project Great ape organoids to reconstruct uniquely human development
Researcher (PI) Jarrett CAMP
Host Institution (HI) INSTITUT FUR MOLEKULARE UND KLINISCHE OPHTHALMOLOGIE BASEL
Call Details Starting Grant (StG), LS2, ERC-2018-STG
Summary Humans diverged from our closest living relatives, chimpanzees and other great apes, 6-10 million years ago. Since this divergence, our ancestors acquired genetic changes that enhanced cognition, altered metabolism, and endowed our species with an adaptive capacity to colonize the entire planet and reshape the biosphere. Through genome comparisons between modern humans, Neandertals, chimpanzees and other apes we have identified genetic changes that likely contribute to innovations in human metabolic and cognitive physiology. However, it has been difficult to assess the functional effects of these genetic changes due to the lack of cell culture systems that recapitulate great ape organ complexity. Human and chimpanzee pluripotent stem cells (PSCs) can self-organize into three-dimensional (3D) tissues that recapitulate the morphology, function, and genetic programs controlling organ development. Our vision is to use organoids to study the changes that set modern humans apart from our closest evolutionary relatives as well as all other organisms on the planet. In ANTHROPOID we will generate a great ape developmental cell atlas using cortex, liver, and small intestine organoids. We will use single-cell transcriptomics and chromatin accessibility to identify cell type-specific features of transcriptome divergence at cellular resolution. We will dissect enhancer evolution using single-cell genomic screens and ancestralize human cells to resurrect pre-human cellular phenotypes. ANTHROPOID utilizes quantitative and state-of-the-art methods to explore exciting high-risk questions at multiple branches of the modern human lineage. This project is a ground breaking starting point to replay evolution and tackle the ancient question of what makes us uniquely human?
Summary
Humans diverged from our closest living relatives, chimpanzees and other great apes, 6-10 million years ago. Since this divergence, our ancestors acquired genetic changes that enhanced cognition, altered metabolism, and endowed our species with an adaptive capacity to colonize the entire planet and reshape the biosphere. Through genome comparisons between modern humans, Neandertals, chimpanzees and other apes we have identified genetic changes that likely contribute to innovations in human metabolic and cognitive physiology. However, it has been difficult to assess the functional effects of these genetic changes due to the lack of cell culture systems that recapitulate great ape organ complexity. Human and chimpanzee pluripotent stem cells (PSCs) can self-organize into three-dimensional (3D) tissues that recapitulate the morphology, function, and genetic programs controlling organ development. Our vision is to use organoids to study the changes that set modern humans apart from our closest evolutionary relatives as well as all other organisms on the planet. In ANTHROPOID we will generate a great ape developmental cell atlas using cortex, liver, and small intestine organoids. We will use single-cell transcriptomics and chromatin accessibility to identify cell type-specific features of transcriptome divergence at cellular resolution. We will dissect enhancer evolution using single-cell genomic screens and ancestralize human cells to resurrect pre-human cellular phenotypes. ANTHROPOID utilizes quantitative and state-of-the-art methods to explore exciting high-risk questions at multiple branches of the modern human lineage. This project is a ground breaking starting point to replay evolution and tackle the ancient question of what makes us uniquely human?
Max ERC Funding
1 500 000 €
Duration
Start date: 2019-06-01, End date: 2024-05-31
Project acronym AXPLAST
Project Deep brain imaging of cellular mechanisms of sensory processing and learning
Researcher (PI) Jan GRUNDEMANN
Host Institution (HI) UNIVERSITAT BASEL
Call Details Starting Grant (StG), LS5, ERC-2018-STG
Summary Learning and memory are the basis of our behaviour and mental well-being. Understanding the mechanisms of structural and cellular plasticity in defined neuronal circuits in vivo will be crucial to elucidate principles of circuit-specific memory formation and their relation to changes in neuronal ensemble dynamics.
Structural plasticity studies were technically limited to cortex, excluding deep brain areas like the amygdala, and mainly focussed on the input site (dendritic spines), whilst the plasticity of the axon initial segment (AIS), a neuron’s site of output generation, was so far not studied in vivo. Length and location of the AIS are plastic and strongly affects a neurons spike output. However, it remains unknown if AIS plasticity regulates neuronal activity upon learning in vivo.
We will combine viral expression of AIS live markers and genetically-encoded Ca2+-sensors with novel deep brain imaging techniques via gradient index (GRIN) lenses to investigate how AIS location and length are regulated upon associative learning in amygdala circuits in vivo. Two-photon time-lapse imaging of the AIS of amygdala neurons upon fear conditioning will help us to track learning-driven AIS location dynamics. Next, we will combine miniature microscope imaging of neuronal activity in freely moving animals with two-photon imaging to link AIS location, length and plasticity to the intrinsic activity as well as learning-related response plasticity of amygdala neurons during fear learning and extinction in vivo. Finally, we will test if AIS plasticity is a general cellular plasticity mechanisms in brain areas afferent to the amygdala, e.g. thalamus.
Using a combination of two-photon and miniature microscopy imaging to map structural dynamics of defined neural circuits in the amygdala and its thalamic input areas will provide fundamental insights into the cellular mechanisms underlying sensory processing upon learning and relate network level plasticity with the cellular level.
Summary
Learning and memory are the basis of our behaviour and mental well-being. Understanding the mechanisms of structural and cellular plasticity in defined neuronal circuits in vivo will be crucial to elucidate principles of circuit-specific memory formation and their relation to changes in neuronal ensemble dynamics.
Structural plasticity studies were technically limited to cortex, excluding deep brain areas like the amygdala, and mainly focussed on the input site (dendritic spines), whilst the plasticity of the axon initial segment (AIS), a neuron’s site of output generation, was so far not studied in vivo. Length and location of the AIS are plastic and strongly affects a neurons spike output. However, it remains unknown if AIS plasticity regulates neuronal activity upon learning in vivo.
We will combine viral expression of AIS live markers and genetically-encoded Ca2+-sensors with novel deep brain imaging techniques via gradient index (GRIN) lenses to investigate how AIS location and length are regulated upon associative learning in amygdala circuits in vivo. Two-photon time-lapse imaging of the AIS of amygdala neurons upon fear conditioning will help us to track learning-driven AIS location dynamics. Next, we will combine miniature microscope imaging of neuronal activity in freely moving animals with two-photon imaging to link AIS location, length and plasticity to the intrinsic activity as well as learning-related response plasticity of amygdala neurons during fear learning and extinction in vivo. Finally, we will test if AIS plasticity is a general cellular plasticity mechanisms in brain areas afferent to the amygdala, e.g. thalamus.
Using a combination of two-photon and miniature microscopy imaging to map structural dynamics of defined neural circuits in the amygdala and its thalamic input areas will provide fundamental insights into the cellular mechanisms underlying sensory processing upon learning and relate network level plasticity with the cellular level.
Max ERC Funding
1 475 475 €
Duration
Start date: 2018-12-01, End date: 2023-11-30
Project acronym BRITE
Project Elucidating the molecular mechanisms underlying brite adipocyte specification and activation
Researcher (PI) Ferdinand VON MEYENN
Host Institution (HI) EIDGENOESSISCHE TECHNISCHE HOCHSCHULE ZUERICH
Call Details Starting Grant (StG), LS4, ERC-2018-STG
Summary Brown adipocytes can dissipate energy in a process called adaptive thermogenesis. Whilst the classical brown adipose tissue (BAT) depots disappear during early life in humans, cold exposure can promote the appearance of brown-like adipocytes within the white adipose tissue (WAT), termed brite (brown-in-white). Increased BAT activity results in increased energy expenditure and has been correlated with leanness in humans. Hence, recruitment of brite adipocytes may constitute a promising therapeutic strategy to treat obesity and its associated metabolic diseases. Despite the beneficial metabolic properties of brown and brite adipocytes, little is known about the molecular mechanisms underlying their specification and activation in vivo. This proposal focuses on understanding the complex biology of thermogenic adipocyte biology by studying the epigenetic and transcriptional aspects of WAT britening and BAT recruitment in vivo to identify pathways of therapeutic relevance and to better define the brite precursor cells. Specific aims are to 1) investigate epigenetic and transcriptional states and heterogeneity in human and mouse adipose tissue; 2) develop a novel time-resolved method to correlate preceding chromatin states and cell fate decisions during adipose tissue remodelling; 3) identify and validate key (drugable) epigenetic and transcriptional regulators involved in brite adipocyte specification. Experimentally, I will use adipose tissue samples from human donors and mouse models, to asses at the single-cell level cellular heterogeneity, transcriptional and epigenetic states, to identify subpopulations, and to define the adaptive responses to cold or β-adrenergic stimulation. Using computational methods and in vitro and in vivo validation experiments, I will define epigenetic and transcriptional networks that control WAT britening, and develop a model of the molecular events underlying adipocyte tissue plasticity.
Summary
Brown adipocytes can dissipate energy in a process called adaptive thermogenesis. Whilst the classical brown adipose tissue (BAT) depots disappear during early life in humans, cold exposure can promote the appearance of brown-like adipocytes within the white adipose tissue (WAT), termed brite (brown-in-white). Increased BAT activity results in increased energy expenditure and has been correlated with leanness in humans. Hence, recruitment of brite adipocytes may constitute a promising therapeutic strategy to treat obesity and its associated metabolic diseases. Despite the beneficial metabolic properties of brown and brite adipocytes, little is known about the molecular mechanisms underlying their specification and activation in vivo. This proposal focuses on understanding the complex biology of thermogenic adipocyte biology by studying the epigenetic and transcriptional aspects of WAT britening and BAT recruitment in vivo to identify pathways of therapeutic relevance and to better define the brite precursor cells. Specific aims are to 1) investigate epigenetic and transcriptional states and heterogeneity in human and mouse adipose tissue; 2) develop a novel time-resolved method to correlate preceding chromatin states and cell fate decisions during adipose tissue remodelling; 3) identify and validate key (drugable) epigenetic and transcriptional regulators involved in brite adipocyte specification. Experimentally, I will use adipose tissue samples from human donors and mouse models, to asses at the single-cell level cellular heterogeneity, transcriptional and epigenetic states, to identify subpopulations, and to define the adaptive responses to cold or β-adrenergic stimulation. Using computational methods and in vitro and in vivo validation experiments, I will define epigenetic and transcriptional networks that control WAT britening, and develop a model of the molecular events underlying adipocyte tissue plasticity.
Max ERC Funding
1 552 620 €
Duration
Start date: 2019-03-01, End date: 2024-02-29
Project acronym CAN-IT-BARRIERS
Project Disruption of systemic and microenvironmental barriers to immunotherapy of antigenic tumors
Researcher (PI) Douglas HANAHAN
Host Institution (HI) ECOLE POLYTECHNIQUE FEDERALE DE LAUSANNE
Call Details Advanced Grant (AdG), LS7, ERC-2018-ADG
Summary The frontier in cancer therapy of orchestrating the immune system to attack tumors is producing unprecedented survival benefit in some patients. The corollary is lack of efficacy both in ostensibly responsive tumor types as well as others that are mostly non-responsive. The basis lies in pre-existing and adaptive resistance mechanisms that circumvent induction of tumor-reactive cytotoxic T cells (CTLs) capable of infiltrating solid tumors and eliminating cancer cells. A priori, cancers induced by expression of human papillomavirus oncogenes should be responsive to immunotherapy: these cancers encode immunogenic neo-antigens – the oncoproteins E6/7 – necessary for their manifestation. Rather, such tumors are poorly responsive to immunotherapies. Results from my lab and others using mouse models of HPV-induced cancer have established an actionable hypothesis: during tumorigenesis, such tumors erect multiple barriers to the induction, infiltration, and killing of cancer cells by tumor antigen-reactive CTLs. These include overarching systemic antigen-nonspecific immunosuppression mediated by expanded populations of myeloid cells in spleen and lymph nodes, complemented by immune response-impairing barriers operative in the tumor microenvironment. A spectrum of models will probe these barriers, genetically and pharmacologically, establishing their functional importance, alone and in concert. A major focus will be on how oncogene-expressing keratinocytes elicit a marked expansion of immunosuppressive myeloid cells in spleen and lymph nodes, and how these myeloid cells in turn inhibit development and activation of CD8 T cells and antigen-presenting dendritic cells. Then we’ll assess the therapeutic potential of barrier-breaking strategies combined with immuno-stimulatory modalities. This project will deliver new knowledge about multi-faceted barriers to immunotherapy in these refractory cancers, helping lay the groundwork for efficacious immunotherapy.
Summary
The frontier in cancer therapy of orchestrating the immune system to attack tumors is producing unprecedented survival benefit in some patients. The corollary is lack of efficacy both in ostensibly responsive tumor types as well as others that are mostly non-responsive. The basis lies in pre-existing and adaptive resistance mechanisms that circumvent induction of tumor-reactive cytotoxic T cells (CTLs) capable of infiltrating solid tumors and eliminating cancer cells. A priori, cancers induced by expression of human papillomavirus oncogenes should be responsive to immunotherapy: these cancers encode immunogenic neo-antigens – the oncoproteins E6/7 – necessary for their manifestation. Rather, such tumors are poorly responsive to immunotherapies. Results from my lab and others using mouse models of HPV-induced cancer have established an actionable hypothesis: during tumorigenesis, such tumors erect multiple barriers to the induction, infiltration, and killing of cancer cells by tumor antigen-reactive CTLs. These include overarching systemic antigen-nonspecific immunosuppression mediated by expanded populations of myeloid cells in spleen and lymph nodes, complemented by immune response-impairing barriers operative in the tumor microenvironment. A spectrum of models will probe these barriers, genetically and pharmacologically, establishing their functional importance, alone and in concert. A major focus will be on how oncogene-expressing keratinocytes elicit a marked expansion of immunosuppressive myeloid cells in spleen and lymph nodes, and how these myeloid cells in turn inhibit development and activation of CD8 T cells and antigen-presenting dendritic cells. Then we’ll assess the therapeutic potential of barrier-breaking strategies combined with immuno-stimulatory modalities. This project will deliver new knowledge about multi-faceted barriers to immunotherapy in these refractory cancers, helping lay the groundwork for efficacious immunotherapy.
Max ERC Funding
2 500 000 €
Duration
Start date: 2020-01-01, End date: 2024-12-31
Project acronym CELLTYPESANDCIRCUITS
Project Neural circuit function in the retina of mice and humans
Researcher (PI) Botond Roska
Host Institution (HI) FRIEDRICH MIESCHER INSTITUTE FOR BIOMEDICAL RESEARCH FONDATION
Call Details Starting Grant (StG), LS5, ERC-2010-StG_20091118
Summary The mammalian brain is assembled from thousands of neuronal cell types that are organized into distinct circuits to perform behaviourally relevant computations. To gain mechanistic insights about brain function and to treat specific diseases of the nervous system it is crucial to understand what these local circuits are computing and how they achieve these computations. By examining the structure and function of a few genetically identified and experimentally accessible neural circuits we plan to address fundamental questions about the functional architecture of neural circuits. First, are cell types assigned to a unique functional circuit with a well-defined function or do they participate in multiple circuits (multitasking cell types), adjusting their role depending on the state of these circuits? Second, does a neural circuit perform a single computation or depending on the information content of its inputs can it carry out radically different functions? Third, how, among the large number of other cell types, do the cells belonging to the same functional circuit connect together during development? We use the mouse retina as a model system to address these questions. Finally, we will study the structure and function of a specialised neural circuit in the human fovea that enables humans to read. We predict that our insights into the mechanism of multitasking, network switches and the development of selective connectivity will be instructive to study similar phenomena in other brain circuits. Knowledge of the structure and function of the human fovea will open up new opportunities to correlate human retinal function with human visual behaviour and our genetic technologies to study human foveal function will allow us and others to design better strategies for restoring vision for the blind.
Summary
The mammalian brain is assembled from thousands of neuronal cell types that are organized into distinct circuits to perform behaviourally relevant computations. To gain mechanistic insights about brain function and to treat specific diseases of the nervous system it is crucial to understand what these local circuits are computing and how they achieve these computations. By examining the structure and function of a few genetically identified and experimentally accessible neural circuits we plan to address fundamental questions about the functional architecture of neural circuits. First, are cell types assigned to a unique functional circuit with a well-defined function or do they participate in multiple circuits (multitasking cell types), adjusting their role depending on the state of these circuits? Second, does a neural circuit perform a single computation or depending on the information content of its inputs can it carry out radically different functions? Third, how, among the large number of other cell types, do the cells belonging to the same functional circuit connect together during development? We use the mouse retina as a model system to address these questions. Finally, we will study the structure and function of a specialised neural circuit in the human fovea that enables humans to read. We predict that our insights into the mechanism of multitasking, network switches and the development of selective connectivity will be instructive to study similar phenomena in other brain circuits. Knowledge of the structure and function of the human fovea will open up new opportunities to correlate human retinal function with human visual behaviour and our genetic technologies to study human foveal function will allow us and others to design better strategies for restoring vision for the blind.
Max ERC Funding
1 499 000 €
Duration
Start date: 2010-11-01, End date: 2015-10-31
Project acronym CENGIN
Project Deciphering and engineering centriole assembly
Researcher (PI) Pierre Jörg GÖNCZY
Host Institution (HI) ECOLE POLYTECHNIQUE FEDERALE DE LAUSANNE
Call Details Advanced Grant (AdG), LS3, ERC-2018-ADG
Summary Deciphering and engineering the assembly of cellular organelles is a key pursuit in biology. The centriole is an evolutionarily conserved organelle well suited for this goal, and which is crucial for cell signaling, motility and division. The centriole exhibits a striking 9-fold radial symmetry of microtubules around a likewise symmetrical cartwheel containing stacked ring-bearing structures. Components essential for generating this remarkable architecture from alga to man have been identified. A next critical step is to engineer assays to probe the dynamics of centriole assembly with molecular precision to fully understand how these components together build a functional organelle. Our ambitious research proposal aims at taking groundbreaking steps in this direction through four specific aims:
1) Reconstituting cartwheel ring assembly dynamics. We will use high-speed AFM (HS-AFM) to dissect the biophysics of SAS-6 ring polymer dynamics at the root of cartwheel assembly. We will also use HS-AFM to analyze monobodies against SAS-6, as well as engineer surfaces and DNA origamis to further dissect ring assembly.
2) Deciphering ring stacking mechanisms. We will use cryo-ET to identify SAS-6 features that direct stacking of ring structures and set cartwheel height. Moreover, we will develop an HS-AFM stacking assay and a reconstituted stacking assay from human cells.
3) Understanding peripheral element contributions to centriole biogenesis. We will dissect the function of the peripheral centriole pinhead protein Cep135/Bld10p, as well as identify and likewise dissect peripheral A-C linker proteins. Furthermore, we will further engineer the HS-AFM assay to include such peripheral components.
4) Dissecting de novo centriole assembly mechanisms. We will dissect de novo centriole formation in human cells and water fern. We will also explore whether de novo formation involves a phase separation mechanism and repurpose the HS-AFM assay to probe de novo organelle biogenes
Summary
Deciphering and engineering the assembly of cellular organelles is a key pursuit in biology. The centriole is an evolutionarily conserved organelle well suited for this goal, and which is crucial for cell signaling, motility and division. The centriole exhibits a striking 9-fold radial symmetry of microtubules around a likewise symmetrical cartwheel containing stacked ring-bearing structures. Components essential for generating this remarkable architecture from alga to man have been identified. A next critical step is to engineer assays to probe the dynamics of centriole assembly with molecular precision to fully understand how these components together build a functional organelle. Our ambitious research proposal aims at taking groundbreaking steps in this direction through four specific aims:
1) Reconstituting cartwheel ring assembly dynamics. We will use high-speed AFM (HS-AFM) to dissect the biophysics of SAS-6 ring polymer dynamics at the root of cartwheel assembly. We will also use HS-AFM to analyze monobodies against SAS-6, as well as engineer surfaces and DNA origamis to further dissect ring assembly.
2) Deciphering ring stacking mechanisms. We will use cryo-ET to identify SAS-6 features that direct stacking of ring structures and set cartwheel height. Moreover, we will develop an HS-AFM stacking assay and a reconstituted stacking assay from human cells.
3) Understanding peripheral element contributions to centriole biogenesis. We will dissect the function of the peripheral centriole pinhead protein Cep135/Bld10p, as well as identify and likewise dissect peripheral A-C linker proteins. Furthermore, we will further engineer the HS-AFM assay to include such peripheral components.
4) Dissecting de novo centriole assembly mechanisms. We will dissect de novo centriole formation in human cells and water fern. We will also explore whether de novo formation involves a phase separation mechanism and repurpose the HS-AFM assay to probe de novo organelle biogenes
Max ERC Funding
2 500 000 €
Duration
Start date: 2019-09-01, End date: 2024-08-31
Project acronym CIRCATRANS
Project Control of mouse metabolism by circadian clock-coordinated mRNA translation
Researcher (PI) Frédéric Bruno Martin Gachon
Host Institution (HI) NESTEC SA
Call Details Starting Grant (StG), LS1, ERC-2010-StG_20091118
Summary The mammalian circadian clock plays a fundamental role in the liver by regulating fatty acid, glucose and xenobiotic metabolism. Impairment of this rhythm has been show to lead to diverse pathologies including metabolic syndrome. At present, it is supposed that the circadian clock regulates metabolism mostly by regulating the expression of liver enzymes at the transcriptional level. We have now collected evidence that post-transcriptional regulations play also an important role in this regulation. Particularly, recent results from our laboratory show that the circadian clock can synchronize mRNA translation in mouse liver through rhythmic activation of the Target Of Rapamycin Complex 1 (TORC1) with a 12-hours period. Based on this unexpected observation, we plan to identify the genes rhythmically translated in the mouse liver as well as the mechanisms involved in this translation. Indeed, our initial observations suggest a cap-independent translation during the day and a cap-dependent translation during the night. Identification of the different complexes involved in translation at this two different times and their correlation with the sequence, structure, and/or function of the translated genes will provide new insight into the action of the circadian clock on animal metabolism. In parallel, we will identify the signalling pathways involved in the rhythmic activation of TORC1 in mouse liver. Finally, we will study the consequences of a deregulated rhythmic translation in circadian clock-deficient mice on the metabolism and the longevity of these animals. Perturbations of the circadian clock have been linked to numerous pathologies, including obesity, type 2 diabetes and cancer. Our project on the importance of circadian clock-coordinated translation will likely reveal new findings in the field of regulation of animal metabolism by the circadian clock.
Summary
The mammalian circadian clock plays a fundamental role in the liver by regulating fatty acid, glucose and xenobiotic metabolism. Impairment of this rhythm has been show to lead to diverse pathologies including metabolic syndrome. At present, it is supposed that the circadian clock regulates metabolism mostly by regulating the expression of liver enzymes at the transcriptional level. We have now collected evidence that post-transcriptional regulations play also an important role in this regulation. Particularly, recent results from our laboratory show that the circadian clock can synchronize mRNA translation in mouse liver through rhythmic activation of the Target Of Rapamycin Complex 1 (TORC1) with a 12-hours period. Based on this unexpected observation, we plan to identify the genes rhythmically translated in the mouse liver as well as the mechanisms involved in this translation. Indeed, our initial observations suggest a cap-independent translation during the day and a cap-dependent translation during the night. Identification of the different complexes involved in translation at this two different times and their correlation with the sequence, structure, and/or function of the translated genes will provide new insight into the action of the circadian clock on animal metabolism. In parallel, we will identify the signalling pathways involved in the rhythmic activation of TORC1 in mouse liver. Finally, we will study the consequences of a deregulated rhythmic translation in circadian clock-deficient mice on the metabolism and the longevity of these animals. Perturbations of the circadian clock have been linked to numerous pathologies, including obesity, type 2 diabetes and cancer. Our project on the importance of circadian clock-coordinated translation will likely reveal new findings in the field of regulation of animal metabolism by the circadian clock.
Max ERC Funding
1 475 831 €
Duration
Start date: 2011-03-01, End date: 2016-02-29
Project acronym COMPUSLANG
Project Neural and computational determinants of left cerebral dominance in speech and language
Researcher (PI) Anne-Lise Mamessier
Host Institution (HI) UNIVERSITE DE GENEVE
Call Details Starting Grant (StG), LS5, ERC-2010-StG_20091118
Summary More than a century after Wernicke and Broca established that speech perception and production rely on temporal and prefrontal cortices of the left brain hemisphere, the biological determinants for this organization are still unknown. While functional neuroanatomy has been described in great detail, the neuroscience of language still lacks a physiologically plausible model of the neuro-computational mechanisms for coding and decoding of speech acoustic signal. We propose to fill this gap by testing the biological validity and exploring the computational implications of one promising proposal, the Asymmetric Sampling in Time theory. AST assumes that speech signals are analysed in parallel at multiple timescales and that these timescales differ between left and right cerebral hemispheres. This theory is original and provocative as it implies that a single computational difference, distinct integration windows in right and left auditory cortices could be sufficient to explain why speech is preferentially processed by the left brain, and possible even why the human brain has evolved toward such an asymmetric functional organization. Our proposal has four goals: 1/ to validate, invalidate or amend AST on the basis of physiological experiments in healthy human subjects including functional magnetic resonance imaging (fMRI), combined electroencephalography (EEG) and fMRI, magnetoencephalography (MEG) and subdural electrocorticography (EcoG), 2/ to use computational modeling to probe those aspects of the theory that currently remain inaccessible to empirical testing (evaluation, assessment), 3/ to apply AST to binaural artificial hearing with cochlear implants, 4/ to test for disorders of auditory sampling in autism and dyslexia, two language neurodevelopmental pathologies in which a genetic basis implicates the physiological underpinnings of AST, and 5/ to assess potential generalisation of AST to linguistic action in the context of speech production.
Summary
More than a century after Wernicke and Broca established that speech perception and production rely on temporal and prefrontal cortices of the left brain hemisphere, the biological determinants for this organization are still unknown. While functional neuroanatomy has been described in great detail, the neuroscience of language still lacks a physiologically plausible model of the neuro-computational mechanisms for coding and decoding of speech acoustic signal. We propose to fill this gap by testing the biological validity and exploring the computational implications of one promising proposal, the Asymmetric Sampling in Time theory. AST assumes that speech signals are analysed in parallel at multiple timescales and that these timescales differ between left and right cerebral hemispheres. This theory is original and provocative as it implies that a single computational difference, distinct integration windows in right and left auditory cortices could be sufficient to explain why speech is preferentially processed by the left brain, and possible even why the human brain has evolved toward such an asymmetric functional organization. Our proposal has four goals: 1/ to validate, invalidate or amend AST on the basis of physiological experiments in healthy human subjects including functional magnetic resonance imaging (fMRI), combined electroencephalography (EEG) and fMRI, magnetoencephalography (MEG) and subdural electrocorticography (EcoG), 2/ to use computational modeling to probe those aspects of the theory that currently remain inaccessible to empirical testing (evaluation, assessment), 3/ to apply AST to binaural artificial hearing with cochlear implants, 4/ to test for disorders of auditory sampling in autism and dyslexia, two language neurodevelopmental pathologies in which a genetic basis implicates the physiological underpinnings of AST, and 5/ to assess potential generalisation of AST to linguistic action in the context of speech production.
Max ERC Funding
1 500 000 €
Duration
Start date: 2011-02-01, End date: 2016-01-31
Project acronym CRISPR2.0
Project Microbial genome defence pathways: from molecular mechanisms to next-generation molecular tools
Researcher (PI) Martin JINEK
Host Institution (HI) UNIVERSITAT ZURICH
Call Details Consolidator Grant (CoG), LS1, ERC-2018-COG
Summary The constant arms race between prokaryotic microbes and their molecular parasites such as viruses, plasmids and transposons has driven the evolution of complex genome defence mechanisms. The CRISPR-Cas defence systems provide adaptive RNA-guided immunity against invasive nucleic acid elements. CRISPR-associated effector nucleases such as Cas9, Cas12a and Cas13 have emerged as powerful tools for precision genome editing, gene expression control and nucleic acid detection. However, these technologies suffer from drawbacks that limit their efficacy and versatility, necessitating the search for additional exploitable molecular activities. Building on our recent structural and biochemical studies, the goal of this project is to investigate the molecular architectures and mechanisms of CRISPR-associated systems and other genome defence mechanisms, aiming not only to shed light on their biological roles but also inform their technological development. Specifically, the proposed studies will examine (i) the molecular basis of cyclic oligoadenylate signalling in type III CRISPR-Cas systems, (ii) the mechanism of transposon-associated type I CRISPR-Cas systems and their putative function in RNA-guided DNA transposition, and (iii) molecular activities associated with recently described non-CRISPR defence systems. Collectively, the proposed studies will advance our understanding of the molecular functions of genome defence mechanisms in shaping the evolution of prokaryotic genomes and make critical contributions to their development as novel genetic engineering tools.
Summary
The constant arms race between prokaryotic microbes and their molecular parasites such as viruses, plasmids and transposons has driven the evolution of complex genome defence mechanisms. The CRISPR-Cas defence systems provide adaptive RNA-guided immunity against invasive nucleic acid elements. CRISPR-associated effector nucleases such as Cas9, Cas12a and Cas13 have emerged as powerful tools for precision genome editing, gene expression control and nucleic acid detection. However, these technologies suffer from drawbacks that limit their efficacy and versatility, necessitating the search for additional exploitable molecular activities. Building on our recent structural and biochemical studies, the goal of this project is to investigate the molecular architectures and mechanisms of CRISPR-associated systems and other genome defence mechanisms, aiming not only to shed light on their biological roles but also inform their technological development. Specifically, the proposed studies will examine (i) the molecular basis of cyclic oligoadenylate signalling in type III CRISPR-Cas systems, (ii) the mechanism of transposon-associated type I CRISPR-Cas systems and their putative function in RNA-guided DNA transposition, and (iii) molecular activities associated with recently described non-CRISPR defence systems. Collectively, the proposed studies will advance our understanding of the molecular functions of genome defence mechanisms in shaping the evolution of prokaryotic genomes and make critical contributions to their development as novel genetic engineering tools.
Max ERC Funding
1 996 525 €
Duration
Start date: 2019-05-01, End date: 2024-04-30
Project acronym CTLANDROS
Project Reactive Oxygen Species in CTL-mediated Cell Death: from Mechanism to Applications
Researcher (PI) Denis Martinvalet
Host Institution (HI) UNIVERSITE DE GENEVE
Call Details Starting Grant (StG), LS6, ERC-2010-StG_20091118
Summary Cytotoxic T lymphocytes (CTL) and natural killer (NK) cells release granzyme and perforin from cytotoxic granules into the immune synapse to induce apoptosis of target cells that are either virus-infected or cancerous. Granzyme A activates a caspase-independent apoptotic pathway and induces mitochondrial damage characterized by superoxide anion production and loss of the mitochondrial transmembrane potential, without disrupting the integrity of the mitochondrial outer membrane; while causing single-stranded DNA damage. GzmB induces both caspase-dependent and caspase-independent cell death. In the caspase-dependent pathway, mitochondrial functions are altered as evidenced by the loss of mitochondrial transmembrane potential and the generation of reactive oxygen species (ROS). The mitochondrial outer membrane (MOM) is disrupted, resulting in the release of apoptogenic factors. To date, research on mitochondrial-dependent apoptosis has focused on mitochondrial outer membrane permeabilization (MOMP) however whether the generation of ROS is incidental or essential to the execution of apoptosis remains unclear. Like human GzmA, human GzmB promotes cell death in a ROS-dependent manner. Preliminary data suggest that human GzmB can induce ROS in a MOMP-independent manner as Bax and Bak double knockout MEF cells treated with human GzmB and perforin still display a robust ROS production and dye in an ROS-dependent manner. Since GzmA and GzmB induce cell death in a ROS-dependent manner, we hypothesize that oxygen free radicals are central to the execution of programmed cell death induced by the cytotoxic granules. Therefore, the goal of this proposal is to dissect the key molecular events triggered by ROS that lead to Citotoxic Tcell-induced target cell death. A combination of biochemical, genetic and proteomic approaches in association with Electron Spin Resonance (ESR) spectroscopy methodology will be used to unravel the essential role ROS play in CTL-mediated killing.
Summary
Cytotoxic T lymphocytes (CTL) and natural killer (NK) cells release granzyme and perforin from cytotoxic granules into the immune synapse to induce apoptosis of target cells that are either virus-infected or cancerous. Granzyme A activates a caspase-independent apoptotic pathway and induces mitochondrial damage characterized by superoxide anion production and loss of the mitochondrial transmembrane potential, without disrupting the integrity of the mitochondrial outer membrane; while causing single-stranded DNA damage. GzmB induces both caspase-dependent and caspase-independent cell death. In the caspase-dependent pathway, mitochondrial functions are altered as evidenced by the loss of mitochondrial transmembrane potential and the generation of reactive oxygen species (ROS). The mitochondrial outer membrane (MOM) is disrupted, resulting in the release of apoptogenic factors. To date, research on mitochondrial-dependent apoptosis has focused on mitochondrial outer membrane permeabilization (MOMP) however whether the generation of ROS is incidental or essential to the execution of apoptosis remains unclear. Like human GzmA, human GzmB promotes cell death in a ROS-dependent manner. Preliminary data suggest that human GzmB can induce ROS in a MOMP-independent manner as Bax and Bak double knockout MEF cells treated with human GzmB and perforin still display a robust ROS production and dye in an ROS-dependent manner. Since GzmA and GzmB induce cell death in a ROS-dependent manner, we hypothesize that oxygen free radicals are central to the execution of programmed cell death induced by the cytotoxic granules. Therefore, the goal of this proposal is to dissect the key molecular events triggered by ROS that lead to Citotoxic Tcell-induced target cell death. A combination of biochemical, genetic and proteomic approaches in association with Electron Spin Resonance (ESR) spectroscopy methodology will be used to unravel the essential role ROS play in CTL-mediated killing.
Max ERC Funding
1 500 000 €
Duration
Start date: 2011-05-01, End date: 2016-04-30
Project acronym DiRECT
Project Directly reprogrammed renal cells for targeted medicine
Researcher (PI) Soeren LIENKAMP
Host Institution (HI) UNIVERSITAT ZURICH
Call Details Starting Grant (StG), LS3, ERC-2018-STG
Summary The global incidence of kidney disease is on the rise, but little progress has been made to develop novel therapies or preventative measures.
New methods to generated renal tissue in vitro hold great promise for regenerative medicine and the prospect of organ replacement. Most of the strategies employed differentiate induced pluripotent stem cells (iPSCs) into kidney organoids, which can be derived from patient tissue.
Direct reprogramming is an alternative approach to convert one cell type into another using cell fate specifying transcription factors. We were the first to develop a method to directly reprogram mouse and human fibroblasts to kidney cells (induced renal tubular epithelial cells - iRECs) without the need for pluripotent cells. Morphological, transcriptomic and functional analyses found that directly reprogrammed iRECs are remarkably similar to native renal tubular cells. Direct reprogramming is fast, technically simple and scalable.
This proposal aims to establish direct reprogramming in nephrology and develop novel in vitro models for kidney diseases that primarily affect the renal tubules. We will unravel the mechanics of how only four transcription factors can change the morphology and function of fibroblasts towards a renal tubule cell identity. These insights will be used to identify alternative routes to directly reprogram tubule cells with increased efficiency and accuracy. We will identify cell type specifying factors for reprogramming of tubular segment specific cell types. Finally, we will use of reprogrammed kidney cells to establish new in vitro models for autosomal dominant polycystic kidney disease and nephronophthisis.
Direct reprogramming holds enormous potential to deliver patient specific disease models for diagnostic and therapeutic applications in the age of personalized and targeted medicine.
Summary
The global incidence of kidney disease is on the rise, but little progress has been made to develop novel therapies or preventative measures.
New methods to generated renal tissue in vitro hold great promise for regenerative medicine and the prospect of organ replacement. Most of the strategies employed differentiate induced pluripotent stem cells (iPSCs) into kidney organoids, which can be derived from patient tissue.
Direct reprogramming is an alternative approach to convert one cell type into another using cell fate specifying transcription factors. We were the first to develop a method to directly reprogram mouse and human fibroblasts to kidney cells (induced renal tubular epithelial cells - iRECs) without the need for pluripotent cells. Morphological, transcriptomic and functional analyses found that directly reprogrammed iRECs are remarkably similar to native renal tubular cells. Direct reprogramming is fast, technically simple and scalable.
This proposal aims to establish direct reprogramming in nephrology and develop novel in vitro models for kidney diseases that primarily affect the renal tubules. We will unravel the mechanics of how only four transcription factors can change the morphology and function of fibroblasts towards a renal tubule cell identity. These insights will be used to identify alternative routes to directly reprogram tubule cells with increased efficiency and accuracy. We will identify cell type specifying factors for reprogramming of tubular segment specific cell types. Finally, we will use of reprogrammed kidney cells to establish new in vitro models for autosomal dominant polycystic kidney disease and nephronophthisis.
Direct reprogramming holds enormous potential to deliver patient specific disease models for diagnostic and therapeutic applications in the age of personalized and targeted medicine.
Max ERC Funding
1 499 917 €
Duration
Start date: 2019-03-01, End date: 2024-02-29
Project acronym DNA-AMP
Project DNA Adduct Molecular Probes: Elucidating the Diet-Cancer Connection at Chemical Resolution
Researcher (PI) Shana Jocette Sturla
Host Institution (HI) EIDGENOESSISCHE TECHNISCHE HOCHSCHULE ZUERICH
Call Details Starting Grant (StG), LS7, ERC-2010-StG_20091118
Summary Bulky DNA adducts formed from chemical carcinogens dictate structure, reactivity, and mechanism of chemical-biological reactions; therefore, their identification is central to evaluating and mitigating cancer risk. Natural food components, or others associated with certain food preparations or metabolic conversions, initiate potentially damaging genetic mutations after forming DNA adducts, which contribute critically to carcinogenesis, despite the fact that they are typically repaired biochemically and they are formed at extremely low levels. This situation places significant limitations on our ability to understand the role of formation, repair, and mutagenesis on the basis of the complex DNA reactivity profiles of food components. The long-term goals of this research are to contribute basic knowledge and advanced experimental tools required to understand, on the basis of chemical structure, the contributions of chronic, potentially adverse, dietary chemical carcinogen exposure to cancer development. It is proposed that a new class of synthetic nucleosides, devised on the basis of preliminary discoveries made in the independent laboratory of the applicant, will serve as molecular probes for bulky DNA adducts and can be effectively used to study and AMPlify, i.e. as a sensitive diagnostic tool, low levels of chemically-specific modes of DNA damage. The proposed research is a chemical biology-based approach to the study of carcinogenesis. Experiments involve chemical synthesis, thermodynamic and kinetic characterization DNA-DNA and enzyme-DNA interactions, and nanoparticle-based molecular probes. The proposal describes a potentially ground-breaking approach for profiling the biological reactivities of chemical carcinogens, and we expect to gain fundamental knowledge and chemical tools that can contribute to the prevention of diseases influenced by gene-environment interactions.
Summary
Bulky DNA adducts formed from chemical carcinogens dictate structure, reactivity, and mechanism of chemical-biological reactions; therefore, their identification is central to evaluating and mitigating cancer risk. Natural food components, or others associated with certain food preparations or metabolic conversions, initiate potentially damaging genetic mutations after forming DNA adducts, which contribute critically to carcinogenesis, despite the fact that they are typically repaired biochemically and they are formed at extremely low levels. This situation places significant limitations on our ability to understand the role of formation, repair, and mutagenesis on the basis of the complex DNA reactivity profiles of food components. The long-term goals of this research are to contribute basic knowledge and advanced experimental tools required to understand, on the basis of chemical structure, the contributions of chronic, potentially adverse, dietary chemical carcinogen exposure to cancer development. It is proposed that a new class of synthetic nucleosides, devised on the basis of preliminary discoveries made in the independent laboratory of the applicant, will serve as molecular probes for bulky DNA adducts and can be effectively used to study and AMPlify, i.e. as a sensitive diagnostic tool, low levels of chemically-specific modes of DNA damage. The proposed research is a chemical biology-based approach to the study of carcinogenesis. Experiments involve chemical synthesis, thermodynamic and kinetic characterization DNA-DNA and enzyme-DNA interactions, and nanoparticle-based molecular probes. The proposal describes a potentially ground-breaking approach for profiling the biological reactivities of chemical carcinogens, and we expect to gain fundamental knowledge and chemical tools that can contribute to the prevention of diseases influenced by gene-environment interactions.
Max ERC Funding
1 500 000 €
Duration
Start date: 2010-09-01, End date: 2015-08-31
Project acronym DYNACLOCK
Project Dynamic protein-DNA interactomes and circadian transcription regulatory networks in mammals
Researcher (PI) Felix Naef
Host Institution (HI) ECOLE POLYTECHNIQUE FEDERALE DE LAUSANNE
Call Details Starting Grant (StG), LS2, ERC-2010-StG_20091118
Summary The aim of this project is to understand the dynamics of protein-DNA interactomes underlying circadian oscillators in mammals, and how these shape circadian transcriptional output programs. Specifically our goal is to solve a fundamental issue in circadian biology: the phase specificity problem underlying circadian gene expression. We have taken a challenging and original multi-disciplinary approach in which molecular biology experiments will be tightly interlinked with computational analyses and biophysical modeling. The approach will generate time resolved protein-DNA interactomes in mouse liver for several key circadian repressors at unprecedented resolution. These experiments will be complemented with chromosome conformation capture (3C) experiments to monitor how looping interactions and 3D genome structure rearrange during the circadian cycle, which will inform on how circadian transcription networks use long-range gene regulatory mechanisms. Novel computational algorithms based on biophysical principles will be developed and implemented to optimally analyze interactome and 3C datasets. For the latter, statistical models from polymer physics will be used to reconstruct the chromatin networks and interaction maps from the 3C data. At the detailed level of individual cells, we will investigate transcription bursts, and how those are involved in the control of circadian gene expression. In particular we will exploit high temporal resolution bioluminescence reporters using a biophysical model of transcription coupled with a Hidden Markov Model (HMM). Through our innovative approach, we expect that the data generated and state-of-the-art analyses performed will lead novel insight into the role and mechanics of circadian transcription in controlling circadian outputs in mammals.
Summary
The aim of this project is to understand the dynamics of protein-DNA interactomes underlying circadian oscillators in mammals, and how these shape circadian transcriptional output programs. Specifically our goal is to solve a fundamental issue in circadian biology: the phase specificity problem underlying circadian gene expression. We have taken a challenging and original multi-disciplinary approach in which molecular biology experiments will be tightly interlinked with computational analyses and biophysical modeling. The approach will generate time resolved protein-DNA interactomes in mouse liver for several key circadian repressors at unprecedented resolution. These experiments will be complemented with chromosome conformation capture (3C) experiments to monitor how looping interactions and 3D genome structure rearrange during the circadian cycle, which will inform on how circadian transcription networks use long-range gene regulatory mechanisms. Novel computational algorithms based on biophysical principles will be developed and implemented to optimally analyze interactome and 3C datasets. For the latter, statistical models from polymer physics will be used to reconstruct the chromatin networks and interaction maps from the 3C data. At the detailed level of individual cells, we will investigate transcription bursts, and how those are involved in the control of circadian gene expression. In particular we will exploit high temporal resolution bioluminescence reporters using a biophysical model of transcription coupled with a Hidden Markov Model (HMM). Through our innovative approach, we expect that the data generated and state-of-the-art analyses performed will lead novel insight into the role and mechanics of circadian transcription in controlling circadian outputs in mammals.
Max ERC Funding
1 500 000 €
Duration
Start date: 2011-03-01, End date: 2016-02-29
Project acronym EngineeringBAP
Project Engineering brain activity patterns for therapeutics of neuropsychiatric and neurological disorders
Researcher (PI) Mehmet Fatih YANIK
Host Institution (HI) EIDGENOESSISCHE TECHNISCHE HOCHSCHULE ZUERICH
Call Details Consolidator Grant (CoG), LS5, ERC-2018-COG
Summary Neuropsychiatric and neurological disorders are complex dysfunctions of neuronal circuits. Their treatment
has been limited by the lack of non-invasive methods for measuring the underlying circuit dysfunctions, and
for direct and localized modifications of these circuits. We propose minimally invasive technologies for
measuring brain activity and functional connectivity patterns, and for manipulating them directly in vivo to
correct the abnormal behavioural phenotypes (in rodents with potential scalability to non-human primates and
humans). First, we present a proof-of-principle study on mutant zebrafish, in which we correct whole-brain
level abnormal activity patterns and behaviours by using large-scale single-neuron resolution measurements,
and by simultaneously modulating multiple sub-networks via neuromodulator cocktails. Next, we present
strong preliminary data in rodents and our plan: (1) For manipulating brain circuits in rodents/primates noninvasively,
we will develop technologies that can deliver receptive-specific neuromodulators to spatially
precise brain targets without opening/damaging the blood brain barrier. These methods will employ engineered
ultrasound pulses and drug carrying microparticles we designed. (2) For reading out the brain circuits in
rodents/primates, we will develop flexible low-power neuromorphic μECoG circuits that can detect single
neuron signals from superficial cortical layers of many cortical areas simultaneously. (3) Finally, these novel
technologies will be comprehensively evaluated on a mouse model of obsessive compulsivity and anxiety
using a battery of behavioural tasks to reverse the pathological symptoms (beyond what is achievable by
existing approaches). This project constitutes a major step towards the development and testing of minimallyinvasive
and high-precision technologies for manipulating brain activity patterns, which can impact both our
understanding of the brain and treatment of intractable brain disorders.
Summary
Neuropsychiatric and neurological disorders are complex dysfunctions of neuronal circuits. Their treatment
has been limited by the lack of non-invasive methods for measuring the underlying circuit dysfunctions, and
for direct and localized modifications of these circuits. We propose minimally invasive technologies for
measuring brain activity and functional connectivity patterns, and for manipulating them directly in vivo to
correct the abnormal behavioural phenotypes (in rodents with potential scalability to non-human primates and
humans). First, we present a proof-of-principle study on mutant zebrafish, in which we correct whole-brain
level abnormal activity patterns and behaviours by using large-scale single-neuron resolution measurements,
and by simultaneously modulating multiple sub-networks via neuromodulator cocktails. Next, we present
strong preliminary data in rodents and our plan: (1) For manipulating brain circuits in rodents/primates noninvasively,
we will develop technologies that can deliver receptive-specific neuromodulators to spatially
precise brain targets without opening/damaging the blood brain barrier. These methods will employ engineered
ultrasound pulses and drug carrying microparticles we designed. (2) For reading out the brain circuits in
rodents/primates, we will develop flexible low-power neuromorphic μECoG circuits that can detect single
neuron signals from superficial cortical layers of many cortical areas simultaneously. (3) Finally, these novel
technologies will be comprehensively evaluated on a mouse model of obsessive compulsivity and anxiety
using a battery of behavioural tasks to reverse the pathological symptoms (beyond what is achievable by
existing approaches). This project constitutes a major step towards the development and testing of minimallyinvasive
and high-precision technologies for manipulating brain activity patterns, which can impact both our
understanding of the brain and treatment of intractable brain disorders.
Max ERC Funding
1 998 984 €
Duration
Start date: 2019-10-01, End date: 2024-09-30
Project acronym EPICROP
Project Dissecting epistasis for enhanced crop productivity
Researcher (PI) Sebastian Soyk
Host Institution (HI) UNIVERSITE DE LAUSANNE
Call Details Starting Grant (StG), LS2, ERC-2018-STG
Summary A major goal in plant biology is to understand how naturally occurring genetic variation leads to quantitative differences in economically important traits. Efforts to navigate the genotype-to-phenotype map are often focused on linear genetic interactions. As a result, crop breeding is mainly driven by loci with predictable additive effects. However, it has become clear that quantitative trait variation often results from perturbations of complex genetic networks. Thus, understanding epistasis, or interactions between genes, is key for our ability to predictably improve crops. To meet this challenge, this project will reveal and dissect epistatic interactions in gene regulatory networks that guide stem cell differentiation in the model crop tomato. In the first aim, I will utilize exhaustive allelic series for epistatic MADS-box genes that quantitatively regulate flower and fruit production as an experimental model system to study fundamental principles of epistasis that can be applied to other genetic networks. Genome-wide transcript profiling will be used to reveal molecular signatures of epistasis and potential targets for predictable crop improvement by advanced CRISPR/Cas9 gene editing technology. Further, my preliminary data suggests that epistasis is widespread and important across major productivity traits in tomato. Thus, in a second aim, I will access this untapped resource of cryptic genetic variation by sensitizing a tomato diversity panel for weak epistatic effects from unknown natural modifier loci of stem cell differentiation using trans-acting CRISPR/Cas9 editing cassettes. This screen represents a new approach to mutagenesis in plants with potential to reveal cryptic variation in other system. The outcomes of this project will advance our knowledge in a fundamental area of plant genome biology, help uncover and understand the functional architecture of epistasis, and have potential to bring significant improvements to agriculture.
Summary
A major goal in plant biology is to understand how naturally occurring genetic variation leads to quantitative differences in economically important traits. Efforts to navigate the genotype-to-phenotype map are often focused on linear genetic interactions. As a result, crop breeding is mainly driven by loci with predictable additive effects. However, it has become clear that quantitative trait variation often results from perturbations of complex genetic networks. Thus, understanding epistasis, or interactions between genes, is key for our ability to predictably improve crops. To meet this challenge, this project will reveal and dissect epistatic interactions in gene regulatory networks that guide stem cell differentiation in the model crop tomato. In the first aim, I will utilize exhaustive allelic series for epistatic MADS-box genes that quantitatively regulate flower and fruit production as an experimental model system to study fundamental principles of epistasis that can be applied to other genetic networks. Genome-wide transcript profiling will be used to reveal molecular signatures of epistasis and potential targets for predictable crop improvement by advanced CRISPR/Cas9 gene editing technology. Further, my preliminary data suggests that epistasis is widespread and important across major productivity traits in tomato. Thus, in a second aim, I will access this untapped resource of cryptic genetic variation by sensitizing a tomato diversity panel for weak epistatic effects from unknown natural modifier loci of stem cell differentiation using trans-acting CRISPR/Cas9 editing cassettes. This screen represents a new approach to mutagenesis in plants with potential to reveal cryptic variation in other system. The outcomes of this project will advance our knowledge in a fundamental area of plant genome biology, help uncover and understand the functional architecture of epistasis, and have potential to bring significant improvements to agriculture.
Max ERC Funding
1 499 903 €
Duration
Start date: 2019-08-01, End date: 2024-07-31
Project acronym EPIGENOME
Project Understanding epigenetic mechanisms of complex genome editing in eukaryotes
Researcher (PI) Mariusz Nowacki
Host Institution (HI) UNIVERSITAET BERN
Call Details Starting Grant (StG), LS1, ERC-2010-StG_20091118
Summary The scientific goal of this proposal is to contribute to our understanding of RNA-mediated epigenetic mechanisms of genome regulation in eukaryotes. Choosing ciliated protozoa as model organisms gives a wonderful opportunity to study the incredibly complex epigenetic mechanism of programming large-scale developmental rearrangements of the genome. This involves extensive rearrangements of the germline DNA, including elimination of up to 95% of the genome. The massive DNA rearrangement makes ciliates the perfect model organism to study this aspect of germline-soma differentiation. This process is proposed to be regulated by an RNA-mediated homology-dependent comparison of the germline and somatic genomes. Ciliate’s genomic subtraction is one of the most fascinating examples of the use of RNA-mediated epigenetic regulation, and of a specialized RNA interference pathway, to convey non-Mendelian inheritance in eukaryotes. The ‘genome scanning’ model raises many interesting questions, which are also relevant to other RNA-mediated regulation systems. One of the most intriguing is a ‘thermodynamic’ problem: the model assumes that a very complex population of small RNAs representing the entire germline genome can be compared to longer transcripts representing the entire rearranged maternal genome, resulting in the efficient selection of germline-specific scnRNAs, which are able to target DNA deletions in the developing nucleus. How is it possible that the truly enormous number of pairing interactions implied can occur in such a short time, just a few hours? RNA-RNA pairing interactions would probably have to be assisted by a dedicated molecular machinery. This proposal focuses on characterizing proteins and RNAs that can orchestrate the massive genome rearrangements in ciliates.
Summary
The scientific goal of this proposal is to contribute to our understanding of RNA-mediated epigenetic mechanisms of genome regulation in eukaryotes. Choosing ciliated protozoa as model organisms gives a wonderful opportunity to study the incredibly complex epigenetic mechanism of programming large-scale developmental rearrangements of the genome. This involves extensive rearrangements of the germline DNA, including elimination of up to 95% of the genome. The massive DNA rearrangement makes ciliates the perfect model organism to study this aspect of germline-soma differentiation. This process is proposed to be regulated by an RNA-mediated homology-dependent comparison of the germline and somatic genomes. Ciliate’s genomic subtraction is one of the most fascinating examples of the use of RNA-mediated epigenetic regulation, and of a specialized RNA interference pathway, to convey non-Mendelian inheritance in eukaryotes. The ‘genome scanning’ model raises many interesting questions, which are also relevant to other RNA-mediated regulation systems. One of the most intriguing is a ‘thermodynamic’ problem: the model assumes that a very complex population of small RNAs representing the entire germline genome can be compared to longer transcripts representing the entire rearranged maternal genome, resulting in the efficient selection of germline-specific scnRNAs, which are able to target DNA deletions in the developing nucleus. How is it possible that the truly enormous number of pairing interactions implied can occur in such a short time, just a few hours? RNA-RNA pairing interactions would probably have to be assisted by a dedicated molecular machinery. This proposal focuses on characterizing proteins and RNAs that can orchestrate the massive genome rearrangements in ciliates.
Max ERC Funding
1 500 000 €
Duration
Start date: 2010-11-01, End date: 2015-10-31
Project acronym EURIBIO
Project Dissecting the biogenesis of eukaryotic ribosomal subunits
Researcher (PI) Vikram Govind Panse
Host Institution (HI) EIDGENOESSISCHE TECHNISCHE HOCHSCHULE ZUERICH
Call Details Starting Grant (StG), LS1, ERC-2010-StG_20091118
Summary In all living cells, the important task of protein synthesis is carried out by the ribosome. A substantial amount of cellular energy and resources is utilized to manufacture ribosomal subunits. In contrast to prokaryotes, eukaryotic ribosome assembly requires a multitude of conserved non-ribosomal trans-acting factors, which transiently associate with pre-ribosomal particles at distinct assembly stages and perform specific maturation steps.
Large-scale proteomic approaches in budding yeast, have rapidly expanded the inventory of trans-acting factors (~200). However, little is known regarding their precise site(s) of action and the role(s) of these factors during pre-ribosome assembly. Upon accomplishing their task, majority of the trans-acting factors, are typically released from maturing pre-ribosomes already in the nucleolus/nucleus. Strikingly, a handful of factors remain associated with pre-ribosomes and facilitate their export into the cytoplasm. Release of these factors constitutes “late cytoplasmic maturation events” which render exported pre-ribosomes translation competent. In this proposal we will exploit the powerful model organism budding yeast to:
(1) Develop novel biochemical tools to elucidate the molecular environment of trans-acting factors on the surface of pre-ribosomal particles. These analyses will provide us a low-resolution biochemical map of a maturing pre-ribosome.
(2) Exploit the powerful combination of genetic and high-throughput visual screening approaches in budding yeast to unravel novel “late cytoplasmic maturation steps” in the 60S biogenesis pathway.
Together, my research proposal aims to contribute significantly to our current knowledge regarding the construction and nuclear export of eukaryotic pre-ribosomes. Our analysis will lead us to general principles that underlie the dynamic assembly/dissassembly of large macromolecular ribonucleo-protein complexes.
Summary
In all living cells, the important task of protein synthesis is carried out by the ribosome. A substantial amount of cellular energy and resources is utilized to manufacture ribosomal subunits. In contrast to prokaryotes, eukaryotic ribosome assembly requires a multitude of conserved non-ribosomal trans-acting factors, which transiently associate with pre-ribosomal particles at distinct assembly stages and perform specific maturation steps.
Large-scale proteomic approaches in budding yeast, have rapidly expanded the inventory of trans-acting factors (~200). However, little is known regarding their precise site(s) of action and the role(s) of these factors during pre-ribosome assembly. Upon accomplishing their task, majority of the trans-acting factors, are typically released from maturing pre-ribosomes already in the nucleolus/nucleus. Strikingly, a handful of factors remain associated with pre-ribosomes and facilitate their export into the cytoplasm. Release of these factors constitutes “late cytoplasmic maturation events” which render exported pre-ribosomes translation competent. In this proposal we will exploit the powerful model organism budding yeast to:
(1) Develop novel biochemical tools to elucidate the molecular environment of trans-acting factors on the surface of pre-ribosomal particles. These analyses will provide us a low-resolution biochemical map of a maturing pre-ribosome.
(2) Exploit the powerful combination of genetic and high-throughput visual screening approaches in budding yeast to unravel novel “late cytoplasmic maturation steps” in the 60S biogenesis pathway.
Together, my research proposal aims to contribute significantly to our current knowledge regarding the construction and nuclear export of eukaryotic pre-ribosomes. Our analysis will lead us to general principles that underlie the dynamic assembly/dissassembly of large macromolecular ribonucleo-protein complexes.
Max ERC Funding
1 500 000 €
Duration
Start date: 2010-09-01, End date: 2016-07-31
Project acronym EVOMORPHYS
Project Identifying how Evolution exploits physical properties of tissues to generate the complexity and diversity of Life
Researcher (PI) Michel Charles MILINKOVITCH
Host Institution (HI) UNIVERSITE DE GENEVE
Call Details Advanced Grant (AdG), LS8, ERC-2018-ADG
Summary My project focuses on answering one fundamental question: what are the drivers of Life’s morphological complexity and diversity? I claim that this question can only be addressed by a Newtonian-Darwinian synthesis that considers how Evolution exploits the physical properties of living matter. I will investigate how the evolutionary process explores the phase space of possible interactions between physical (mechanics, reaction-diffusion) and biological (cell signalling, proliferation, migration) processes and generates configurations that compute functional phenotypes. In particular, I will combine experiments in biology and physics, as well as mathematical models and Artificial-Life (ALife) numerical simulations. The latter will be based on physics’ first principles, symmetry-breaking processes and a genetic algorithm. First, I will investigate how geometry affects signalling by (i) imaging the embryonic development of colour patterns and skin geometries of multiple squamate species with various scale-to-colour pattern correspondences, (ii) generating CRISPR/Cas9 scaleless mutants in two lizard species to study the effect of skin 3D geometry on colour patterning, and (iii) performing ALife experiments to explore how the evolutionary process can modify signalling events and exploit geometry to generate new patterns. Second, I will analyse how growth can affect geometry by (i) performing in-silico experiments where coupling between growth and morphogenesis is systematically explored and (ii) evaluating how much the in-silico model captures morphologies generated with physics laboratory experiments using 3D layered polymeric gels. Third, I will build a Newtonian-Darwinian framework by coupling geometry, signalling, growth and mechanics in extensive open-ended ALife experiments. The results of the EVOMORPHYS project will constitute a novel framework for understanding how Evolution exploits physics to generate the morphological diversity and complexity of Life forms.
Summary
My project focuses on answering one fundamental question: what are the drivers of Life’s morphological complexity and diversity? I claim that this question can only be addressed by a Newtonian-Darwinian synthesis that considers how Evolution exploits the physical properties of living matter. I will investigate how the evolutionary process explores the phase space of possible interactions between physical (mechanics, reaction-diffusion) and biological (cell signalling, proliferation, migration) processes and generates configurations that compute functional phenotypes. In particular, I will combine experiments in biology and physics, as well as mathematical models and Artificial-Life (ALife) numerical simulations. The latter will be based on physics’ first principles, symmetry-breaking processes and a genetic algorithm. First, I will investigate how geometry affects signalling by (i) imaging the embryonic development of colour patterns and skin geometries of multiple squamate species with various scale-to-colour pattern correspondences, (ii) generating CRISPR/Cas9 scaleless mutants in two lizard species to study the effect of skin 3D geometry on colour patterning, and (iii) performing ALife experiments to explore how the evolutionary process can modify signalling events and exploit geometry to generate new patterns. Second, I will analyse how growth can affect geometry by (i) performing in-silico experiments where coupling between growth and morphogenesis is systematically explored and (ii) evaluating how much the in-silico model captures morphologies generated with physics laboratory experiments using 3D layered polymeric gels. Third, I will build a Newtonian-Darwinian framework by coupling geometry, signalling, growth and mechanics in extensive open-ended ALife experiments. The results of the EVOMORPHYS project will constitute a novel framework for understanding how Evolution exploits physics to generate the morphological diversity and complexity of Life forms.
Max ERC Funding
2 499 070 €
Duration
Start date: 2019-08-01, End date: 2024-07-31
Project acronym FuncMAB
Project High-throughput single-cell phenotypic analysis of functional antibody repertoires
Researcher (PI) Klaus EYER
Host Institution (HI) EIDGENOESSISCHE TECHNISCHE HOCHSCHULE ZUERICH
Call Details Starting Grant (StG), LS9, ERC-2018-STG
Summary Antibodies play an important role ensuring successful protection after vaccination. Upon injection, antigen-binding antibodies are generated to prime the host’s immune system for future encounters with the threat. These responses are highly heterogeneous, with each cell contributing with a single antibody variant to the complexity. Each antibody variant furthermore can recognize a different antigen/epitope with varying specificity and affinity. The immunological function induced is related to those parameters.
Depending on the nature of the threat, required protective functional antibodies vary. Therefore, also each vaccination against those threads needs to trigger a specific functional antibody repertoire. Presently, induced functional antibody repertoires have not yet been studied sufficiently, mostly due to the lack of technologies that enable analysing these repertoires with high enough throughput and resolution. Consequently, the mechanisms behind the evolution of these functional repertoires, and the influence of vaccination on these repertoires remain poorly understood.
An innovative technology combined with a methodical approach to vaccinations will enable the FuncMab research team to generate data sets needed for the understanding of immunological processes that result in different functional antibody repertoires. Herein, antibodies are analysed on the individual cell level in high-throughput using specific bioassays that target various antibody functions and their biophysical parameters, generating high-resolution data. These functional repertoires are followed over time and evolutionary changes can be linked to introduced vaccine variations, allowing a quantitative approach to study the changes within the repertoires. These in-depth data sets will not only allow understanding interactions between vaccine components and their generated immune responses, but also propels this project to the forefront of creating a new generation of successful vaccines
Summary
Antibodies play an important role ensuring successful protection after vaccination. Upon injection, antigen-binding antibodies are generated to prime the host’s immune system for future encounters with the threat. These responses are highly heterogeneous, with each cell contributing with a single antibody variant to the complexity. Each antibody variant furthermore can recognize a different antigen/epitope with varying specificity and affinity. The immunological function induced is related to those parameters.
Depending on the nature of the threat, required protective functional antibodies vary. Therefore, also each vaccination against those threads needs to trigger a specific functional antibody repertoire. Presently, induced functional antibody repertoires have not yet been studied sufficiently, mostly due to the lack of technologies that enable analysing these repertoires with high enough throughput and resolution. Consequently, the mechanisms behind the evolution of these functional repertoires, and the influence of vaccination on these repertoires remain poorly understood.
An innovative technology combined with a methodical approach to vaccinations will enable the FuncMab research team to generate data sets needed for the understanding of immunological processes that result in different functional antibody repertoires. Herein, antibodies are analysed on the individual cell level in high-throughput using specific bioassays that target various antibody functions and their biophysical parameters, generating high-resolution data. These functional repertoires are followed over time and evolutionary changes can be linked to introduced vaccine variations, allowing a quantitative approach to study the changes within the repertoires. These in-depth data sets will not only allow understanding interactions between vaccine components and their generated immune responses, but also propels this project to the forefront of creating a new generation of successful vaccines
Max ERC Funding
1 500 000 €
Duration
Start date: 2019-02-01, End date: 2024-01-31
Project acronym GEOMETRYCELLCYCLE
Project Geometric control of the cell cycle in the fission yeast
Researcher (PI) Sophie Genevieve Elisabeth Martin Benton
Host Institution (HI) UNIVERSITE DE LAUSANNE
Call Details Starting Grant (StG), LS3, ERC-2010-StG_20091118
Summary Cell cycle progression is monitored by checkpoints that ensure the fidelity of cell division and prevent unrestricted cell proliferation. Checkpoints also serve to couple cell size with division – a mechanism important to adapt to changing environmental conditions.
While most studies on cell size homeostasis have focused on the links between size and biosynthetic activity, we have recently discovered a novel geometry-sensing mechanism by which fission yeast cells couple cell length with entry into mitosis. Conceptually, the system is remarkably simple: it is composed of a signal – the protein kinase Pom1 – forming concentration gradients from the ends of the cells, which inhibits a sensor – the protein kinase Cdr2, itself an activator of mitotic entry – placed at the cell equator. Since Pom1 concentration at the cell middle is higher in short cells than in long cells, this suggests a model where Pom1 inhibits Cdr2 until the cell has reached a sufficient length.
These findings open a conceptually new way of thinking about cell size homeostasis and suggest that cell polarity and cell shape have important effect on cell cycle progression. The proposed project investigates the mechanisms and functional importance of this geometry-sensing system through four specific aims:
Aim 1. Defining and modeling the molecular mechanisms of Pom1 gradient formation
Aim 2. Dissecting the mechanisms of Pom1 action
Aim 3. Investigating the influence of altered cell shape on cell proliferation
Aim 4. Exploring the effect of environmental stresses to the Pom1-Cdr2 system
By combining genetic, biochemical, physical, live-imaging and modeling approaches, this project will provide an integrated understanding of how cell geometry can be perceived at the molecular level and how this information is transduced to control cell proliferation. This work will have wide-ranging implication for our understanding of gradient formation, cell size homeostasis, and the role of cell polarity in proliferation. It will thus be of interest to cell, developmental and cancer biologists alike.
Summary
Cell cycle progression is monitored by checkpoints that ensure the fidelity of cell division and prevent unrestricted cell proliferation. Checkpoints also serve to couple cell size with division – a mechanism important to adapt to changing environmental conditions.
While most studies on cell size homeostasis have focused on the links between size and biosynthetic activity, we have recently discovered a novel geometry-sensing mechanism by which fission yeast cells couple cell length with entry into mitosis. Conceptually, the system is remarkably simple: it is composed of a signal – the protein kinase Pom1 – forming concentration gradients from the ends of the cells, which inhibits a sensor – the protein kinase Cdr2, itself an activator of mitotic entry – placed at the cell equator. Since Pom1 concentration at the cell middle is higher in short cells than in long cells, this suggests a model where Pom1 inhibits Cdr2 until the cell has reached a sufficient length.
These findings open a conceptually new way of thinking about cell size homeostasis and suggest that cell polarity and cell shape have important effect on cell cycle progression. The proposed project investigates the mechanisms and functional importance of this geometry-sensing system through four specific aims:
Aim 1. Defining and modeling the molecular mechanisms of Pom1 gradient formation
Aim 2. Dissecting the mechanisms of Pom1 action
Aim 3. Investigating the influence of altered cell shape on cell proliferation
Aim 4. Exploring the effect of environmental stresses to the Pom1-Cdr2 system
By combining genetic, biochemical, physical, live-imaging and modeling approaches, this project will provide an integrated understanding of how cell geometry can be perceived at the molecular level and how this information is transduced to control cell proliferation. This work will have wide-ranging implication for our understanding of gradient formation, cell size homeostasis, and the role of cell polarity in proliferation. It will thus be of interest to cell, developmental and cancer biologists alike.
Max ERC Funding
1 500 000 €
Duration
Start date: 2010-09-01, End date: 2016-08-31
