Project acronym DHISP
Project Dorsal Horn Interneurons in Sensory Processing
Researcher (PI) Hanns Ulrich Zeilhofer
Host Institution (HI) UNIVERSITAT ZURICH
Call Details Advanced Grant (AdG), LS5, ERC-2009-AdG
Summary Chronic pain syndromes are to a large extent due to maladaptive plastic changes in the CNS. A CNS area particularly relevant for such changes is the spinal dorsal horn, where inputs from nociceptive and non-nociceptive fibers undergo their first synaptic integration. This area harbors a sophisticated network of interneurons, which function as a gate-control unit for incoming sensory signals. Several different types of interneurons can be distinguished based e.g. on their neurotransmitter and neuropeptide content. Despite more than 40 years of research, our knowledge about the integration of these neurons in dorsal horn circuits and their contribution to sensory processing is still very limited. This proposal aims at a comprehensive characterization of the dorsal horn neuronal network under normal conditions and in chronic pain states with a focus on inhibitory interneurons. A genome-wide analysis of the gene expression profile shall be made from defined dorsal horn interneurons genetically tagged with fluorescent markers and isolated by fluorescence activated cell sorting. A functional characterization of the connectivity of these neurons in spinal cord slices and of their role in in vivo sensory processing shall be achieved with optogenetic tools (channelrhodopsin-2), which permit activation of these neurons with light. Finally, behavioral analyses shall be made in mice after diphteria toxin-mediated ablation of defined interneuron types. All three approaches shall be applied to naïve mice and to mice with inflammatory or neuropathic pain. The results from these studies will improve our understanding of the malfunctioning of sensory processing in chronic pain states and will provide the basis for novel approaches to the prevention or reversal of chronic pain states.
Summary
Chronic pain syndromes are to a large extent due to maladaptive plastic changes in the CNS. A CNS area particularly relevant for such changes is the spinal dorsal horn, where inputs from nociceptive and non-nociceptive fibers undergo their first synaptic integration. This area harbors a sophisticated network of interneurons, which function as a gate-control unit for incoming sensory signals. Several different types of interneurons can be distinguished based e.g. on their neurotransmitter and neuropeptide content. Despite more than 40 years of research, our knowledge about the integration of these neurons in dorsal horn circuits and their contribution to sensory processing is still very limited. This proposal aims at a comprehensive characterization of the dorsal horn neuronal network under normal conditions and in chronic pain states with a focus on inhibitory interneurons. A genome-wide analysis of the gene expression profile shall be made from defined dorsal horn interneurons genetically tagged with fluorescent markers and isolated by fluorescence activated cell sorting. A functional characterization of the connectivity of these neurons in spinal cord slices and of their role in in vivo sensory processing shall be achieved with optogenetic tools (channelrhodopsin-2), which permit activation of these neurons with light. Finally, behavioral analyses shall be made in mice after diphteria toxin-mediated ablation of defined interneuron types. All three approaches shall be applied to naïve mice and to mice with inflammatory or neuropathic pain. The results from these studies will improve our understanding of the malfunctioning of sensory processing in chronic pain states and will provide the basis for novel approaches to the prevention or reversal of chronic pain states.
Max ERC Funding
2 467 000 €
Duration
Start date: 2010-05-01, 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 DiSCo MRI SFN
Project Developing Integrated Susceptibility and Conductivity MRI for Next Generation Structural and Functional Neuroimaging
Researcher (PI) Karin SHMUELI
Host Institution (HI) UNIVERSITY COLLEGE LONDON
Call Details Consolidator Grant (CoG), LS5, ERC-2017-COG
Summary MRI is indispensable in the diagnosis of neurodegenerative diseases. These are poorly understood while their prevalence and socio-economic burden continue to rise. Structural and functional MRI can provide biomarkers for early diagnosis and potential therapeutic intervention. My research vision is to develop novel MRI methods for structural and functional mapping of tissue magnetic susceptibility and electrical conductivity as these show great promise for neuroimaging in diseases such as Alzheimer’s (AD).
Susceptibility mapping (SM), which I pioneered, is uniquely sensitive to tissue composition including iron content affected in AD while conductivity mapping (CM) probably reflects cellular disruption in AD. Resting-state functional MRI (rsfMRI) reveals how AD affects brain networks without any tasks or stimulation equipment. However, each technique currently needs a separate time-consuming MRI scan. I will develop an integrated scan for simultaneous structural SM and CM, and rsfMRI functional connectivity characterisation. This efficient scan, ideal for AD patients, will reveal totally new resting-state networks based on electromagnetic properties: resting-state functional SM and resting-state functional CM for the first time. As changes in blood susceptibility underlie fMRI, rsfSM should measure functional connectivity more directly. This also makes it sensitive to physiological noise so I will develop noise removal methods building on fMRI techniques I established. Initial fSM studies have been at 7 Tesla but I will target the more widespread 3T field to maximise applicability. As a leader in both SM and rsfMRI physiological noise removal I have the ideal background to integrate SM and CM with fMRI and extend them for ground-breaking functional electromagnetic connectivity. This research will yield a rich set of novel, multimodal MRI contrasts to allow development of new combined structural and functional biomarkers for early diagnosis of AD and other diseases.
Summary
MRI is indispensable in the diagnosis of neurodegenerative diseases. These are poorly understood while their prevalence and socio-economic burden continue to rise. Structural and functional MRI can provide biomarkers for early diagnosis and potential therapeutic intervention. My research vision is to develop novel MRI methods for structural and functional mapping of tissue magnetic susceptibility and electrical conductivity as these show great promise for neuroimaging in diseases such as Alzheimer’s (AD).
Susceptibility mapping (SM), which I pioneered, is uniquely sensitive to tissue composition including iron content affected in AD while conductivity mapping (CM) probably reflects cellular disruption in AD. Resting-state functional MRI (rsfMRI) reveals how AD affects brain networks without any tasks or stimulation equipment. However, each technique currently needs a separate time-consuming MRI scan. I will develop an integrated scan for simultaneous structural SM and CM, and rsfMRI functional connectivity characterisation. This efficient scan, ideal for AD patients, will reveal totally new resting-state networks based on electromagnetic properties: resting-state functional SM and resting-state functional CM for the first time. As changes in blood susceptibility underlie fMRI, rsfSM should measure functional connectivity more directly. This also makes it sensitive to physiological noise so I will develop noise removal methods building on fMRI techniques I established. Initial fSM studies have been at 7 Tesla but I will target the more widespread 3T field to maximise applicability. As a leader in both SM and rsfMRI physiological noise removal I have the ideal background to integrate SM and CM with fMRI and extend them for ground-breaking functional electromagnetic connectivity. This research will yield a rich set of novel, multimodal MRI contrasts to allow development of new combined structural and functional biomarkers for early diagnosis of AD and other diseases.
Max ERC Funding
1 721 726 €
Duration
Start date: 2019-04-01, End date: 2024-03-31
Project acronym DISEASE
Project Disease Risk And Immune Strategies In Social Insects
Researcher (PI) Nathalie STROEYMEYT
Host Institution (HI) UNIVERSITY OF BRISTOL
Call Details Starting Grant (StG), LS8, ERC-2018-STG
Summary Group-living has been predicted to have opposing effects on disease risk and immune strategies. First, since repeated contacts between individuals facilitate pathogen transmission, sociality may favour high investment in personal immunity. Alternatively, because social animals can limit disease spread through collective sanitary actions (e.g., mutual grooming) or organisational features (e.g., division of the group’s social network into distinct subsets), sociality may instead favour low investment in personal immunity. The overall goal of this project is to experimentally test these conflicting predictions in ants using advanced data collection and analytical tools. I will first quantify the effect of social organisation on disease transmission using a combination of automated behavioural tracking, social network analysis, and empirical tracking of transmission markers (fluorescent beads). Experimental network manipulations and controlled disease seeding by a robotic ant will allow key predictions from network epidemiology to be tested, with broad implications for disease management strategies. I will then study the effect of colony size on social network structure and disease transmission, and how this in turn affects investment in personal immunity. This will shed light on far-reaching hypotheses about the effect of group size on social organisation ('size-complexity’ hypothesis) and immune investment (‘density-dependent prophylaxis’). Finally, I will explore whether prolonged pathogen pressure induces colonies to reinforce the transmission-inhibiting aspects of their social organisation (e.g., colony fragmentation) or to invest more in personal immunity. This project will represent the first empirical investigation of the role of social organisation in disease risk management, and allow its importance to be compared with other immune strategies. This will constitute a significant advance in our understanding of the complex feedback between sociality and health.
Summary
Group-living has been predicted to have opposing effects on disease risk and immune strategies. First, since repeated contacts between individuals facilitate pathogen transmission, sociality may favour high investment in personal immunity. Alternatively, because social animals can limit disease spread through collective sanitary actions (e.g., mutual grooming) or organisational features (e.g., division of the group’s social network into distinct subsets), sociality may instead favour low investment in personal immunity. The overall goal of this project is to experimentally test these conflicting predictions in ants using advanced data collection and analytical tools. I will first quantify the effect of social organisation on disease transmission using a combination of automated behavioural tracking, social network analysis, and empirical tracking of transmission markers (fluorescent beads). Experimental network manipulations and controlled disease seeding by a robotic ant will allow key predictions from network epidemiology to be tested, with broad implications for disease management strategies. I will then study the effect of colony size on social network structure and disease transmission, and how this in turn affects investment in personal immunity. This will shed light on far-reaching hypotheses about the effect of group size on social organisation ('size-complexity’ hypothesis) and immune investment (‘density-dependent prophylaxis’). Finally, I will explore whether prolonged pathogen pressure induces colonies to reinforce the transmission-inhibiting aspects of their social organisation (e.g., colony fragmentation) or to invest more in personal immunity. This project will represent the first empirical investigation of the role of social organisation in disease risk management, and allow its importance to be compared with other immune strategies. This will constitute a significant advance in our understanding of the complex feedback between sociality and health.
Max ERC Funding
1 499 995 €
Duration
Start date: 2019-04-01, End date: 2024-03-31
Project acronym DiSect
Project The Tumour Stroma as a Driver of Clonal Selection
Researcher (PI) Claus JORGENSEN
Host Institution (HI) THE UNIVERSITY OF MANCHESTER
Call Details Consolidator Grant (CoG), LS4, ERC-2017-COG
Summary Pancreatic ductal adenocarcinomas (PDA) are complex heterocellular tumours characterised by extensive desmoplasia. Tumour and stromal host cells actively engage to establish reciprocal signalling loops, which drive cancer progression, resistance to treatment and evasion of immune surveillance. However, the specificity and directionality of these interactions are incompletely characterised.
We have previously shown that tumour cells expressing the main oncogenic driver (KRASG12D) co-opt stromal fibroblasts to elicit a reciprocal signal, which activate tumour cell IGF-1R and AXL receptor tyrosine kinases. Importantly, these signals enable tumour cells to engage additional signalling pathways not activated when oncogenic KRAS is expressed in homogeneous tumour cell cultures. Therefore, to fully appreciate tumour cell signalling, studies should be undertaken within the context of the tumour stroma.
Early stages of PDA display a gradual accumulation of mutations where activated KRAS is accompanied by loss of tumour suppressors CDKN2A, TP53 and SMAD4. Simultaneously, there is an accumulation of infiltrating stromal cells. To address how PDA cells differ in their interaction with the infiltrating stroma, we will use in vitro co-cultures to study how PDA cells with frequent genetic aberrations recruit and interact with host stromal cells. We will combine our unique methodologies for cell-specific labelling with global proteomics and phosphoproteomics analysis to discern cell-specific signalling between tumour and stroma cells. Following, we will analyse the impact of the tumour stroma on clonal selection and use computational modelling to identify which cell autonomous and non-cell autonomous signals drive progression. Delineating how reciprocal signalling regulates early tumour cell signalling and clonal selection is critical to define pro-tumorigenic from restrictive stromal elements in order to improve combination therapies.
Summary
Pancreatic ductal adenocarcinomas (PDA) are complex heterocellular tumours characterised by extensive desmoplasia. Tumour and stromal host cells actively engage to establish reciprocal signalling loops, which drive cancer progression, resistance to treatment and evasion of immune surveillance. However, the specificity and directionality of these interactions are incompletely characterised.
We have previously shown that tumour cells expressing the main oncogenic driver (KRASG12D) co-opt stromal fibroblasts to elicit a reciprocal signal, which activate tumour cell IGF-1R and AXL receptor tyrosine kinases. Importantly, these signals enable tumour cells to engage additional signalling pathways not activated when oncogenic KRAS is expressed in homogeneous tumour cell cultures. Therefore, to fully appreciate tumour cell signalling, studies should be undertaken within the context of the tumour stroma.
Early stages of PDA display a gradual accumulation of mutations where activated KRAS is accompanied by loss of tumour suppressors CDKN2A, TP53 and SMAD4. Simultaneously, there is an accumulation of infiltrating stromal cells. To address how PDA cells differ in their interaction with the infiltrating stroma, we will use in vitro co-cultures to study how PDA cells with frequent genetic aberrations recruit and interact with host stromal cells. We will combine our unique methodologies for cell-specific labelling with global proteomics and phosphoproteomics analysis to discern cell-specific signalling between tumour and stroma cells. Following, we will analyse the impact of the tumour stroma on clonal selection and use computational modelling to identify which cell autonomous and non-cell autonomous signals drive progression. Delineating how reciprocal signalling regulates early tumour cell signalling and clonal selection is critical to define pro-tumorigenic from restrictive stromal elements in order to improve combination therapies.
Max ERC Funding
1 969 768 €
Duration
Start date: 2018-06-01, End date: 2023-05-31
Project acronym DIVERSITY
Project Evolution of Pathogen and Host Diversity
Researcher (PI) Sunetra Gupta
Host Institution (HI) THE CHANCELLOR, MASTERS AND SCHOLARS OF THE UNIVERSITY OF OXFORD
Call Details Advanced Grant (AdG), LS8, ERC-2010-AdG_20100317
Summary The study of host-pathogen systems is of central importance to the control of infectious disease, but also provides unique opportunities to observe evolution in action. Many pathogen species have diversified under selection pressures from the host; conversely, genes that are important in host defence also exhibit high degrees of polymorphism. This proposal divides into two parts: (1) the evolution of pathogen diversity under host immune selection, and (2) the evolution of host diversity under pathogen selection. I have developed a body of theoretical work showing that discrete population structures can arise through immune selection rather than limitations on genetic exchange. The predictions of this framework concerning the structure and dynamics of antigenic, metabolic and virulence genes will be empirically tested using three different systems: the bacterial pathogen, Neisseira meningitidis, the influenza virus, and the malaria parasite, Plasmodium falciparum. The current theory will also be expanded and modified to address a number of outstanding questions such whether it can explain the occurrence of influenza pandemics. With regard to host diversity, we will be attempting to validate and extend a novel framework incoporating epistatic interactions between malaria-protective genetic disorders of haemoglobin to understand their intriguing geographical distribution and their mode of action against the malarial disease. We will also be exploring the potential of mechanisms that can organise pathogens into discrete strains to generate patterns among host genes responsible for pathogen recognition, such as the Major Histocompatibility Complex. The co-evolution of hosts and pathogens under immune selection thus forms the ultimate theme of this proposal.
Summary
The study of host-pathogen systems is of central importance to the control of infectious disease, but also provides unique opportunities to observe evolution in action. Many pathogen species have diversified under selection pressures from the host; conversely, genes that are important in host defence also exhibit high degrees of polymorphism. This proposal divides into two parts: (1) the evolution of pathogen diversity under host immune selection, and (2) the evolution of host diversity under pathogen selection. I have developed a body of theoretical work showing that discrete population structures can arise through immune selection rather than limitations on genetic exchange. The predictions of this framework concerning the structure and dynamics of antigenic, metabolic and virulence genes will be empirically tested using three different systems: the bacterial pathogen, Neisseira meningitidis, the influenza virus, and the malaria parasite, Plasmodium falciparum. The current theory will also be expanded and modified to address a number of outstanding questions such whether it can explain the occurrence of influenza pandemics. With regard to host diversity, we will be attempting to validate and extend a novel framework incoporating epistatic interactions between malaria-protective genetic disorders of haemoglobin to understand their intriguing geographical distribution and their mode of action against the malarial disease. We will also be exploring the potential of mechanisms that can organise pathogens into discrete strains to generate patterns among host genes responsible for pathogen recognition, such as the Major Histocompatibility Complex. The co-evolution of hosts and pathogens under immune selection thus forms the ultimate theme of this proposal.
Max ERC Funding
1 670 632 €
Duration
Start date: 2011-06-01, End date: 2017-05-31
Project acronym Division
Project Division of Labour and the Evolution of Complexity
Researcher (PI) Stuart WEST
Host Institution (HI) THE CHANCELLOR, MASTERS AND SCHOLARS OF THE UNIVERSITY OF OXFORD
Call Details Advanced Grant (AdG), LS8, ERC-2018-ADG
Summary Division of labour is fundamental to the evolution of life on earth, allowing genes to work together to form genomes, cells to build organisms, pathogens to escape immune attack, and eusocial insect societies to achieve ecological dominance. Consequently, if we want to understand how life on earth evolved, we need to understand why division of labour does or, just as importantly, does not evolve. There are two major outstanding problems for our understanding of division of labour: First, how can we explain why division of labour has evolved with some traits, in some species, but not others? Given the potential benefits of dividing labour, why does it not arise more frequently in cooperative species? Second, in cases where division of labour has evolved, how can we explain the form that it takes? Why do factors such as the degree of specialisation, or mechanism used to produce different phenotypes, vary across species? I will combine my social evolution expertise with novel synthetic and genomic approaches to address these problems. I will explain the distribution and form of division of labour in the natural world, with an interdisciplinary research programme, divided into four work packages: (1) I will provide the first experimental test of the fundamental assumption that division of labour provides an efficiency benefit, by synthetically manipulating bacteria. (2) I will test how selection has acted for and against the evolution of division of labour in natural populations of bacteria, using novel genomic analysis techniques. (3) I will determine why division of labour evolved in some species, but not others, with an across species study on insects, and experimental evolution of bacteria. (4) I will establish a new field of research on why different species use different mechanisms to divide labour: genetic differences, environmental cues, or random assignment of roles. I will develop theory to explain this variation, and test this theory experimentally.
Summary
Division of labour is fundamental to the evolution of life on earth, allowing genes to work together to form genomes, cells to build organisms, pathogens to escape immune attack, and eusocial insect societies to achieve ecological dominance. Consequently, if we want to understand how life on earth evolved, we need to understand why division of labour does or, just as importantly, does not evolve. There are two major outstanding problems for our understanding of division of labour: First, how can we explain why division of labour has evolved with some traits, in some species, but not others? Given the potential benefits of dividing labour, why does it not arise more frequently in cooperative species? Second, in cases where division of labour has evolved, how can we explain the form that it takes? Why do factors such as the degree of specialisation, or mechanism used to produce different phenotypes, vary across species? I will combine my social evolution expertise with novel synthetic and genomic approaches to address these problems. I will explain the distribution and form of division of labour in the natural world, with an interdisciplinary research programme, divided into four work packages: (1) I will provide the first experimental test of the fundamental assumption that division of labour provides an efficiency benefit, by synthetically manipulating bacteria. (2) I will test how selection has acted for and against the evolution of division of labour in natural populations of bacteria, using novel genomic analysis techniques. (3) I will determine why division of labour evolved in some species, but not others, with an across species study on insects, and experimental evolution of bacteria. (4) I will establish a new field of research on why different species use different mechanisms to divide labour: genetic differences, environmental cues, or random assignment of roles. I will develop theory to explain this variation, and test this theory experimentally.
Max ERC Funding
2 491 766 €
Duration
Start date: 2020-01-01, End date: 2024-12-31
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 DNA-DOCK
Project Precision Docking of Very Large DNA Cargos in Mammalian Genomes
Researcher (PI) Imre Berger
Host Institution (HI) UNIVERSITY OF BRISTOL
Call Details Advanced Grant (AdG), LS9, ERC-2018-ADG
Summary Gene editing has developed at breath-taking speed. In particular CRISPR/Cas9 provides a tool-set thousands of researchers worldwide now utilize with unprecedented ease to edit genes, catalysing a broad range of biomedical and industrial applications. Gene synthesis technologies producing thousands of base pairs of synthetic DNA have become affordable. Current gene editing technology is highly effective for local, small genomic DNA edits and insertions. To unlock the full potential of this revolution, however, our capacities to disrupt or rewrite small local elements of code must be complemented by equal capacities to efficiently insert very large synthetic DNA cargos with a wide range of functions into genomic sites. Large designer cargos would carry multicomponent DNA circuitry including programmable and fine-tuneable functionalities, representing the vital interface between gene editing which is the state-of-the-art at present, and genome engineering, which is the future. This challenge remained largely unaddressed to date.
We aspire to resolve this bottleneck by creating ground-breaking, generally applicable, easy-to-use technology to enable docking of large DNA cargos with base pair precision and unparalleled efficiency into mammalian genomes. To achieve our ambitious goals, we will apply a whole array of sophisticated tools. We will unlock a small non-human virus to rational design, creating safe, flexible and easy-to-produce, large capacity DNA delivery nanodevices with unmatched transduction capability. We will exploit a range of techniques including Darwinian in vitro selection/evolution to accomplish unprecedented precision DNA integration efficiency into genomic sites. We will use parallelized DNA assembly methods to generate multifunctional circuits, to accelerate T cell engineering, resolving unmet needs. Once we accomplish our tasks, our technology has the potential to be exceptionally rewarding to the scientific, industrial and medical communities.
Summary
Gene editing has developed at breath-taking speed. In particular CRISPR/Cas9 provides a tool-set thousands of researchers worldwide now utilize with unprecedented ease to edit genes, catalysing a broad range of biomedical and industrial applications. Gene synthesis technologies producing thousands of base pairs of synthetic DNA have become affordable. Current gene editing technology is highly effective for local, small genomic DNA edits and insertions. To unlock the full potential of this revolution, however, our capacities to disrupt or rewrite small local elements of code must be complemented by equal capacities to efficiently insert very large synthetic DNA cargos with a wide range of functions into genomic sites. Large designer cargos would carry multicomponent DNA circuitry including programmable and fine-tuneable functionalities, representing the vital interface between gene editing which is the state-of-the-art at present, and genome engineering, which is the future. This challenge remained largely unaddressed to date.
We aspire to resolve this bottleneck by creating ground-breaking, generally applicable, easy-to-use technology to enable docking of large DNA cargos with base pair precision and unparalleled efficiency into mammalian genomes. To achieve our ambitious goals, we will apply a whole array of sophisticated tools. We will unlock a small non-human virus to rational design, creating safe, flexible and easy-to-produce, large capacity DNA delivery nanodevices with unmatched transduction capability. We will exploit a range of techniques including Darwinian in vitro selection/evolution to accomplish unprecedented precision DNA integration efficiency into genomic sites. We will use parallelized DNA assembly methods to generate multifunctional circuits, to accelerate T cell engineering, resolving unmet needs. Once we accomplish our tasks, our technology has the potential to be exceptionally rewarding to the scientific, industrial and medical communities.
Max ERC Funding
2 498 578 €
Duration
Start date: 2019-09-01, End date: 2024-08-31
Project acronym DROPFAT
Project Biogenesis of lipid droplets and lipid homeostasis
Researcher (PI) Pedro Nuno Chaves Simoes De Carvalho
Host Institution (HI) THE CHANCELLOR, MASTERS AND SCHOLARS OF THE UNIVERSITY OF OXFORD
Call Details Starting Grant (StG), LS3, ERC-2012-StG_20111109
Summary Organisms and cells face a myriad of environmental changes with periods of nutrient surplus and shortage. It is therefore not surprising that in all kingdoms of life, cells have evolved the means to store energy and thereby minimize the effects of environmental fluctuations. While the capability for energy storage has obvious advantages, deregulated energy accumulation can also be detrimental and is the hallmark of many diseases such as obesity.
In most cells energy is stored as neutral lipids in a dedicated cellular compartment, the lipid droplets (LDs). LDs are found in virtually every eukaryotic cell and play a central role in cellular lipid and energy metabolism. Despite their ubiquitous presence and importance, the physiology of LDs is poorly understood. LDs are composed of a single lipid layer and therefore distinct from all other cellular compartments. How do LDs originate at the endoplasmic reticulum (ER) and what is the machinery involved? How is the size, number and the storage capacity of the LDs regulated? How are specific proteins and lipids targeted to LDs? Addressing these questions is fundamental for understanding the “life cycle” of LDs and for a global picture of the cellular energy homeostasis.
The main goal of this proposal is to reveal the molecular mechanisms controlling neutral lipid dynamics and their storage in LDs. We will focus specifically on the role of the endoplasmic reticulum in the biogenesis of LDs. First, we will identify the ER protein complexes required for LD formation and regulation. Second, we will develop an assay to dissect the targeting of proteins to LDs. Finally, we will develop a cell-free system that recapitulates the biogenesis of LDs in vitro. Altogether, our strategy constitutes a systematic, in-depth analysis of LD dynamics and will lead to significant insight on the mechanisms of cellular energy storage. Our findings will likely offer a better understanding of human pathologies such as obesity and lipodistrophies
Summary
Organisms and cells face a myriad of environmental changes with periods of nutrient surplus and shortage. It is therefore not surprising that in all kingdoms of life, cells have evolved the means to store energy and thereby minimize the effects of environmental fluctuations. While the capability for energy storage has obvious advantages, deregulated energy accumulation can also be detrimental and is the hallmark of many diseases such as obesity.
In most cells energy is stored as neutral lipids in a dedicated cellular compartment, the lipid droplets (LDs). LDs are found in virtually every eukaryotic cell and play a central role in cellular lipid and energy metabolism. Despite their ubiquitous presence and importance, the physiology of LDs is poorly understood. LDs are composed of a single lipid layer and therefore distinct from all other cellular compartments. How do LDs originate at the endoplasmic reticulum (ER) and what is the machinery involved? How is the size, number and the storage capacity of the LDs regulated? How are specific proteins and lipids targeted to LDs? Addressing these questions is fundamental for understanding the “life cycle” of LDs and for a global picture of the cellular energy homeostasis.
The main goal of this proposal is to reveal the molecular mechanisms controlling neutral lipid dynamics and their storage in LDs. We will focus specifically on the role of the endoplasmic reticulum in the biogenesis of LDs. First, we will identify the ER protein complexes required for LD formation and regulation. Second, we will develop an assay to dissect the targeting of proteins to LDs. Finally, we will develop a cell-free system that recapitulates the biogenesis of LDs in vitro. Altogether, our strategy constitutes a systematic, in-depth analysis of LD dynamics and will lead to significant insight on the mechanisms of cellular energy storage. Our findings will likely offer a better understanding of human pathologies such as obesity and lipodistrophies
Max ERC Funding
1 475 282 €
Duration
Start date: 2013-02-01, End date: 2018-01-31
Project acronym Droso-parasite
Project Drosophila as a model host to study infections by kinetoplastid parasites
Researcher (PI) Petros Ligoxygakis
Host Institution (HI) THE CHANCELLOR, MASTERS AND SCHOLARS OF THE UNIVERSITY OF OXFORD
Call Details Starting Grant (StG), LS6, ERC-2012-StG_20111109
Summary For the vast majority of vector borne parasites the ability to overcome the insect midgut defences is central to transmission. However, for many such diseases we know virtually nothing about the molecular mechanisms involved. For vectors such as tsetse flies and sand flies the prospects for rapidly improving our understanding of key interactions occurring in the midgut when challenged by parasites is bleak. This is because the ‘tool box’ required untangling the interactions is very unlikely to be rapidly developed. For example, there is no realistic prospect of producing transgenic technology for tsetse flies because eggs are inaccessible due to intrauterine development of larvae; maintenance of multiple lines of either sand or tsetse flies permitting genetic studies is impossible because of the cost and complexity of culturing colonies; bioinformatic resources are still in their infancy. In this application we suggest that under these circumstances a comparative approach, in which kinetoplastid interactions in Drosophila melanogaster are studied in the first instance, will permit us to make significant progress in understanding the more important cases of insect-parasite interactions (Trypanosome brucei spp in tsetse and Leishmania in sandflies). Herpetomonas ampelophilae is a natural kinetoplastid parasite of Drosophila melanogaster, which establishes infection in the midgut of the fruit fly and can go on to invade the salivary glands. We now have this protozoan in culture and intend, through a combination of genomics, cell biology and RNAi experiments to identify the gut-specific host genomic contingent involved in parasite challenge. In addition, we will study the interaction between the indigenous flora and the parasite and the role of the former in protecting the host from parasite infection. These studies will outline the major immune pathways and interactions by which insects and their gut microflora respond to kinetoplastid challenge in the midgut.
Summary
For the vast majority of vector borne parasites the ability to overcome the insect midgut defences is central to transmission. However, for many such diseases we know virtually nothing about the molecular mechanisms involved. For vectors such as tsetse flies and sand flies the prospects for rapidly improving our understanding of key interactions occurring in the midgut when challenged by parasites is bleak. This is because the ‘tool box’ required untangling the interactions is very unlikely to be rapidly developed. For example, there is no realistic prospect of producing transgenic technology for tsetse flies because eggs are inaccessible due to intrauterine development of larvae; maintenance of multiple lines of either sand or tsetse flies permitting genetic studies is impossible because of the cost and complexity of culturing colonies; bioinformatic resources are still in their infancy. In this application we suggest that under these circumstances a comparative approach, in which kinetoplastid interactions in Drosophila melanogaster are studied in the first instance, will permit us to make significant progress in understanding the more important cases of insect-parasite interactions (Trypanosome brucei spp in tsetse and Leishmania in sandflies). Herpetomonas ampelophilae is a natural kinetoplastid parasite of Drosophila melanogaster, which establishes infection in the midgut of the fruit fly and can go on to invade the salivary glands. We now have this protozoan in culture and intend, through a combination of genomics, cell biology and RNAi experiments to identify the gut-specific host genomic contingent involved in parasite challenge. In addition, we will study the interaction between the indigenous flora and the parasite and the role of the former in protecting the host from parasite infection. These studies will outline the major immune pathways and interactions by which insects and their gut microflora respond to kinetoplastid challenge in the midgut.
Max ERC Funding
1 110 126 €
Duration
Start date: 2013-03-01, End date: 2018-02-28
Project acronym DROSOPHILAINFECTION
Project Genetic variation in the susceptibility of Drosophila to infection
Researcher (PI) Francis Michael Jiggins
Host Institution (HI) THE CHANCELLOR MASTERS AND SCHOLARS OF THE UNIVERSITY OF CAMBRIDGE
Call Details Starting Grant (StG), LS8, ERC-2011-StG_20101109
Summary Insects vary in their susceptibility to viral infection, and this variation affects disease transmission by vectors and the survival of beneficial insects. Identifying the genes that cause this variation will provide insights into both the molecular interactions between insects and their parasites, and the processes that maintain this variation in populations. We propose to do this in Drosophila, where genome-wide association studies are now possible thanks to the publication of large numbers of genome sequences. Furthermore, new techniques allow the sequence of Drosophila genes to be precisely altered, which will allow the exact molecular changes affecting resistance to be confirmed experimentally. Using these powerful techniques, we will first identify genes that affect resistance to a diverse panel of different viruses, which will allow us to understand the molecular and cellular basis of how resistance to different groups of viruses evolves in nature. Next, we will repeat this analysis using different isolates of the same virus, to identify the molecular basis of the ‘specific’ resistance commonly observed in invertebrates, where different host genotypes are resistant to different parasite genotypes. Once we have identified the polymorphisms that affect resistance, we can then use these results to examine the evolutionary processes that maintain this variation in populations: are alleles that increase resistance costly, how has natural selection acted on the polymorphisms, and is there more variation if the virus has naturally coevolved with Drosophila than if the virus was isolated from another insect. Finally, by hybridising D. melanogaster to D. simulans, we will extend these experiments to identify genes that cause species to differ in resistance, which will reveal the molecular basis of how resistance evolves over millions of years and how viruses adapt to their hosts.
Summary
Insects vary in their susceptibility to viral infection, and this variation affects disease transmission by vectors and the survival of beneficial insects. Identifying the genes that cause this variation will provide insights into both the molecular interactions between insects and their parasites, and the processes that maintain this variation in populations. We propose to do this in Drosophila, where genome-wide association studies are now possible thanks to the publication of large numbers of genome sequences. Furthermore, new techniques allow the sequence of Drosophila genes to be precisely altered, which will allow the exact molecular changes affecting resistance to be confirmed experimentally. Using these powerful techniques, we will first identify genes that affect resistance to a diverse panel of different viruses, which will allow us to understand the molecular and cellular basis of how resistance to different groups of viruses evolves in nature. Next, we will repeat this analysis using different isolates of the same virus, to identify the molecular basis of the ‘specific’ resistance commonly observed in invertebrates, where different host genotypes are resistant to different parasite genotypes. Once we have identified the polymorphisms that affect resistance, we can then use these results to examine the evolutionary processes that maintain this variation in populations: are alleles that increase resistance costly, how has natural selection acted on the polymorphisms, and is there more variation if the virus has naturally coevolved with Drosophila than if the virus was isolated from another insect. Finally, by hybridising D. melanogaster to D. simulans, we will extend these experiments to identify genes that cause species to differ in resistance, which will reveal the molecular basis of how resistance evolves over millions of years and how viruses adapt to their hosts.
Max ERC Funding
1 498 072 €
Duration
Start date: 2011-11-01, End date: 2017-10-31
Project acronym DROSOPHILASIGNALING
Project Signaling Pathways Controlling Patterning, Growth and Final Size of Drosophila Limbs
Researcher (PI) Konrad Basler
Host Institution (HI) UNIVERSITAT ZURICH
Call Details Advanced Grant (AdG), LS3, ERC-2008-AdG
Summary Developmental biology seeks not only to learn more about the fundamental processes of growth and pattern per se, but to understand how they synergize to enable the morphogenesis of multicellular organisms. Our goal is to perform real-time analyses of these developmental processes in an intact developing organ. By applying a vital imaging approach, we can circumvent the normal limitations of inferring cellular dynamics from static images or molecular data, and obtain the real dynamic view of growth and patterning. The wing imaginal disc of Drosophila, which starts out as a simple epithelial structure and gives rise to a precisely structured adult limb, will serve as an ideal model system. This system has the combined advantages of relative simplicity and genetic tractability. We will create several innovations that expand the current toolkit and thus facilitate the detailed dissection of growth and patterning. A key early step will be to develop novel reporters to dynamically and faithfully monitor signaling cascades involved in growth and patterning, such as the Dpp and Hippo pathways. We will also implement quantification techniques that are currently being set up in collaboration with an experimental physicist, to deduce, and alter, the mechanical forces that develop in the cells of a growing tissue. The large amount of quantitative data that will be generated allow us derive computational models of the individual pathways and their interaction. The focus of the study will be to answer the following questions: 1) Is the Hippo pathway regulated spatially and temporally, and by what signaling pathways? 2) Do mechanical forces play a pivotal controlling role in organ morphogenesis? 3) What are the global effects on growth, when pathways controlling patterning, cell competition or compensatory proliferation are perturbed? The proposed project will bring the approaches taken to define the mechanisms underlying and controlling growth and patterning to the next level.
Summary
Developmental biology seeks not only to learn more about the fundamental processes of growth and pattern per se, but to understand how they synergize to enable the morphogenesis of multicellular organisms. Our goal is to perform real-time analyses of these developmental processes in an intact developing organ. By applying a vital imaging approach, we can circumvent the normal limitations of inferring cellular dynamics from static images or molecular data, and obtain the real dynamic view of growth and patterning. The wing imaginal disc of Drosophila, which starts out as a simple epithelial structure and gives rise to a precisely structured adult limb, will serve as an ideal model system. This system has the combined advantages of relative simplicity and genetic tractability. We will create several innovations that expand the current toolkit and thus facilitate the detailed dissection of growth and patterning. A key early step will be to develop novel reporters to dynamically and faithfully monitor signaling cascades involved in growth and patterning, such as the Dpp and Hippo pathways. We will also implement quantification techniques that are currently being set up in collaboration with an experimental physicist, to deduce, and alter, the mechanical forces that develop in the cells of a growing tissue. The large amount of quantitative data that will be generated allow us derive computational models of the individual pathways and their interaction. The focus of the study will be to answer the following questions: 1) Is the Hippo pathway regulated spatially and temporally, and by what signaling pathways? 2) Do mechanical forces play a pivotal controlling role in organ morphogenesis? 3) What are the global effects on growth, when pathways controlling patterning, cell competition or compensatory proliferation are perturbed? The proposed project will bring the approaches taken to define the mechanisms underlying and controlling growth and patterning to the next level.
Max ERC Funding
2 310 000 €
Duration
Start date: 2009-02-01, End date: 2014-01-31
Project acronym DrosoSpiro
Project The Drosophila-Spiroplasma interaction as a model to dissect the molecular mechanisms underlying insect endosymbiosis
Researcher (PI) Bruno Lemaitre
Host Institution (HI) ECOLE POLYTECHNIQUE FEDERALE DE LAUSANNE
Call Details Advanced Grant (AdG), LS8, ERC-2013-ADG
Summary Virtually every species of insect harbors facultative bacterial endosymbionts that are transmitted from females to their offspring, often in the egg cytoplasm. These symbionts play crucial roles in the biology of their hosts. Many manipulate host reproduction in order to spread within host populations. Others increase the fitness of their hosts under certain conditions. For example, increasing tolerance to heat or protecting their hosts against natural enemies. Over the past decade, our understanding of insect endosymbionts has shifted from seeing them as fascinating oddities to being ubiquitous and central to the biology of their hosts, including many of high economic and medical importance. However, in spite of growing interest in endosymbionts, very little is known about the molecular mechanisms underlying most endosymbiont-insect interactions. For instance, the basis of the main phenotypes caused by endosymbionts, including diverse reproductive manipulations or symbiont-protective immunity, remains largely enigmatic. The goal of the present application is to fill this gap by dissecting the interaction between Drosophila and its native endosymbiont Spiroplasma poulsonii. This project will use a broad range of approaches ranging from molecular genetic to genomics to dissect the molecular mechanisms underlying key features of the symbiosis, including vertical transmission, male killing, regulation of symbiont growth, and symbiont-mediated protection against parasitic wasps. We believe that the fundamental knowledge generated on the Drosophila-Spiroplasma interaction will serve as a paradigm for other endosymbiont-insect interactions that are less amenable to genetic studies.
Summary
Virtually every species of insect harbors facultative bacterial endosymbionts that are transmitted from females to their offspring, often in the egg cytoplasm. These symbionts play crucial roles in the biology of their hosts. Many manipulate host reproduction in order to spread within host populations. Others increase the fitness of their hosts under certain conditions. For example, increasing tolerance to heat or protecting their hosts against natural enemies. Over the past decade, our understanding of insect endosymbionts has shifted from seeing them as fascinating oddities to being ubiquitous and central to the biology of their hosts, including many of high economic and medical importance. However, in spite of growing interest in endosymbionts, very little is known about the molecular mechanisms underlying most endosymbiont-insect interactions. For instance, the basis of the main phenotypes caused by endosymbionts, including diverse reproductive manipulations or symbiont-protective immunity, remains largely enigmatic. The goal of the present application is to fill this gap by dissecting the interaction between Drosophila and its native endosymbiont Spiroplasma poulsonii. This project will use a broad range of approaches ranging from molecular genetic to genomics to dissect the molecular mechanisms underlying key features of the symbiosis, including vertical transmission, male killing, regulation of symbiont growth, and symbiont-mediated protection against parasitic wasps. We believe that the fundamental knowledge generated on the Drosophila-Spiroplasma interaction will serve as a paradigm for other endosymbiont-insect interactions that are less amenable to genetic studies.
Max ERC Funding
1 963 926 €
Duration
Start date: 2014-05-01, End date: 2019-04-30
Project acronym DrugE3CRLs
Project Probing Druggability of Multisubunit Complexes:
E3 Cullin RING Ligases
Researcher (PI) Alessio Ciulli
Host Institution (HI) UNIVERSITY OF DUNDEE
Call Details Starting Grant (StG), LS7, ERC-2012-StG_20111109
Summary This proposal is centred on the development and application of chemical tools to probe molecular recognition of multiprotein complexes. Although much effort has been devoted to targeting protein-protein interactions using small molecules, these have focused to date on individual gene products or truncated domains, which however do not reflect the physiological organization and activity of many functional proteins. Few successes have been achieved, yet many of the key physical determinants of druggability of surfaces within native protein complexes have remained elusive. The aim of this project is to shed light upon this problem by chemically interrogating biological systems that rely on several subunits working in concert rather than on single proteins working alone. As model system we will investigate the Cullin RING Ligases (CRLs), the largest superfamily of multisubunit E3 ligases in humans. These enzymatic machines are responsible for the recognition, poly-ubiquitination and targeting of substrate proteins to the proteasome for degradation. Many members of this family have crucial roles in cellular physiology and homeostatis, are implicated in a wide range of diseases and are attractive targets for drug discovery. Two interdependent lines of enquiry will be followed. First, we will screen for and elucidate the binding of small molecular fragments and short peptides to identify new druggable surfaces and interfaces on CRLs and their components. Second, we will exploit the nature of the interactions to develop novel chemical probes of CRLs. As the probes are selected and optimised for binding rather than for a particular functional outcome, diverse mechanisms of action are envisaged beyond conventional disruption of the interaction. The successes of this interdisciplinary research will provide a step change in how we interrogate protein-protein interactions of functional and pathological pathways with impact in many areas of chemical biology and drug discovery.
Summary
This proposal is centred on the development and application of chemical tools to probe molecular recognition of multiprotein complexes. Although much effort has been devoted to targeting protein-protein interactions using small molecules, these have focused to date on individual gene products or truncated domains, which however do not reflect the physiological organization and activity of many functional proteins. Few successes have been achieved, yet many of the key physical determinants of druggability of surfaces within native protein complexes have remained elusive. The aim of this project is to shed light upon this problem by chemically interrogating biological systems that rely on several subunits working in concert rather than on single proteins working alone. As model system we will investigate the Cullin RING Ligases (CRLs), the largest superfamily of multisubunit E3 ligases in humans. These enzymatic machines are responsible for the recognition, poly-ubiquitination and targeting of substrate proteins to the proteasome for degradation. Many members of this family have crucial roles in cellular physiology and homeostatis, are implicated in a wide range of diseases and are attractive targets for drug discovery. Two interdependent lines of enquiry will be followed. First, we will screen for and elucidate the binding of small molecular fragments and short peptides to identify new druggable surfaces and interfaces on CRLs and their components. Second, we will exploit the nature of the interactions to develop novel chemical probes of CRLs. As the probes are selected and optimised for binding rather than for a particular functional outcome, diverse mechanisms of action are envisaged beyond conventional disruption of the interaction. The successes of this interdisciplinary research will provide a step change in how we interrogate protein-protein interactions of functional and pathological pathways with impact in many areas of chemical biology and drug discovery.
Max ERC Funding
1 499 904 €
Duration
Start date: 2013-05-01, End date: 2018-04-30
Project acronym DRYLIFE
Project Surviving the dry state: engineering a desiccation-tolerant mammalian cell
Researcher (PI) Alan Tunnacliffe
Host Institution (HI) THE CHANCELLOR MASTERS AND SCHOLARS OF THE UNIVERSITY OF CAMBRIDGE
Call Details Advanced Grant (AdG), LS9, ERC-2008-AdG
Summary Certain plants, animals and micro-organisms are able to dry out completely and yet remain viable, a phenomenon known as anhydrobiosis ( life without water ), or desiccation tolerance. This proposal addresses the molecular mechanisms responsible for desiccation tolerance and aims to confer these mechanisms on desiccation-sensitive mammalian cells, establishing a new field in biotechnology: a form of synthetic biology we have called anhydrobiotic engineering. One feature of anhydrobiotic organisms is the production of many examples of highly hydrophilic proteins (or hydrophilins ) in preparation for severe dehydration. Although data are limited, these hydrophilins are suggested to fulfil various roles in preserving homeostasis of the desiccating cell, including the maintenance of protein, nucleic acid and membrane structure. The proposed project will investigate the function of hydrophilins, engineer these and other elements as desiccation protection modules, and introduce modules into mammalian cell lines. By combining protection modules and using an iterative deployment strategy, we aim to achieve an engineered mammalian cell with high viability in the dried state. Anhydrobiotic engineering will find applications in cell banking, e.g. of hybridoma collections, and cell-based technologies including tissue engineering. Principles established should be applicable to agriculture, where drought-resistant crops, or desiccation-tolerant biopesticides are envisaged. The PI has a distinguished record of achievement in several disciplines in the life sciences and biotechnology, in both academia and industry. Publications in Nature, Science and other leading journals include contributions in human genomics, the molecular genetics of the immune system and inherited disease, the molecular cell biology and biochemistry of desiccation tolerance, and invertebrate genetics. The PI is also an inventor on licensed patents and patent applications in two different fields.
Summary
Certain plants, animals and micro-organisms are able to dry out completely and yet remain viable, a phenomenon known as anhydrobiosis ( life without water ), or desiccation tolerance. This proposal addresses the molecular mechanisms responsible for desiccation tolerance and aims to confer these mechanisms on desiccation-sensitive mammalian cells, establishing a new field in biotechnology: a form of synthetic biology we have called anhydrobiotic engineering. One feature of anhydrobiotic organisms is the production of many examples of highly hydrophilic proteins (or hydrophilins ) in preparation for severe dehydration. Although data are limited, these hydrophilins are suggested to fulfil various roles in preserving homeostasis of the desiccating cell, including the maintenance of protein, nucleic acid and membrane structure. The proposed project will investigate the function of hydrophilins, engineer these and other elements as desiccation protection modules, and introduce modules into mammalian cell lines. By combining protection modules and using an iterative deployment strategy, we aim to achieve an engineered mammalian cell with high viability in the dried state. Anhydrobiotic engineering will find applications in cell banking, e.g. of hybridoma collections, and cell-based technologies including tissue engineering. Principles established should be applicable to agriculture, where drought-resistant crops, or desiccation-tolerant biopesticides are envisaged. The PI has a distinguished record of achievement in several disciplines in the life sciences and biotechnology, in both academia and industry. Publications in Nature, Science and other leading journals include contributions in human genomics, the molecular genetics of the immune system and inherited disease, the molecular cell biology and biochemistry of desiccation tolerance, and invertebrate genetics. The PI is also an inventor on licensed patents and patent applications in two different fields.
Max ERC Funding
2 494 963 €
Duration
Start date: 2009-01-01, End date: 2014-09-30
Project acronym DURABLERESISTANCE
Project Durable resistance against fungal plant pathogens
Researcher (PI) Beat Keller
Host Institution (HI) UNIVERSITAT ZURICH
Call Details Advanced Grant (AdG), LS9, ERC-2009-AdG
Summary Plants and their pathogens are in a constant process of co-evolution. Consequently, many of the known defense genes of plants against fungal pathogens are rapidly loosing effectiveness under agricultural conditions. However, there are examples for durable resistance. It is one of the main research questions in plant biology to determine the genetic basis of such naturally occurring resistance and to understand the underlying biochemical and molecular cause for durability. This durability is characterized by the apparent inability of the pathogen to adapt to the resistance mechanism. The molecular understanding of durable resistance will contribute to future attempts to develop such resistance by design. We want to use two approaches towards understanding and developing durable resistance: the first one is based on the naturally occurring durable resistance gene Lr34 against rust and mildew diseases in wheat. This gene was recently isolated in our group and it encodes a putative ABC type of transporter protein, providing a possible link between non-host and durable resistance. Its function in resistance will be studied by genetic and biochemical approaches in the crop plant wheat, as there is no Lr34-type of resistance characterized in any other plant. However, there is a close Lr34-homolog in rice and its function will be investigated in this diploid system. The second approach will be based on natural diversity found in a specific resistance gene, conferring strong, but not durable resistance. This diversity will be used for a designed improvement of durability by developing new proteins or protein combinations to which the pathogen can not adapt. We will use the 15 naturally occurring alleles of the Pm3 powdery mildew resistance genes to identify the structural basis of specific interactions. Based on this characterization, we will develop intragenic or gene combination pyramiding strategies to obtain more broad-spectrum and more durable resistance.
Summary
Plants and their pathogens are in a constant process of co-evolution. Consequently, many of the known defense genes of plants against fungal pathogens are rapidly loosing effectiveness under agricultural conditions. However, there are examples for durable resistance. It is one of the main research questions in plant biology to determine the genetic basis of such naturally occurring resistance and to understand the underlying biochemical and molecular cause for durability. This durability is characterized by the apparent inability of the pathogen to adapt to the resistance mechanism. The molecular understanding of durable resistance will contribute to future attempts to develop such resistance by design. We want to use two approaches towards understanding and developing durable resistance: the first one is based on the naturally occurring durable resistance gene Lr34 against rust and mildew diseases in wheat. This gene was recently isolated in our group and it encodes a putative ABC type of transporter protein, providing a possible link between non-host and durable resistance. Its function in resistance will be studied by genetic and biochemical approaches in the crop plant wheat, as there is no Lr34-type of resistance characterized in any other plant. However, there is a close Lr34-homolog in rice and its function will be investigated in this diploid system. The second approach will be based on natural diversity found in a specific resistance gene, conferring strong, but not durable resistance. This diversity will be used for a designed improvement of durability by developing new proteins or protein combinations to which the pathogen can not adapt. We will use the 15 naturally occurring alleles of the Pm3 powdery mildew resistance genes to identify the structural basis of specific interactions. Based on this characterization, we will develop intragenic or gene combination pyramiding strategies to obtain more broad-spectrum and more durable resistance.
Max ERC Funding
2 100 000 €
Duration
Start date: 2010-04-01, End date: 2015-03-31
Project acronym DUT-signal
Project dUTPase Signalling: from Phage to Eukaryotes
Researcher (PI) Jose Rafael Penades Casanova
Host Institution (HI) UNIVERSITY OF GLASGOW
Call Details Advanced Grant (AdG), LS6, ERC-2014-ADG
Summary dUTPases (DUTs) are enzymes that regulate cellular dUTP levels to prevent the misincorporation of uracil into DNA. Recently however, DUTs have been involved in the control of relevant cellular processes. How these regulatory functions are controlled remains unsolved. The recent elucidation of the mechanistic role of DUTs in the transfer of staphylococcal pathogenicity islands (SaPIs) by our group has revealed an entirely novel and surprising strategy involving DUTs in signalling. Namely, we have demonstrated that in addition to the 5 classical domains present in all the trimeric DUTs, staphylococcal phage-encoded DUT proteins possess an extra region (Motif VI) involved in SaPI de-repression by binding to the SaPI-encoded repressor (Stl). Although this domain is necessary, it does not suffice to induce the SaPI cycle. Unexpectedly, the strongly conserved DUT motif V is also inherently involved in mediating de-repression. Crystallographic and mutagenic analyses have demonstrated that binding to dUTP orders the C-terminal motif V of phage-encoded DUTs, potentially rendering these proteins in the conformation required for SaPI de-repression. In contrast, conversion into the apo state conformation by the hydrolysis of the bound dUTP disorders motif V and generates a protein that is unable to induce the SaPI cycle. Analogously, previous work demonstrated that the trimeric rat DUT interacts with the transcriptional factor PPARα, an interaction that depends on an “extra” N-terminal motif VI present in the DUT protein and requires the C-terminal domain contribution, strongly supporting in general the mechanism involving DUTs in signalling. In summary, our results suggest that DUTs define a widespread family of signalling molecules that acts analogously to eukaryotic G-proteins. This project stems from this ground-breaking result, and will investigate the biological role of DUTs as signalling molecules, opening up the possibility to establish dUTP as a new second messenger.
Summary
dUTPases (DUTs) are enzymes that regulate cellular dUTP levels to prevent the misincorporation of uracil into DNA. Recently however, DUTs have been involved in the control of relevant cellular processes. How these regulatory functions are controlled remains unsolved. The recent elucidation of the mechanistic role of DUTs in the transfer of staphylococcal pathogenicity islands (SaPIs) by our group has revealed an entirely novel and surprising strategy involving DUTs in signalling. Namely, we have demonstrated that in addition to the 5 classical domains present in all the trimeric DUTs, staphylococcal phage-encoded DUT proteins possess an extra region (Motif VI) involved in SaPI de-repression by binding to the SaPI-encoded repressor (Stl). Although this domain is necessary, it does not suffice to induce the SaPI cycle. Unexpectedly, the strongly conserved DUT motif V is also inherently involved in mediating de-repression. Crystallographic and mutagenic analyses have demonstrated that binding to dUTP orders the C-terminal motif V of phage-encoded DUTs, potentially rendering these proteins in the conformation required for SaPI de-repression. In contrast, conversion into the apo state conformation by the hydrolysis of the bound dUTP disorders motif V and generates a protein that is unable to induce the SaPI cycle. Analogously, previous work demonstrated that the trimeric rat DUT interacts with the transcriptional factor PPARα, an interaction that depends on an “extra” N-terminal motif VI present in the DUT protein and requires the C-terminal domain contribution, strongly supporting in general the mechanism involving DUTs in signalling. In summary, our results suggest that DUTs define a widespread family of signalling molecules that acts analogously to eukaryotic G-proteins. This project stems from this ground-breaking result, and will investigate the biological role of DUTs as signalling molecules, opening up the possibility to establish dUTP as a new second messenger.
Max ERC Funding
2 246 192 €
Duration
Start date: 2015-12-01, End date: 2020-11-30
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 dynamicmodifications
Project Complexity and dynamics of nucleic acids modifications in vivo
Researcher (PI) Petra Hajkova
Host Institution (HI) IMPERIAL COLLEGE OF SCIENCE TECHNOLOGY AND MEDICINE
Call Details Consolidator Grant (CoG), LS2, ERC-2014-CoG
Summary Development of any organism starts with a totipotent cell (zygote). Through series of cell divisions and differentiation processes this cell will eventually give rise to the whole organism containing hundreds of specialised cell. While the cells at the onset of development have the capacity to generate all cell types (ie are toti-or pluripotent), this developmental capacity is progressively lost as the cells undertake cell fate decisions. At the molecular level, the memory of these events is laid down in a complex layer of epigenetic modifications at both the DNA and the chromatin level. Unidirectional character of the developmental progress dictates that the key acquired epigenetic modifications are stable and inherited through subsequent cell divisions. This paradigm is, however, challenged during cellular reprogramming that requires de-differentiation (nuclear transfer, induced pluripotent stem cells, wound healing and regeneration in lower organisms) or a change in cell fate (transdifferentiation). Despite intense efforts of numerous research teams, the molecular mechanisms of these processes remain enigmatic.
In order to understand cellular reprogramming at the molecular level, this proposal takes advantage of epigenetic reprogramming processes that occur naturally during mouse development. By using mouse fertilised zygote and mouse developing primordial germ cells we will investigate novel molecular components implicated in the genome-wide erasure of DNA methylation. Additionally, by using a unique combination of the developmental models with the state of the art ultra-sensitive LC/MS and genomics approaches we propose to investigate the dynamics and the interplay between DNA and RNA modifications during these key periods of embryonic development characterised by genome-wide epigenetic changes . Our work will thus provide new fundamental insights into a complex dynamics and interactions between epigenetic modifications that underlie epigenetic reprogramming
Summary
Development of any organism starts with a totipotent cell (zygote). Through series of cell divisions and differentiation processes this cell will eventually give rise to the whole organism containing hundreds of specialised cell. While the cells at the onset of development have the capacity to generate all cell types (ie are toti-or pluripotent), this developmental capacity is progressively lost as the cells undertake cell fate decisions. At the molecular level, the memory of these events is laid down in a complex layer of epigenetic modifications at both the DNA and the chromatin level. Unidirectional character of the developmental progress dictates that the key acquired epigenetic modifications are stable and inherited through subsequent cell divisions. This paradigm is, however, challenged during cellular reprogramming that requires de-differentiation (nuclear transfer, induced pluripotent stem cells, wound healing and regeneration in lower organisms) or a change in cell fate (transdifferentiation). Despite intense efforts of numerous research teams, the molecular mechanisms of these processes remain enigmatic.
In order to understand cellular reprogramming at the molecular level, this proposal takes advantage of epigenetic reprogramming processes that occur naturally during mouse development. By using mouse fertilised zygote and mouse developing primordial germ cells we will investigate novel molecular components implicated in the genome-wide erasure of DNA methylation. Additionally, by using a unique combination of the developmental models with the state of the art ultra-sensitive LC/MS and genomics approaches we propose to investigate the dynamics and the interplay between DNA and RNA modifications during these key periods of embryonic development characterised by genome-wide epigenetic changes . Our work will thus provide new fundamental insights into a complex dynamics and interactions between epigenetic modifications that underlie epigenetic reprogramming
Max ERC Funding
2 000 000 €
Duration
Start date: 2015-08-01, End date: 2020-07-31
