Project acronym DEPTH
Project DEsigning new Paths in The differentiation Hyperspace
Researcher (PI) Giovanni Cesareni
Host Institution (HI) UNIVERSITA DEGLI STUDI DI ROMA TOR VERGATA
Call Details Advanced Grant (AdG), LS2, ERC-2012-ADG_20120314
Summary The adult human organism contains heterogeneous reservoirs of pluripotent stem cells characterized by a diversified differentiation potential. Understanding their biology at a system level would advance our ability to selectively activate and control their differentiation potential. Aside from the basic implications this would represent a substantial progress in regenerative medicine by providing a rational framework for using small molecules to control cell trans-determination and reprogramming.
Here we propose a combined experimental and modelling approach to assemble a predictive model of mesoderm stem cell differentiation. Different cell states are identified by a vector in the differentiation hyperspace, the coordinates of the vector being the activation levels of a large number of nodes of a logic model linking the cell signalling network to the transcription regulatory network.
The premise of this proposal is that differentiation is equivalent to rewiring the cell regulatory network as a consequence of induced perturbation of the gene expression program. This process can be rationally controlled by perturbing specific nodes of the signalling network that in turn control transcription factor activation. We will develop this novel strategy using the mesoangioblast ex vivo differentiation system. Mesoangioblasts are one of the many different types of mesoderm stem/progenitor cells that exhibit myogenic potential. Ex vivo, they readily differentiate into striated muscle. However, under appropriate conditions they can also differentiate, into smooth muscle and adipocytes, albeit less efficiently. We will start by assembling, training and optimizing different predictive models for the undifferentiated mesoangioblast. Next by a combination of experiments and modelling approaches we will learn how, by perturbing the signalling models with different inhibitors and activators we can rewire the cell networks to induce trans-determination or reprogramming.
Summary
The adult human organism contains heterogeneous reservoirs of pluripotent stem cells characterized by a diversified differentiation potential. Understanding their biology at a system level would advance our ability to selectively activate and control their differentiation potential. Aside from the basic implications this would represent a substantial progress in regenerative medicine by providing a rational framework for using small molecules to control cell trans-determination and reprogramming.
Here we propose a combined experimental and modelling approach to assemble a predictive model of mesoderm stem cell differentiation. Different cell states are identified by a vector in the differentiation hyperspace, the coordinates of the vector being the activation levels of a large number of nodes of a logic model linking the cell signalling network to the transcription regulatory network.
The premise of this proposal is that differentiation is equivalent to rewiring the cell regulatory network as a consequence of induced perturbation of the gene expression program. This process can be rationally controlled by perturbing specific nodes of the signalling network that in turn control transcription factor activation. We will develop this novel strategy using the mesoangioblast ex vivo differentiation system. Mesoangioblasts are one of the many different types of mesoderm stem/progenitor cells that exhibit myogenic potential. Ex vivo, they readily differentiate into striated muscle. However, under appropriate conditions they can also differentiate, into smooth muscle and adipocytes, albeit less efficiently. We will start by assembling, training and optimizing different predictive models for the undifferentiated mesoangioblast. Next by a combination of experiments and modelling approaches we will learn how, by perturbing the signalling models with different inhibitors and activators we can rewire the cell networks to induce trans-determination or reprogramming.
Max ERC Funding
2 639 804 €
Duration
Start date: 2013-04-01, End date: 2018-09-30
Project acronym DEVOCHROMO
Project Chromosome structure and genome organization in early mammalian development
Researcher (PI) Peter Fraser
Host Institution (HI) THE BABRAHAM INSTITUTE
Call Details Advanced Grant (AdG), LS2, ERC-2013-ADG
Summary "The spatial organization of the genome inside the cell nucleus is tissue-specific and has been linked to several nuclear processes including gene activation, gene silencing, genomic imprinting, gene co-regulation, genome maintenance, DNA replication, DNA repair, chromosomal translocations and X chromosome inactivation. In fact, just about any nuclear/genome function has a spatial component that has been implicated in its control. We know surprisingly little about chromosome conformation and spatial organization or how they are established. The extent to which they are a cause or consequence of genome functions are current topics of considerable debate, however emerging data from my group and many other groups world-wide indicate that nuclear location and organization are drivers of genome functions, which in cooperation with other features including epigenetic marks, non-coding RNAs and trans-factor binding bring about genome control. Thus, genome spatial organization can be considered on a par with other epigenetic features that together contribute to overall genome control. The classical paradigm of early mammalian development arguably represents the most dramatic and yet least understood process of genome reprogramming, where a single cell undergoes a series of divisions to ultimately give rise to the hundreds of different cell types found in a mature organism. Study of pre-implantation embryo development is hindered by the very nature of the life form, composed of extremely low cell numbers at each stage, which severely limits the options for investigation. My lab has recently developed a novel technique called single cell Hi-C, which has the power to detect tens of thousands of simultaneous chromatin contacts from a single cell. In this application I propose to apply this technology to study chromosome structure and genome organization during mouse pre-implantation development along with single cell transcriptome analyses from the same cells."
Summary
"The spatial organization of the genome inside the cell nucleus is tissue-specific and has been linked to several nuclear processes including gene activation, gene silencing, genomic imprinting, gene co-regulation, genome maintenance, DNA replication, DNA repair, chromosomal translocations and X chromosome inactivation. In fact, just about any nuclear/genome function has a spatial component that has been implicated in its control. We know surprisingly little about chromosome conformation and spatial organization or how they are established. The extent to which they are a cause or consequence of genome functions are current topics of considerable debate, however emerging data from my group and many other groups world-wide indicate that nuclear location and organization are drivers of genome functions, which in cooperation with other features including epigenetic marks, non-coding RNAs and trans-factor binding bring about genome control. Thus, genome spatial organization can be considered on a par with other epigenetic features that together contribute to overall genome control. The classical paradigm of early mammalian development arguably represents the most dramatic and yet least understood process of genome reprogramming, where a single cell undergoes a series of divisions to ultimately give rise to the hundreds of different cell types found in a mature organism. Study of pre-implantation embryo development is hindered by the very nature of the life form, composed of extremely low cell numbers at each stage, which severely limits the options for investigation. My lab has recently developed a novel technique called single cell Hi-C, which has the power to detect tens of thousands of simultaneous chromatin contacts from a single cell. In this application I propose to apply this technology to study chromosome structure and genome organization during mouse pre-implantation development along with single cell transcriptome analyses from the same cells."
Max ERC Funding
2 401 393 €
Duration
Start date: 2014-02-01, End date: 2019-01-31
Project acronym DIATOMITE
Project Genome-enabled dissection of marine diatom ecophysiology
Researcher (PI) Chris Bowler
Host Institution (HI) CENTRE NATIONAL DE LA RECHERCHE SCIENTIFIQUE CNRS
Call Details Advanced Grant (AdG), LS2, ERC-2011-ADG_20110310
Summary "Diatoms are the most successful group of eukaryotic phytoplankton in the modern ocean. Recently completed whole genome sequences have revealed a wealth of information about the evolutionary origins and metabolic adaptations that may have led to their ecological success. A major finding is that they have acquired genes both from their endosymbiotic ancestors and by horizontal gene transfer from marine bacteria. This unique melting pot of genes encodes novel and largely unexplored capacities for metabolic management. The project will address the current gap in knowledge about the physiological functions of diatom gene products and about the evolutionary mechanisms that have led to diatom success in contemporary oceans. We will exploit genome-enabled approaches to pioneer new research topics addressing:
1. How has diatom evolution enabled interactions between chloroplasts and mitochondria that have provided diatoms with physiological and metabolic innovations?
2. What are the relative contributions of DNA sequence variation and epigenetic processes in diatom adaptive dynamics?
By combining these questions, we will uniquely be able to identify sentinel genes that have driven major physiological and metabolic innovations in diatoms, and will explore the mechanisms that have selected and molded them during diatom evolution. We will focus our studies largely on diatom responses to nutrients, in particular nitrate and iron, and will exploit the advantages of Phaeodactylum tricornutum as a model diatom species for reverse genetics. The proposed studies will revisit textbook understanding of photosynthesis and nitrogen metabolism, and will refine hypotheses about why diatoms dominate in contemporary ocean settings. By placing our studies in evolutionary and ecological contexts, in particular by examining the contribution of epigenetic processes in diatoms, our work will furthermore provide insights into how the environment selects for fitness in phytoplankton."
Summary
"Diatoms are the most successful group of eukaryotic phytoplankton in the modern ocean. Recently completed whole genome sequences have revealed a wealth of information about the evolutionary origins and metabolic adaptations that may have led to their ecological success. A major finding is that they have acquired genes both from their endosymbiotic ancestors and by horizontal gene transfer from marine bacteria. This unique melting pot of genes encodes novel and largely unexplored capacities for metabolic management. The project will address the current gap in knowledge about the physiological functions of diatom gene products and about the evolutionary mechanisms that have led to diatom success in contemporary oceans. We will exploit genome-enabled approaches to pioneer new research topics addressing:
1. How has diatom evolution enabled interactions between chloroplasts and mitochondria that have provided diatoms with physiological and metabolic innovations?
2. What are the relative contributions of DNA sequence variation and epigenetic processes in diatom adaptive dynamics?
By combining these questions, we will uniquely be able to identify sentinel genes that have driven major physiological and metabolic innovations in diatoms, and will explore the mechanisms that have selected and molded them during diatom evolution. We will focus our studies largely on diatom responses to nutrients, in particular nitrate and iron, and will exploit the advantages of Phaeodactylum tricornutum as a model diatom species for reverse genetics. The proposed studies will revisit textbook understanding of photosynthesis and nitrogen metabolism, and will refine hypotheses about why diatoms dominate in contemporary ocean settings. By placing our studies in evolutionary and ecological contexts, in particular by examining the contribution of epigenetic processes in diatoms, our work will furthermore provide insights into how the environment selects for fitness in phytoplankton."
Max ERC Funding
2 423 320 €
Duration
Start date: 2012-06-01, End date: 2017-05-31
Project acronym DICIG
Project Dynamic Interplay between Eukaryotic Chromosomes: Impact on Genome Stability
Researcher (PI) Romain Nicolas André Koszul
Host Institution (HI) INSTITUT PASTEUR
Call Details Starting Grant (StG), LS2, ERC-2010-StG_20091118
Summary The structure and role of the DNA molecule raise fascinating questions regarding its dynamics, i.e. not only the tri-dimensional reorganisation associated with functional events at short time-scale, but also the structural changes, i.e. rearrangements, that occur in the chromosome over generations. It is increasingly obvious that the physical properties of both the chromosomes and their environment the nucleoplasm, the nuclear periphery, cytoskeleton, etc. are playing important roles in the dynamic changes observed. For instance, we recently showed that chromosome movements during mid-prophase of meiosis in budding yeast result from a trans-acting force generated at the level of the global cytoskeleton network, suggesting that extranuclear mechanical trans-acting signals could also regulate chromosomal metabolism in other ways. Our objectives are to make important contributions to the understanding of the mechanical and functional interplay between the cytoskeleton, the nuclear periphery, and chromosomes through in vitro and in vivo interdisciplinary approaches. We will investigate three questions of fundamental importance: i) the potential transmission and function of mechanical forces from the cytoskeleton to chromatin during interphase, ii) the physical principles that govern chromosome reorganization under mechanical force in vitro, and iii) the global chromatin dynamics during the fundamental S phase and its impact on genome stability. We will use a combination of high-resolution imaging, micromanipulation, and high-throughput molecular techniques (chromosome conformation capture and ChIP-Seq) to reach our goals. Most of these studies will be performed in budding yeast, but will have repercussions in our understanding of higher eukaryotes metabolism.
Summary
The structure and role of the DNA molecule raise fascinating questions regarding its dynamics, i.e. not only the tri-dimensional reorganisation associated with functional events at short time-scale, but also the structural changes, i.e. rearrangements, that occur in the chromosome over generations. It is increasingly obvious that the physical properties of both the chromosomes and their environment the nucleoplasm, the nuclear periphery, cytoskeleton, etc. are playing important roles in the dynamic changes observed. For instance, we recently showed that chromosome movements during mid-prophase of meiosis in budding yeast result from a trans-acting force generated at the level of the global cytoskeleton network, suggesting that extranuclear mechanical trans-acting signals could also regulate chromosomal metabolism in other ways. Our objectives are to make important contributions to the understanding of the mechanical and functional interplay between the cytoskeleton, the nuclear periphery, and chromosomes through in vitro and in vivo interdisciplinary approaches. We will investigate three questions of fundamental importance: i) the potential transmission and function of mechanical forces from the cytoskeleton to chromatin during interphase, ii) the physical principles that govern chromosome reorganization under mechanical force in vitro, and iii) the global chromatin dynamics during the fundamental S phase and its impact on genome stability. We will use a combination of high-resolution imaging, micromanipulation, and high-throughput molecular techniques (chromosome conformation capture and ChIP-Seq) to reach our goals. Most of these studies will be performed in budding yeast, but will have repercussions in our understanding of higher eukaryotes metabolism.
Max ERC Funding
1 497 000 €
Duration
Start date: 2011-06-01, End date: 2017-05-31
Project acronym DMR-CODE
Project Decoding the Mammalian transcriptional Regulatory code in development and stimulatory responses
Researcher (PI) Ido Amit
Host Institution (HI) WEIZMANN INSTITUTE OF SCIENCE
Call Details Starting Grant (StG), LS2, ERC-2012-StG_20111109
Summary Transcription factors (TF) regulate genome function by controlling gene expression. Comprehensive characterization of the in vivo binding of TF to the DNA in relevant primary models is a critical step towards a global understanding of the human genome. Recent advances in high-throughput genomic technologies provide an extraordinary opportunity to develop and apply systematic approaches to learn the underline principles and mechanisms of mammalian transcriptional networks. The premise of this proposal is that a tractable set of rules govern how cells commit to a specific cell type or respond to the environment, and that these rules are coded in regulatory elements in the genome. Currently our understanding of the mammalian regulatory code is hampered by the difficulty of directly measuring in vivo binding of large numbers of TFs to DNA across multiple primary cell types and their natural response to physiological stimuli.
Here, we overcome this bottleneck by systematically exploring the genomic binding network of 1. All relevant TFs of key hematopoietic cells in both steady state and under relevant stimuli. 2. Follow the changes in TF networks as cells differentiate 3. Use these models to engineer cell states and responses. To achieve these goals, we developed a new method for automated high throughput ChIP coupled to sequencing (HT-ChIP-Seq). We used this method to measure binding of 40 TFs in 4 time points following stimulation of dendritic cells with pathogen components. We find that TFs vary substantially in their binding dynamics, genomic localization, number of binding events, and degree of interaction with other TFs. The analysis of this data suggests that the TF network is hierarchically organized, and composed of different types of TFs, cell differentiation factors, factors that prime for gene induction, and factors that bind more specifically and dynamically. This proposal revisits and challenges the current understanding of the mammalian regulatory code.
Summary
Transcription factors (TF) regulate genome function by controlling gene expression. Comprehensive characterization of the in vivo binding of TF to the DNA in relevant primary models is a critical step towards a global understanding of the human genome. Recent advances in high-throughput genomic technologies provide an extraordinary opportunity to develop and apply systematic approaches to learn the underline principles and mechanisms of mammalian transcriptional networks. The premise of this proposal is that a tractable set of rules govern how cells commit to a specific cell type or respond to the environment, and that these rules are coded in regulatory elements in the genome. Currently our understanding of the mammalian regulatory code is hampered by the difficulty of directly measuring in vivo binding of large numbers of TFs to DNA across multiple primary cell types and their natural response to physiological stimuli.
Here, we overcome this bottleneck by systematically exploring the genomic binding network of 1. All relevant TFs of key hematopoietic cells in both steady state and under relevant stimuli. 2. Follow the changes in TF networks as cells differentiate 3. Use these models to engineer cell states and responses. To achieve these goals, we developed a new method for automated high throughput ChIP coupled to sequencing (HT-ChIP-Seq). We used this method to measure binding of 40 TFs in 4 time points following stimulation of dendritic cells with pathogen components. We find that TFs vary substantially in their binding dynamics, genomic localization, number of binding events, and degree of interaction with other TFs. The analysis of this data suggests that the TF network is hierarchically organized, and composed of different types of TFs, cell differentiation factors, factors that prime for gene induction, and factors that bind more specifically and dynamically. This proposal revisits and challenges the current understanding of the mammalian regulatory code.
Max ERC Funding
1 500 000 €
Duration
Start date: 2012-10-01, End date: 2017-09-30
Project acronym DOGPSYCH
Project Canine models of human psychiatric disease: identifying novel anxiety genes with the help of man's best friend
Researcher (PI) Hannes Tapani Lohi
Host Institution (HI) HELSINGIN YLIOPISTO
Call Details Starting Grant (StG), LS2, ERC-2010-StG_20091118
Summary Anxiety disorders include different forms of pathological fear and anxiety and rank among the most common health concerns in human medicine. Millions of people become affected every year, and many of them do not respond to treatments. Anxiety disorders are heritable, but genetically complex. As a result, traditional gene mapping methods in the human population with prominent locus and allelic heterogeneity have not succeeded. Similarly, rodents have provided some insights into the circuitry of anxiety, but naturally occurring versions do not exist and gene deletion studies have not provided adequate models. To break through and identify new anxiety genes, I propose a novel and unique approach that resorts to man s best friend, dog. Taking advantage of the exaggerated genetic homogeneity characteristic of purebred dogs, recent genomics tools and the existence of naturally occurring heritable behaviour disorders in dogs can remedy the current lack of a suitable animal model of human psychiatric disorders. I propose to collect and perform a genome-wide association study in four breed-specific anxiety traits in dogs representing the three major forms of human anxiety: compulsive pacing and tail-chasing, noise phobia, and shyness corresponding to human OCD, panic disorder and social phobia, respectively. Canine anxiety disorders respond to human medications and other phenomenological studies suggest a share biological mechanism in both species. The proposed research has the potential to discover new genetic risk factors, which eventually will shed light on the biological basis of common neuropsychiatric disorders in both dog and human, provide insight into etiological mechanisms, enable identification of individuals at high-risk for adverse health outcomes, and facilitate development of tailored treatments.
Summary
Anxiety disorders include different forms of pathological fear and anxiety and rank among the most common health concerns in human medicine. Millions of people become affected every year, and many of them do not respond to treatments. Anxiety disorders are heritable, but genetically complex. As a result, traditional gene mapping methods in the human population with prominent locus and allelic heterogeneity have not succeeded. Similarly, rodents have provided some insights into the circuitry of anxiety, but naturally occurring versions do not exist and gene deletion studies have not provided adequate models. To break through and identify new anxiety genes, I propose a novel and unique approach that resorts to man s best friend, dog. Taking advantage of the exaggerated genetic homogeneity characteristic of purebred dogs, recent genomics tools and the existence of naturally occurring heritable behaviour disorders in dogs can remedy the current lack of a suitable animal model of human psychiatric disorders. I propose to collect and perform a genome-wide association study in four breed-specific anxiety traits in dogs representing the three major forms of human anxiety: compulsive pacing and tail-chasing, noise phobia, and shyness corresponding to human OCD, panic disorder and social phobia, respectively. Canine anxiety disorders respond to human medications and other phenomenological studies suggest a share biological mechanism in both species. The proposed research has the potential to discover new genetic risk factors, which eventually will shed light on the biological basis of common neuropsychiatric disorders in both dog and human, provide insight into etiological mechanisms, enable identification of individuals at high-risk for adverse health outcomes, and facilitate development of tailored treatments.
Max ERC Funding
1 381 807 €
Duration
Start date: 2010-10-01, End date: 2015-09-30
Project acronym DOUBLE-UP
Project The importance of gene and genome duplications for natural and artificial organism populations
Researcher (PI) Yves Eddy Philomena Van De Peer
Host Institution (HI) VIB VZW
Call Details Advanced Grant (AdG), LS2, ERC-2012-ADG_20120314
Summary The long-term establishment of ancient organisms that have undergone whole genome duplications has been exceedingly rare. On the other hand, tens of thousands of now-living species are polyploid and contain multiple copies of their genome. The paucity of ancient genome duplications and the existence of so many species that are currently polyploid provide an interesting and fascinating enigma. A question that remains is whether these older genome duplications have survived by coincidence or because they did occur at very specific times, for instance during major ecological upheavals and periods of extinction. It has indeed been proposed that chromosome doubling conveys greater stress tolerance by fostering slower development, delayed reproduction and longer life span. Furthermore, polyploids have also been considered to have greater ability to colonize new or disturbed habitats. If polyploidy allowed many plant lineages to survive and adapt during global changes, as suggested, we might wonder whether polyploidy will confer a similar advantage in the current period of global warming and general ecological pressure caused by the human race. Given predictions that species extinction is now occurring at as high rates as during previous mass extinctions, will the presumed extra adaptability of polyploid plants mean they will become the dominant species? In the current proposal, we hope to address these questions at different levels through 1) the analysis of whole plant genome sequence data and 2) the in silico modelling of artificial gene regulatory networks to mimic the genomic consequences of genome doubling and how this may affect network structure and dosage balance. Furthermore, we aim at using simulated robotic models running on artificial gene regulatory networks in complex environments to evaluate how both natural and artificial organism populations can potentially benefit from gene and genome duplications for adaptation, survival, and evolution in general.
Summary
The long-term establishment of ancient organisms that have undergone whole genome duplications has been exceedingly rare. On the other hand, tens of thousands of now-living species are polyploid and contain multiple copies of their genome. The paucity of ancient genome duplications and the existence of so many species that are currently polyploid provide an interesting and fascinating enigma. A question that remains is whether these older genome duplications have survived by coincidence or because they did occur at very specific times, for instance during major ecological upheavals and periods of extinction. It has indeed been proposed that chromosome doubling conveys greater stress tolerance by fostering slower development, delayed reproduction and longer life span. Furthermore, polyploids have also been considered to have greater ability to colonize new or disturbed habitats. If polyploidy allowed many plant lineages to survive and adapt during global changes, as suggested, we might wonder whether polyploidy will confer a similar advantage in the current period of global warming and general ecological pressure caused by the human race. Given predictions that species extinction is now occurring at as high rates as during previous mass extinctions, will the presumed extra adaptability of polyploid plants mean they will become the dominant species? In the current proposal, we hope to address these questions at different levels through 1) the analysis of whole plant genome sequence data and 2) the in silico modelling of artificial gene regulatory networks to mimic the genomic consequences of genome doubling and how this may affect network structure and dosage balance. Furthermore, we aim at using simulated robotic models running on artificial gene regulatory networks in complex environments to evaluate how both natural and artificial organism populations can potentially benefit from gene and genome duplications for adaptation, survival, and evolution in general.
Max ERC Funding
2 217 525 €
Duration
Start date: 2013-10-01, End date: 2018-09-30
Project acronym DRUGPROFILBIND
Project Chemogenomic profiling of drug-protein binding by shape, enthalpy/entropy and interaction kinetics
Researcher (PI) Gerhard Friedrich Klebe
Host Institution (HI) PHILIPPS UNIVERSITAET MARBURG
Call Details Advanced Grant (AdG), LS2, ERC-2010-AdG_20100317
Summary Once a new drug target is discovered, screening techniques are applied to detect prospective hits. However, which hit should be taken to the next level of development? This decision is most crucial as it entails huge financial commitments of the subsequent drug optimization. In consequence drugs are only developed against diseases that promise short-term profit. Chemogenomic profiling allows to compile parameters characterizing binding of drug candidates that achieve optimal interference with protein function. Membrane proteins demand different properties than viral ones. Either high isoform selectivity, promiscuous family-wide binding or efficient resistance tolerance is desired. This calls for very different ligand binding characteristics, requiring either enthalpy-/entropy-driven binding, rigid shape complementarity or pronounced residual mobility at the binding site. Interaction kinetics determine on/off-rates and the time a drug spends with its target. Their correct adjustment is essential for drug efficacy. At present chemogenomic binding parameters are rarely available and their correlation with the required target properties is hardly understood. We want to compile a knowledge base from congeneric protein-ligand series to correlate structural, thermodynamic, interaction-kinetic and dynamic behaviour to predict the qualities a lead must meet to optimally address a target. Our studies involve crystal structure analyses, microcalorimetry, molecular dynamics simulations, site-directed mutagenesis and interaction kinetics. This provides a comprehensive picture to productively change our current understanding of drug-protein binding to move from a current trial-and-error to a more efficient rational approach. It provides the opportunity to also consider orphan drugs and address neglected diseases.
Summary
Once a new drug target is discovered, screening techniques are applied to detect prospective hits. However, which hit should be taken to the next level of development? This decision is most crucial as it entails huge financial commitments of the subsequent drug optimization. In consequence drugs are only developed against diseases that promise short-term profit. Chemogenomic profiling allows to compile parameters characterizing binding of drug candidates that achieve optimal interference with protein function. Membrane proteins demand different properties than viral ones. Either high isoform selectivity, promiscuous family-wide binding or efficient resistance tolerance is desired. This calls for very different ligand binding characteristics, requiring either enthalpy-/entropy-driven binding, rigid shape complementarity or pronounced residual mobility at the binding site. Interaction kinetics determine on/off-rates and the time a drug spends with its target. Their correct adjustment is essential for drug efficacy. At present chemogenomic binding parameters are rarely available and their correlation with the required target properties is hardly understood. We want to compile a knowledge base from congeneric protein-ligand series to correlate structural, thermodynamic, interaction-kinetic and dynamic behaviour to predict the qualities a lead must meet to optimally address a target. Our studies involve crystal structure analyses, microcalorimetry, molecular dynamics simulations, site-directed mutagenesis and interaction kinetics. This provides a comprehensive picture to productively change our current understanding of drug-protein binding to move from a current trial-and-error to a more efficient rational approach. It provides the opportunity to also consider orphan drugs and address neglected diseases.
Max ERC Funding
1 754 615 €
Duration
Start date: 2011-05-01, End date: 2016-04-30
Project acronym DSBRECA
Project Relevance of double strand break repair pathway choice in human disease and cancer
Researcher (PI) Pablo Huertas Sanchez
Host Institution (HI) UNIVERSIDAD DE SEVILLA
Call Details Starting Grant (StG), LS2, ERC-2011-StG_20101109
Summary "Double strand breaks (DSBs) repair is essential for normal development. While the complete inability to repair DSBs leads to embryonic lethality and cell death, mutations that hamper this repair cause genetically inherited syndromes, with or without cancer predisposition. The phenotypes associated with these syndromes are extremely varied, and can include growth and mental retardation, ataxia, skeletal abnormalities, immunodeficiency, premature aging, etc. Moreover, DSBs play an extremely relevant role in the biology of cancer. Alterations in the DSBs repair pathways facilitate tumour progression and are selected early on during cancer development. On the other hand, DSBs are the molecular base of radiotherapies and chemotherapies. This double role of DSBs in both, the genesis and treatment of cancer makes the understanding of the mechanisms that control their repair of capital importance in cancer research.
DSBs are repaired by two major mechanisms that compete for the same substrate. Both ends of the DSB can be simple re-joined with little or no processing, a mechanism known as non-homologous end-joining. On the other hand, DSBs can be processed and engaged in a more complex repair pathway called homologous recombination. This pathway uses the information present in a homologue sequence. The balance between these two pathways is exquisitely controlled and its alteration leads to the appearance of chromosomal abnormalities and contribute to the diseases aforementioned. However, and despite its importance, the network controlling the choice between both is poorly understood.
Here, we propose a series of research lines designed to investigate how the choice between both DSBs repair pathways is made, its relevance for cellular and organismal survival and disease, and its potential as a therapeutic target for the treatment of cancer and some genetically inherited disorders."
Summary
"Double strand breaks (DSBs) repair is essential for normal development. While the complete inability to repair DSBs leads to embryonic lethality and cell death, mutations that hamper this repair cause genetically inherited syndromes, with or without cancer predisposition. The phenotypes associated with these syndromes are extremely varied, and can include growth and mental retardation, ataxia, skeletal abnormalities, immunodeficiency, premature aging, etc. Moreover, DSBs play an extremely relevant role in the biology of cancer. Alterations in the DSBs repair pathways facilitate tumour progression and are selected early on during cancer development. On the other hand, DSBs are the molecular base of radiotherapies and chemotherapies. This double role of DSBs in both, the genesis and treatment of cancer makes the understanding of the mechanisms that control their repair of capital importance in cancer research.
DSBs are repaired by two major mechanisms that compete for the same substrate. Both ends of the DSB can be simple re-joined with little or no processing, a mechanism known as non-homologous end-joining. On the other hand, DSBs can be processed and engaged in a more complex repair pathway called homologous recombination. This pathway uses the information present in a homologue sequence. The balance between these two pathways is exquisitely controlled and its alteration leads to the appearance of chromosomal abnormalities and contribute to the diseases aforementioned. However, and despite its importance, the network controlling the choice between both is poorly understood.
Here, we propose a series of research lines designed to investigate how the choice between both DSBs repair pathways is made, its relevance for cellular and organismal survival and disease, and its potential as a therapeutic target for the treatment of cancer and some genetically inherited disorders."
Max ERC Funding
1 416 866 €
Duration
Start date: 2012-01-01, End date: 2016-12-31
Project acronym DSBREPAIR
Project Developmental and Genetic Analysis of DNA Double-Strand Break Repair
Researcher (PI) Marcel Tijsterman
Host Institution (HI) ACADEMISCH ZIEKENHUIS LEIDEN
Call Details Starting Grant (StG), LS2, ERC-2007-StG
Summary The DNA within our cells is constantly being damaged by both environmental and endogenous agents; of the many forms of DNA damage, the DNA double-strand break (DSB) is considered to be most dangerous. Correct processing of DSBs is not only essential for maintaining genomic integrity but is also required in specific biological processes, such as meiotic recombination and V(D)J recombination, in which DNA breaks are deliberately generated. In animals, defects in the proper response to DSBs can thus have different outcomes: cancer predisposition, embryonic lethality, or compromised immunity. Many genes that play a role in the processing of DSBs have been identified over the past decades, mainly by cloning genes that are responsible for specific human genomic instability or immune deficiency syndromes, and by genetic approaches using unicellular eukaryotes and rodent cell lines. It is, however, evident that many components required in higher eukaryotes are not yet known and the identification of those will be a major challenge for future research. Here, we will for the first time systematically test all genes encoded by an animals genome directly for their involvement in the cellular response to DSB in both somatic and germline tissues: we will use our recently developed transgenic animal models (C. elegans) that visualizes repair of a single localized genomic DNA break in genome wide RNAi screenings to identify (and then characterize) the complement of genes that are required to keep our genome stable, and when mutated can predispose humans to cancer. In parallel, we will study the cellular response to single DNA breaks that are artificially generated during different stages of gametogenesis, as well as address the developmental consequences of DSB induction during the earliest stages of embryonic development – an almost completely unexplored area in the field of genome instability and DNA damage responses.
Summary
The DNA within our cells is constantly being damaged by both environmental and endogenous agents; of the many forms of DNA damage, the DNA double-strand break (DSB) is considered to be most dangerous. Correct processing of DSBs is not only essential for maintaining genomic integrity but is also required in specific biological processes, such as meiotic recombination and V(D)J recombination, in which DNA breaks are deliberately generated. In animals, defects in the proper response to DSBs can thus have different outcomes: cancer predisposition, embryonic lethality, or compromised immunity. Many genes that play a role in the processing of DSBs have been identified over the past decades, mainly by cloning genes that are responsible for specific human genomic instability or immune deficiency syndromes, and by genetic approaches using unicellular eukaryotes and rodent cell lines. It is, however, evident that many components required in higher eukaryotes are not yet known and the identification of those will be a major challenge for future research. Here, we will for the first time systematically test all genes encoded by an animals genome directly for their involvement in the cellular response to DSB in both somatic and germline tissues: we will use our recently developed transgenic animal models (C. elegans) that visualizes repair of a single localized genomic DNA break in genome wide RNAi screenings to identify (and then characterize) the complement of genes that are required to keep our genome stable, and when mutated can predispose humans to cancer. In parallel, we will study the cellular response to single DNA breaks that are artificially generated during different stages of gametogenesis, as well as address the developmental consequences of DSB induction during the earliest stages of embryonic development – an almost completely unexplored area in the field of genome instability and DNA damage responses.
Max ERC Funding
1 060 000 €
Duration
Start date: 2008-05-01, End date: 2014-04-30
