Project acronym CANCERLINC
Project Functional and Mecahnistic Roles of Large Intergenic Non-coding RNAs in Cancer
Researcher (PI) Maite Huarte Martinez
Host Institution (HI) FUNDACION PARA LA INVESTIGACION MEDICA APLICADA FIMA
Call Details Starting Grant (StG), LS1, ERC-2011-StG_20101109
Summary Mammalian cells express thousands of RNA molecules structurally similar to protein coding genes –they are large, spliced, poly-adenylated, transcribed by RNA Pol II, with conserved promoters and exonic structures –however lack coding capacity. Although thousands exist, only few of these large intergenic non-coding RNAs (lincRNAs) have been characterized. The few that have, show powerful biological roles as regulators of gene expression by diverse epigenetic and non-epigenetic mechanisms. Significantly, their expression patterns suggest that some lincRNAs are involved in cellular pathways critical in cancer, like the p53 pathway. I explored this association demonstrating that p53 induces the expression of many lincRNAs. One them, named lincRNA-p21, is directly induced by p53 to play a critical role in the p53 response, being required for the global repression of genes that interfere with p53 induction of apoptosis. My results, together with the emerging evidence in the field, suggest that lincRNAs may play key roles in numerous tumor-suppressor and oncogenic pathways, representing an unknown paradigm in cellular transformation. However, their mechanisms of function and biological roles remain largely unexplored.
The goal of this project is to decipher the functional and biological roles of lincRNAs in the context of oncogenic pathways to better understand the cellular mechanisms of gene regulation at the epigenetic and non-epigenetic levels, and be able to implement lincRNA use for diagnostics and therapies. In order to accomplish these goals we will integrate molecular and cell biology techniques with functional genomics approaches and in vivo studies. Importantly, the profiling of patient samples will reveal the relevance of our findings in human disease. Together, the functional study of lincRNAs will not only be crucial for developing improved diagnostics and therapies, but also will help a better understanding of the mechanisms that govern cellular network.
Summary
Mammalian cells express thousands of RNA molecules structurally similar to protein coding genes –they are large, spliced, poly-adenylated, transcribed by RNA Pol II, with conserved promoters and exonic structures –however lack coding capacity. Although thousands exist, only few of these large intergenic non-coding RNAs (lincRNAs) have been characterized. The few that have, show powerful biological roles as regulators of gene expression by diverse epigenetic and non-epigenetic mechanisms. Significantly, their expression patterns suggest that some lincRNAs are involved in cellular pathways critical in cancer, like the p53 pathway. I explored this association demonstrating that p53 induces the expression of many lincRNAs. One them, named lincRNA-p21, is directly induced by p53 to play a critical role in the p53 response, being required for the global repression of genes that interfere with p53 induction of apoptosis. My results, together with the emerging evidence in the field, suggest that lincRNAs may play key roles in numerous tumor-suppressor and oncogenic pathways, representing an unknown paradigm in cellular transformation. However, their mechanisms of function and biological roles remain largely unexplored.
The goal of this project is to decipher the functional and biological roles of lincRNAs in the context of oncogenic pathways to better understand the cellular mechanisms of gene regulation at the epigenetic and non-epigenetic levels, and be able to implement lincRNA use for diagnostics and therapies. In order to accomplish these goals we will integrate molecular and cell biology techniques with functional genomics approaches and in vivo studies. Importantly, the profiling of patient samples will reveal the relevance of our findings in human disease. Together, the functional study of lincRNAs will not only be crucial for developing improved diagnostics and therapies, but also will help a better understanding of the mechanisms that govern cellular network.
Max ERC Funding
1 500 000 €
Duration
Start date: 2012-01-01, End date: 2017-12-31
Project acronym DNATRAFFIC
Project DNA traffic during bacterial cell division
Researcher (PI) François-Xavier Andre Fernand Barre
Host Institution (HI) CENTRE NATIONAL DE LA RECHERCHE SCIENTIFIQUE CNRS
Call Details Starting Grant (StG), LS1, ERC-2011-StG_20101109
Summary The molecular mechanisms that serve to couple DNA replication, chromosome segregation and cell division are largely unknown in bacteria. This led a considerable interest to the study of Escherichia coli FtsK, an essential cell division protein that assembles into DNA-pumps to transfer chromosomal DNA between the two daughter cell compartments during septation. Indeed, our recent work suggests that FtsK might regulate the late stages of septation to ensure DNA is fully cleared from the septum before it is allowed to close. This would be the first example of a cell cycle checkpoint in bacteria.
FtsK-mediated DNA transfer is required in 15% of the cells at each generation in E. coli, in which it serves to promote the resolution of topological problems arising from the circularity of the chromosome by Xer recombination. However, the FtsK checkpoint could be a more general feature of the bacterial cell cycle since FtsK is highly conserved among eubacteria, including species that do not possess a Xer system. Indeed, preliminary results from the lab indicate that DNA transfer by FtsK is required independently of Xer recombination in Vibrio cholerae.
To confirm the existence and the generality of the FtsK checkpoint in bacteria, we will determine the different situations that lead to a requirement for FtsK-mediated DNA transfer by studying chromosome segregation and cell division in V. cholerae. In parallel, we will apply new fluorescent microscopy tools to follow the progression of cell division and chromosome segregation in single live bacterial cells. PALM will notably serve to probe the structure of the FtsK DNA-pumps at a high spatial resolution, FRET will be used to determine their timing of assembly and their interactions with the other cell division proteins, and TIRF will serve to follow in real time their activity with respect to the progression of chromosome dimer resolution, chromosome segregation, and septum closure.
Summary
The molecular mechanisms that serve to couple DNA replication, chromosome segregation and cell division are largely unknown in bacteria. This led a considerable interest to the study of Escherichia coli FtsK, an essential cell division protein that assembles into DNA-pumps to transfer chromosomal DNA between the two daughter cell compartments during septation. Indeed, our recent work suggests that FtsK might regulate the late stages of septation to ensure DNA is fully cleared from the septum before it is allowed to close. This would be the first example of a cell cycle checkpoint in bacteria.
FtsK-mediated DNA transfer is required in 15% of the cells at each generation in E. coli, in which it serves to promote the resolution of topological problems arising from the circularity of the chromosome by Xer recombination. However, the FtsK checkpoint could be a more general feature of the bacterial cell cycle since FtsK is highly conserved among eubacteria, including species that do not possess a Xer system. Indeed, preliminary results from the lab indicate that DNA transfer by FtsK is required independently of Xer recombination in Vibrio cholerae.
To confirm the existence and the generality of the FtsK checkpoint in bacteria, we will determine the different situations that lead to a requirement for FtsK-mediated DNA transfer by studying chromosome segregation and cell division in V. cholerae. In parallel, we will apply new fluorescent microscopy tools to follow the progression of cell division and chromosome segregation in single live bacterial cells. PALM will notably serve to probe the structure of the FtsK DNA-pumps at a high spatial resolution, FRET will be used to determine their timing of assembly and their interactions with the other cell division proteins, and TIRF will serve to follow in real time their activity with respect to the progression of chromosome dimer resolution, chromosome segregation, and septum closure.
Max ERC Funding
1 565 938 €
Duration
Start date: 2012-02-01, End date: 2017-01-31
Project acronym DYMOCHRO
Project Dynamics of modified chromatin domains
Researcher (PI) Fabian, Roman ERDEL
Host Institution (HI) CENTRE NATIONAL DE LA RECHERCHE SCIENTIFIQUE CNRS
Call Details Starting Grant (StG), LS1, ERC-2018-STG
Summary Cellular identity is defined by complex patterns of DNA and histone modifications, which partition our chromosomes and determine how cells interpret the genetic information. For cells to remember who they are, these modifications have to be tightly regulated over time and through cell division. Loss of cellular identity promotes different types of disease including neurological disorders and cancer.
Histone modifications can spread along chromatin and can be transmitted through cell division, giving rise to chromatin position effects and cellular memory. However, the underlying molecular mechanisms are not understood. In particular, we do not know how the size and stability of modified domains is controlled, and we currently lack techniques to study these processes in real-time.
Here, I propose to develop the single-molecule ‘chromatin curtains’ platform to directly visualize spreading and maintenance of histone methylation in a reconstituted system and to compare the resulting domains to those found on individual chromatin fibers isolated from cells. In a complementary approach, I will devise and set up a tunable synthetic circuit that installs and reinforces orthogonal epigenetic modifications in living cells to define the functional modules that are necessary and sufficient for chromatin position effects and cellular memory.
My project combines molecular biophysics with synthetic biology to elucidate the fundamental principles that govern the dynamics of histone modifications to establish and preserve cellular identity. The chromatin curtains platform I will develop complements sequencing-based methods and will make it for the first time possible to directly assess the dynamics of histone modification patterns on single chromatin fibers under native conditions. I anticipate that the insights gained in my project will aid in the design of future strategies to control histone modifications in disease.
Summary
Cellular identity is defined by complex patterns of DNA and histone modifications, which partition our chromosomes and determine how cells interpret the genetic information. For cells to remember who they are, these modifications have to be tightly regulated over time and through cell division. Loss of cellular identity promotes different types of disease including neurological disorders and cancer.
Histone modifications can spread along chromatin and can be transmitted through cell division, giving rise to chromatin position effects and cellular memory. However, the underlying molecular mechanisms are not understood. In particular, we do not know how the size and stability of modified domains is controlled, and we currently lack techniques to study these processes in real-time.
Here, I propose to develop the single-molecule ‘chromatin curtains’ platform to directly visualize spreading and maintenance of histone methylation in a reconstituted system and to compare the resulting domains to those found on individual chromatin fibers isolated from cells. In a complementary approach, I will devise and set up a tunable synthetic circuit that installs and reinforces orthogonal epigenetic modifications in living cells to define the functional modules that are necessary and sufficient for chromatin position effects and cellular memory.
My project combines molecular biophysics with synthetic biology to elucidate the fundamental principles that govern the dynamics of histone modifications to establish and preserve cellular identity. The chromatin curtains platform I will develop complements sequencing-based methods and will make it for the first time possible to directly assess the dynamics of histone modification patterns on single chromatin fibers under native conditions. I anticipate that the insights gained in my project will aid in the design of future strategies to control histone modifications in disease.
Max ERC Funding
1 447 860 €
Duration
Start date: 2019-07-01, End date: 2024-06-30
Project acronym MOLSTRUCTTRANSFO
Project Molecular and Structural Biology of Bacterial Transformation
Researcher (PI) Rémi Fronzes
Host Institution (HI) INSTITUT PASTEUR
Call Details Starting Grant (StG), LS1, ERC-2011-StG_20101109
Summary A common form of gene transfer is the vertical gene transfer between one organism and its offspring during sexual reproduction. However, some organisms, such as bacteria, are able to acquire genetic material independently of sexual reproduction by horizontal gene transfer (HGT). Three mechanisms mediate HGT in bacteria: conjugation, transduction and natural transformation. HGT and the selective pressure exerted by the widespread use antibiotics (in medicine, veterinary medicine, agriculture, animal feeding, etc) are responsible for the rapid spread of antibiotic resistance genes among pathogenic bacteria.
In this proposal, we focus on bacterial transformation systems, also named competence systems. Natural transformation is the acquisition of naked DNA from the extracellular milieu. It is the only programmed process for generalized genetic exchange found in bacteria. This highly efficient and regulated process promotes bacterial genome plasticity and adaptive response of bacteria to changes in their environment. It is essential for bacterial survival and/or virulence and greatly limits efficiency of treatments or vaccine against some pathogenic bacteria.
The architecture and functioning of the membrane protein complexes mediating DNA transfer through the cell envelope during bacterial transformation remain elusive. We want to decipher the molecular mechanism of this transfer. To attain this goal, we will carry out structural biology studies (X-ray crystallography and high resolution electron microscopy) as well as functional and structure-function in vivo studies. We have the ambition to make major contributions to the understanding of bacterial transformation. Ultimately, we hope that our results will also help to find compounds that could block natural transformation in bacterial pathogens.
Summary
A common form of gene transfer is the vertical gene transfer between one organism and its offspring during sexual reproduction. However, some organisms, such as bacteria, are able to acquire genetic material independently of sexual reproduction by horizontal gene transfer (HGT). Three mechanisms mediate HGT in bacteria: conjugation, transduction and natural transformation. HGT and the selective pressure exerted by the widespread use antibiotics (in medicine, veterinary medicine, agriculture, animal feeding, etc) are responsible for the rapid spread of antibiotic resistance genes among pathogenic bacteria.
In this proposal, we focus on bacterial transformation systems, also named competence systems. Natural transformation is the acquisition of naked DNA from the extracellular milieu. It is the only programmed process for generalized genetic exchange found in bacteria. This highly efficient and regulated process promotes bacterial genome plasticity and adaptive response of bacteria to changes in their environment. It is essential for bacterial survival and/or virulence and greatly limits efficiency of treatments or vaccine against some pathogenic bacteria.
The architecture and functioning of the membrane protein complexes mediating DNA transfer through the cell envelope during bacterial transformation remain elusive. We want to decipher the molecular mechanism of this transfer. To attain this goal, we will carry out structural biology studies (X-ray crystallography and high resolution electron microscopy) as well as functional and structure-function in vivo studies. We have the ambition to make major contributions to the understanding of bacterial transformation. Ultimately, we hope that our results will also help to find compounds that could block natural transformation in bacterial pathogens.
Max ERC Funding
1 405 149 €
Duration
Start date: 2012-01-01, End date: 2016-12-31
Project acronym MultiMotif
Project Motif repeats in intrinsically disordered regions of the clathrin mediated endocytosis pathway
Researcher (PI) Sigrid MILLES
Host Institution (HI) CENTRE NATIONAL DE LA RECHERCHE SCIENTIFIQUE CNRS
Call Details Starting Grant (StG), LS1, ERC-2018-STG
Summary Linear motifs are short sequence stretches that occur in intrinsically disordered protein regions (IDRs) lacking stable secondary and tertiary structure, and mediate vital interactions within various biological systems. An exemplary system for the presence of IDRs and a high concentration of linear motifs is the clathrin mediated endocytosis machinery of the eukaryotic cell, where a complex interaction network of IDR-rich adaptor proteins enables both protein and lipid interactions. The molecular mechanism of such interactions, especially when multiple motifs act in concert, is however only poorly understood particularly since the dynamic and flexible nature of IDRs makes them a very difficult object to study. I aim to develop an integrative approach based on single molecule fluorescence and NMR spectroscopies to characterize the molecular principles of IDRs in clathrin mediated endocytosis. A systematic analysis of IDRs with different types of motifs and various interaction partners will not only shed light on the molecular functions of linear motifs within endocytosis, but also on how multiplicities of linear motifs may work in various biological processes in general. In vitro structural studies will be connected with single molecule imaging to relate molecular conformation with function within the cell.
Summary
Linear motifs are short sequence stretches that occur in intrinsically disordered protein regions (IDRs) lacking stable secondary and tertiary structure, and mediate vital interactions within various biological systems. An exemplary system for the presence of IDRs and a high concentration of linear motifs is the clathrin mediated endocytosis machinery of the eukaryotic cell, where a complex interaction network of IDR-rich adaptor proteins enables both protein and lipid interactions. The molecular mechanism of such interactions, especially when multiple motifs act in concert, is however only poorly understood particularly since the dynamic and flexible nature of IDRs makes them a very difficult object to study. I aim to develop an integrative approach based on single molecule fluorescence and NMR spectroscopies to characterize the molecular principles of IDRs in clathrin mediated endocytosis. A systematic analysis of IDRs with different types of motifs and various interaction partners will not only shed light on the molecular functions of linear motifs within endocytosis, but also on how multiplicities of linear motifs may work in various biological processes in general. In vitro structural studies will be connected with single molecule imaging to relate molecular conformation with function within the cell.
Max ERC Funding
1 599 809 €
Duration
Start date: 2019-02-01, End date: 2024-01-31
Project acronym NDOGS
Project Nuclear Dynamic, Organization and Genome Stability
Researcher (PI) Karine Marie Renée Dubrana
Host Institution (HI) COMMISSARIAT A L ENERGIE ATOMIQUE ET AUX ENERGIES ALTERNATIVES
Call Details Starting Grant (StG), LS1, ERC-2011-StG_20101109
Summary The eukaryotic genome is packaged into large-scale chromatin structures occupying distinct domains in the cell nucleus. Nuclear compartmentalization has recently been proposed to play an important role in genome stability but the molecular steps regulated remain to be defined. Focusing on Double strand breaks (DSBs) in response to which cells activate checkpoint and DNA repair pathways, we propose to characterize the spatial and temporal behavior of damaged chromatin and determine how this affects the maintenance of genome integrity. Currently, most studies concerning DSBs signaling and repair have been realized on asynchronous cell populations, which makes it difficult to precisely define the kinetics of events that occur at the cellular level. We thus propose to follow the nuclear localization and dynamics of an inducible DSB concomitantly with the kinetics of checkpoint activation and DNA repair at a single cell level and along the cell cycle. This will be performed using budding yeast as a model system enabling the combination of genetics, molecular biology and advanced live microscopy. We recently demonstrated that DSBs relocated to the nuclear periphery where they contact nuclear pores. This change in localization possibly regulates the choice of the repair pathway through steps that are controlled by post-translational modifications. This proposal aims at dissecting the molecular pathways defining the position of DSBs in the nucleus by performing genetic and proteomic screens, testing the functional consequence of nuclear position for checkpoint activation and DNA repair by driving the DSB to specific nuclear landmarks and, defining the dynamics of DNA damages in different repair contexts. Our project will identify new players in the DNA repair and checkpoint pathways and further our understanding of how the compartmentalization of damaged chromatin into the nucleus regulates these processes to insure the transmission of a stable genome.
Summary
The eukaryotic genome is packaged into large-scale chromatin structures occupying distinct domains in the cell nucleus. Nuclear compartmentalization has recently been proposed to play an important role in genome stability but the molecular steps regulated remain to be defined. Focusing on Double strand breaks (DSBs) in response to which cells activate checkpoint and DNA repair pathways, we propose to characterize the spatial and temporal behavior of damaged chromatin and determine how this affects the maintenance of genome integrity. Currently, most studies concerning DSBs signaling and repair have been realized on asynchronous cell populations, which makes it difficult to precisely define the kinetics of events that occur at the cellular level. We thus propose to follow the nuclear localization and dynamics of an inducible DSB concomitantly with the kinetics of checkpoint activation and DNA repair at a single cell level and along the cell cycle. This will be performed using budding yeast as a model system enabling the combination of genetics, molecular biology and advanced live microscopy. We recently demonstrated that DSBs relocated to the nuclear periphery where they contact nuclear pores. This change in localization possibly regulates the choice of the repair pathway through steps that are controlled by post-translational modifications. This proposal aims at dissecting the molecular pathways defining the position of DSBs in the nucleus by performing genetic and proteomic screens, testing the functional consequence of nuclear position for checkpoint activation and DNA repair by driving the DSB to specific nuclear landmarks and, defining the dynamics of DNA damages in different repair contexts. Our project will identify new players in the DNA repair and checkpoint pathways and further our understanding of how the compartmentalization of damaged chromatin into the nucleus regulates these processes to insure the transmission of a stable genome.
Max ERC Funding
1 499 863 €
Duration
Start date: 2012-02-01, End date: 2018-01-31
Project acronym NextGen IO
Project Exploiting the hypoxia response in T cells for Next-Generation Immuno-Oncology
Researcher (PI) Francisco de Asis PALAZON GARCIA
Host Institution (HI) ASOCIACION CENTRO DE INVESTIGACION COOPERATIVA EN BIOCIENCIAS
Call Details Starting Grant (StG), LS7, ERC-2018-STG
Summary NextGen_IO has a core focus on immuno-oncology, specifically on target discovery and drug development, to exploit several opportunities that the hypoxia pathway in T cells offers for the treatment of cancer. It is well recognised that the clinical response of immunotherapies depends on the ability of T-cells to mount an effective effector response, persist in treated patients and avoid exhaustion and toxicities. Several approaches to immunotherapy have shown promise in clinical trials, especially the use of immune checkpoint inhibitors and, more recently, autologous adoptive T-cell therapies. However, current state-of-the-art immunotherapies are only effective in a small fraction of patients, offering a medical need to be addressed in several cancer types. Importantly, the tumor microenvironment has specific features that impact the immune response, including decreased oxygenation, aberrant vascularization and altered nutrient availability; all these influence the success of immunotherapies. During the last 10 years, my research has been focused on elucidating the role of the oxygen sensing machinery in T cell function, and the link of hypoxia-driven metabolism and epigenetic modifications with T cell differentiation into effector and memory T cells within the context of cancer immunotherapy. The current proposal aims to exploit these previous findings with a multi-disciplinary strategy, to deliver several early-stage drug discovery outputs.
The main objectives are:
1. Development of a novel small molecule inhibitor to modulate the hypoxic response in T cells.
2. Therapeutic target discovery in T cells, focused on hypoxia-driven epigenetic modifications.
3. Development of hypoxia-inducible molecular switches for adoptive T cell therapy.
Successful completion of the project will allow me to further innovate and consolidate my position as a leader in this field, harness this pathway for therapeutic potential and explore potential combinatorial approaches.
Summary
NextGen_IO has a core focus on immuno-oncology, specifically on target discovery and drug development, to exploit several opportunities that the hypoxia pathway in T cells offers for the treatment of cancer. It is well recognised that the clinical response of immunotherapies depends on the ability of T-cells to mount an effective effector response, persist in treated patients and avoid exhaustion and toxicities. Several approaches to immunotherapy have shown promise in clinical trials, especially the use of immune checkpoint inhibitors and, more recently, autologous adoptive T-cell therapies. However, current state-of-the-art immunotherapies are only effective in a small fraction of patients, offering a medical need to be addressed in several cancer types. Importantly, the tumor microenvironment has specific features that impact the immune response, including decreased oxygenation, aberrant vascularization and altered nutrient availability; all these influence the success of immunotherapies. During the last 10 years, my research has been focused on elucidating the role of the oxygen sensing machinery in T cell function, and the link of hypoxia-driven metabolism and epigenetic modifications with T cell differentiation into effector and memory T cells within the context of cancer immunotherapy. The current proposal aims to exploit these previous findings with a multi-disciplinary strategy, to deliver several early-stage drug discovery outputs.
The main objectives are:
1. Development of a novel small molecule inhibitor to modulate the hypoxic response in T cells.
2. Therapeutic target discovery in T cells, focused on hypoxia-driven epigenetic modifications.
3. Development of hypoxia-inducible molecular switches for adoptive T cell therapy.
Successful completion of the project will allow me to further innovate and consolidate my position as a leader in this field, harness this pathway for therapeutic potential and explore potential combinatorial approaches.
Max ERC Funding
1 993 575 €
Duration
Start date: 2019-02-01, End date: 2024-01-31
Project acronym PATHOVIROME
Project Viral metagenomics of human pathologies with unknown etiology
Researcher (PI) Christelle Marie Desnues
Host Institution (HI) CENTRE NATIONAL DE LA RECHERCHE SCIENTIFIQUE CNRS
Call Details Starting Grant (StG), LS7, ERC-2009-StG
Summary While viral infections create an important threat for humanity, our knowledge of the viruses that infect humans is largely incomplete. So far, discovery of new viruses has been limited by the inability to propagate them in cell culture, the lack of serological cross-reactivity, or the absence of conserved genetic element to target by PCR. Thus, numerous acute and chronic diseases with unknown etiology are caused by yet unidentified viruses. Among the highest failure rates in determining the etiological cause of disease, pneumonia, encephalitis, and pericarditis are usually cited. In these cases, the search for unknown viruses is an urgent scientific task. We propose to identify new viruses, both indigenous and pathogenic, using metagenomics (shotgun Sanger sequencing and 454 pyrosequencing) of RNA and DNA from purified viral particles found in clinical samples of individuals presenting encephalitis, pneumonia, or pericarditis diseases without known etiology. Virus-centered bioinformatics methods will be developed to detect close as well as distant relatives of known viral species. Initial viral sequence similarity analysis will be followed by full viral genome reconstruction and phylogenetic analysis. The prevalence, abundance, and geographical distribution of newly identified viruses will then be determined using quantitative real-time PCR and RT-PCR on a 10-year collection of samples from extensively characterized patients.
Summary
While viral infections create an important threat for humanity, our knowledge of the viruses that infect humans is largely incomplete. So far, discovery of new viruses has been limited by the inability to propagate them in cell culture, the lack of serological cross-reactivity, or the absence of conserved genetic element to target by PCR. Thus, numerous acute and chronic diseases with unknown etiology are caused by yet unidentified viruses. Among the highest failure rates in determining the etiological cause of disease, pneumonia, encephalitis, and pericarditis are usually cited. In these cases, the search for unknown viruses is an urgent scientific task. We propose to identify new viruses, both indigenous and pathogenic, using metagenomics (shotgun Sanger sequencing and 454 pyrosequencing) of RNA and DNA from purified viral particles found in clinical samples of individuals presenting encephalitis, pneumonia, or pericarditis diseases without known etiology. Virus-centered bioinformatics methods will be developed to detect close as well as distant relatives of known viral species. Initial viral sequence similarity analysis will be followed by full viral genome reconstruction and phylogenetic analysis. The prevalence, abundance, and geographical distribution of newly identified viruses will then be determined using quantitative real-time PCR and RT-PCR on a 10-year collection of samples from extensively characterized patients.
Max ERC Funding
831 902 €
Duration
Start date: 2010-02-01, End date: 2014-01-31
Project acronym RETROGENOMICS
Project Mechanisms of retrotransposition in humans and consequences on cancer genomic plasticity
Researcher (PI) Gael Pierre Varam Cristofari
Host Institution (HI) INSTITUT NATIONAL DE LA SANTE ET DE LA RECHERCHE MEDICALE
Call Details Starting Grant (StG), LS1, ERC-2009-StG
Summary Retrotransposons are a class of highly repetitive sequences, which are very abundant in the human genome. They disperse by an RNA-based copy-and-paste mechanism, called retrotransposition. This process can drive profound genome rearrangements. Although generally silent, they are expressed in germ cells, in the early embryo, and in embryonic stem cells, which occasionally results in genetic diseases. Retrotransposons are also massively re-expressed in the large majority of cancers, but the importance and consequences of retrotransposition in human tumors have been poorly studied. Somatic retrotransposition is difficult to track in human tissue due to the highly repetitive and dispersed nature of these elements. Thus the questions we wish to address in this research proposal are the following: (i) What cellular pathways control retrotransposon copy number? This will be achieved by combining functional genomics and proteomics approaches to identify positive and negative regulators of retrotransposition in humans. (ii) What are the molecular mechanisms of retrotransposons replication? To answer this question, we will develop a cell-free assay that will contain the complete retrotransposition machinery. (iii) How retrotransposons participate in the normal and pathological remodeling of the human genome? To this purpose we are currently developing innovative approaches to track retrotransposition events in clinical samples, especially in tumor samples. Since LINE-1 elements (L1) are the most active and autonomous retroelements in our genome, we focus, at the moment, our investigations on this family. Understanding how the activity of retrotransposons is controlled will impact our knowledge of the mechanisms that lead to new genetic diseases or to cancer progression. Since mobile genetic elements are becoming important tools in insertional mutagenesis or gene-transfer technologies in mammals, our work should also help to improve their use in mammalian functional genomics.
Summary
Retrotransposons are a class of highly repetitive sequences, which are very abundant in the human genome. They disperse by an RNA-based copy-and-paste mechanism, called retrotransposition. This process can drive profound genome rearrangements. Although generally silent, they are expressed in germ cells, in the early embryo, and in embryonic stem cells, which occasionally results in genetic diseases. Retrotransposons are also massively re-expressed in the large majority of cancers, but the importance and consequences of retrotransposition in human tumors have been poorly studied. Somatic retrotransposition is difficult to track in human tissue due to the highly repetitive and dispersed nature of these elements. Thus the questions we wish to address in this research proposal are the following: (i) What cellular pathways control retrotransposon copy number? This will be achieved by combining functional genomics and proteomics approaches to identify positive and negative regulators of retrotransposition in humans. (ii) What are the molecular mechanisms of retrotransposons replication? To answer this question, we will develop a cell-free assay that will contain the complete retrotransposition machinery. (iii) How retrotransposons participate in the normal and pathological remodeling of the human genome? To this purpose we are currently developing innovative approaches to track retrotransposition events in clinical samples, especially in tumor samples. Since LINE-1 elements (L1) are the most active and autonomous retroelements in our genome, we focus, at the moment, our investigations on this family. Understanding how the activity of retrotransposons is controlled will impact our knowledge of the mechanisms that lead to new genetic diseases or to cancer progression. Since mobile genetic elements are becoming important tools in insertional mutagenesis or gene-transfer technologies in mammals, our work should also help to improve their use in mammalian functional genomics.
Max ERC Funding
1 874 000 €
Duration
Start date: 2010-01-01, End date: 2014-12-31
Project acronym TopSurgeons
Project Understanding the influence of human and organizational factors on surgeon performance to enhance patient outcomes: experimental evaluation of a customized coaching program
Researcher (PI) Antoine DUCLOS
Host Institution (HI) UNIVERSITE LYON 1 CLAUDE BERNARD
Call Details Starting Grant (StG), LS7, ERC-2018-STG
Summary Individual performance of surgeon is a core element of successful surgery that can vary greatly over career for poorly understood reasons. Solutions to optimize physical and mental condition of surgeon during operation have not been thoroughly explored so far, while this may represent basic foundation for delivering high quality surgery. This surgeon-centred outcome research pursues three successive goals: 1-Identifying the key determinants related to surgeon's human factor and operating room organization influencing his/her performance in terms of patient safety and care efficiency; 2-Developing a customized coaching program for surgeons based on the human and organizational factors previously discovered, which includes a charting system for individual parameters and surgical outcomes feedback, profiling of individual surgeon, and standardized modules of improvement; 3-Implementing and measuring the impact of this program on surgical outcomes of a randomized group of surgeons against a control group of non-exposed surgeons. Inspired from previous experiences in the aeronautic and sport arena to improve pilots and athletes performance, our approach will take place in real time at the point of care in close collaboration with front-line personnel. A particular attention will be paid to quantify the influence of several factors that may affect how the surgeon operates every day (physiological stress, sleep quality, physical activities, workload, team composition and unplanned events in operating room). Generated knowledge on these factors will be exploited for identifying deficiencies that, if corrected, could improve surgeon's functional capacity. Solutions to control these factors and achieve optimal outcomes will then be experimentally tested to establish evidence-based standards of surgical practice. Those standards will be adapted to each surgeon's needs and preferences, potentially leading to a certification model for surgeons complying with excellence criteria.
Summary
Individual performance of surgeon is a core element of successful surgery that can vary greatly over career for poorly understood reasons. Solutions to optimize physical and mental condition of surgeon during operation have not been thoroughly explored so far, while this may represent basic foundation for delivering high quality surgery. This surgeon-centred outcome research pursues three successive goals: 1-Identifying the key determinants related to surgeon's human factor and operating room organization influencing his/her performance in terms of patient safety and care efficiency; 2-Developing a customized coaching program for surgeons based on the human and organizational factors previously discovered, which includes a charting system for individual parameters and surgical outcomes feedback, profiling of individual surgeon, and standardized modules of improvement; 3-Implementing and measuring the impact of this program on surgical outcomes of a randomized group of surgeons against a control group of non-exposed surgeons. Inspired from previous experiences in the aeronautic and sport arena to improve pilots and athletes performance, our approach will take place in real time at the point of care in close collaboration with front-line personnel. A particular attention will be paid to quantify the influence of several factors that may affect how the surgeon operates every day (physiological stress, sleep quality, physical activities, workload, team composition and unplanned events in operating room). Generated knowledge on these factors will be exploited for identifying deficiencies that, if corrected, could improve surgeon's functional capacity. Solutions to control these factors and achieve optimal outcomes will then be experimentally tested to establish evidence-based standards of surgical practice. Those standards will be adapted to each surgeon's needs and preferences, potentially leading to a certification model for surgeons complying with excellence criteria.
Max ERC Funding
1 499 818 €
Duration
Start date: 2019-02-01, End date: 2024-01-31
