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 DIDO
Project Innovative drugs targeting IDO molecular dynamics in autoimmunity and neoplasia
Researcher (PI) Ursula Grohmann
Host Institution (HI) UNIVERSITA DEGLI STUDI DI PERUGIA
Call Details Advanced Grant (AdG), LS7, ERC-2013-ADG
Summary "Catabolism of amino acids is an ancient survival strategy that also controls immune responses in mammals. Indoleamine 2,3-dioxygenase (IDO), a tryptophan catabolizing enzyme, is recognized as an authentic regulator of immunity in several physiopathologic conditions, including autoimmune diseases, in which it is often defective, and neoplasia, in which it promotes immune unresponsiveness. The PI’s group recently revealed that IDO does not merely degrade tryptophan and produce immunoregulatory kynurenines but also acts as a signal-transducing molecule independently of its enzyme activity. IDO’s signaling function relies on the presence of phosphorylable motifs in a region (small IDO domain) distant from the catalytic site (large IDO domain). Preliminary data indicate that IDO, depending on microenvironmental conditions, can move among distinct cellular compartments. Thus IDO may be considered a ‘moonligthing’ protein, i.e., an ancestral metabolic molecule that, during evolution, has acquired the DYNAMIC feature of moving intracellularly and switching among distinct functions by changing its conformational state. By means of computational studies, Macchiarulo’s group (team member) has identified distinct conformations of IDO, some of which are associated with optimal catalytic activity of the enzyme whereas others may favor tyrosine phosphorylation of IDO’s small domain. A switch between distinct conformations can be induced by the use of ligands that bind either the catalytic site or an accessory pocket outside the IDO catalytic site. The first aim of DIDO is to decipher the relationships between IDO conformations and multiple functions of the enzyme. A second aim is to identify small molecules with drug-like properties capable of modulating distinct IDO’s molecular conformations in order to either potentiate (a new therapeutic approach in autoimmune diseases) or inhibit (more efficient anti-tumor therapeutic strategy) immunoregulatory signaling ability of IDO."
Summary
"Catabolism of amino acids is an ancient survival strategy that also controls immune responses in mammals. Indoleamine 2,3-dioxygenase (IDO), a tryptophan catabolizing enzyme, is recognized as an authentic regulator of immunity in several physiopathologic conditions, including autoimmune diseases, in which it is often defective, and neoplasia, in which it promotes immune unresponsiveness. The PI’s group recently revealed that IDO does not merely degrade tryptophan and produce immunoregulatory kynurenines but also acts as a signal-transducing molecule independently of its enzyme activity. IDO’s signaling function relies on the presence of phosphorylable motifs in a region (small IDO domain) distant from the catalytic site (large IDO domain). Preliminary data indicate that IDO, depending on microenvironmental conditions, can move among distinct cellular compartments. Thus IDO may be considered a ‘moonligthing’ protein, i.e., an ancestral metabolic molecule that, during evolution, has acquired the DYNAMIC feature of moving intracellularly and switching among distinct functions by changing its conformational state. By means of computational studies, Macchiarulo’s group (team member) has identified distinct conformations of IDO, some of which are associated with optimal catalytic activity of the enzyme whereas others may favor tyrosine phosphorylation of IDO’s small domain. A switch between distinct conformations can be induced by the use of ligands that bind either the catalytic site or an accessory pocket outside the IDO catalytic site. The first aim of DIDO is to decipher the relationships between IDO conformations and multiple functions of the enzyme. A second aim is to identify small molecules with drug-like properties capable of modulating distinct IDO’s molecular conformations in order to either potentiate (a new therapeutic approach in autoimmune diseases) or inhibit (more efficient anti-tumor therapeutic strategy) immunoregulatory signaling ability of IDO."
Max ERC Funding
2 442 078 €
Duration
Start date: 2014-02-01, End date: 2019-01-31
Project acronym DNAMET
Project "DNA methylation, hydroxymethylation and cancer"
Researcher (PI) Kristian Helin
Host Institution (HI) KOBENHAVNS UNIVERSITET
Call Details Advanced Grant (AdG), LS4, ERC-2011-ADG_20110310
Summary "DNA methylation patterns are frequently perturbed in human diseases such as imprinting disorders and cancer. In cancer increased aberrant DNA methylation is believed to work as a silencing mechanism for tumor suppressor genes such as INK4A, RB1 and MLH1. The high frequency of abnormal DNA methylation found in cancer might be due to the inactivation of a proofreading and/or fidelity system regulating the correct patterns of DNA methylation. Currently we have very limited knowledge about such mechanisms.
In this research proposal, we will focus on elucidating the biological function of a novel protein family, which catalyzes the conversion of 5-methyl-cytosine (5-mC) to 5-hydroxymethyl cytosine (5-hmC). By catalyzing this reaction the TET proteins most likely work as DNA demethylases, and they might therefore have a role in regulating DNA methylation fidelity. Interestingly, accumulated data has in the last 2 years shown that TET2 is one of the most frequently mutated genes in various hematological cancers. We propose to investigate the molecular mechanisms by which TET2 regulates normal hematopoiesis, how its inactivation leads to hematopoietic malignancies and how the protein contributes to the regulation of DNA methylation patterns and transcription. Furthermore, we propose several experimental approaches for identifying proteins required for the recruitment of TET proteins to target genes and to analyze their role in the regulation of DNA methylation patterns and in cancer. Finally, we will investigate the potential functional role of 5-hmC and explore the potential mechanisms by which this modification could be erased.
We expect to provide new insights into the biology of DNA methylation, hydroxymethylation and contribute to unravel the roles of TET proteins in normal physiology and cancer."
Summary
"DNA methylation patterns are frequently perturbed in human diseases such as imprinting disorders and cancer. In cancer increased aberrant DNA methylation is believed to work as a silencing mechanism for tumor suppressor genes such as INK4A, RB1 and MLH1. The high frequency of abnormal DNA methylation found in cancer might be due to the inactivation of a proofreading and/or fidelity system regulating the correct patterns of DNA methylation. Currently we have very limited knowledge about such mechanisms.
In this research proposal, we will focus on elucidating the biological function of a novel protein family, which catalyzes the conversion of 5-methyl-cytosine (5-mC) to 5-hydroxymethyl cytosine (5-hmC). By catalyzing this reaction the TET proteins most likely work as DNA demethylases, and they might therefore have a role in regulating DNA methylation fidelity. Interestingly, accumulated data has in the last 2 years shown that TET2 is one of the most frequently mutated genes in various hematological cancers. We propose to investigate the molecular mechanisms by which TET2 regulates normal hematopoiesis, how its inactivation leads to hematopoietic malignancies and how the protein contributes to the regulation of DNA methylation patterns and transcription. Furthermore, we propose several experimental approaches for identifying proteins required for the recruitment of TET proteins to target genes and to analyze their role in the regulation of DNA methylation patterns and in cancer. Finally, we will investigate the potential functional role of 5-hmC and explore the potential mechanisms by which this modification could be erased.
We expect to provide new insights into the biology of DNA methylation, hydroxymethylation and contribute to unravel the roles of TET proteins in normal physiology and cancer."
Max ERC Funding
2 298 000 €
Duration
Start date: 2012-07-01, End date: 2017-06-30
Project acronym EIMS
Project "Early infectious, inflammatory and immune mechanisms in schizophrenia"
Researcher (PI) Preben Bo Mortensen
Host Institution (HI) AARHUS UNIVERSITET
Call Details Advanced Grant (AdG), LS5, ERC-2011-ADG_20110310
Summary "The ambitious goal of this proposal is to identify causal mechanisms in schizophrenia, a devastating disease affecting about 1 percent of the population worldwide, and for which there is no current prevention or cure.
If my team and I are successful, we will discover etiological factors that can be targets for preventive interventions on the general population level and in high-risk groups, as well as inform the development of novel treatments.
I will use a truly unique population-based set of registers and biobanks, based upon a total national Danish birth cohort of more that 1.6 million individuals, and apply a novel combination of epidemiological design and methods and molecular biological techniques to the study of early risk factors for schizophrenia: I propose to combine cohort, nested case-control and case-sibling designs in studies of this total national birth cohort with detailed biological assessment of genetic and environmental risk factors operating during fetal life and around birth, in combination with detailed longitudinal information about the life course of cases, controls and their relatives.
Together with my team, I will for the first time in a human population empirically test a range of novel and specific hypotheses, tied together by a common theoretical framework of inflammatory and immune mechanisms interacting with individual genetic vulnerability during fetal life. Specifically the focus will be on infectious agents, markers of inflammation, effects of maternal auto-antibodies, and interactions with maternal vitamin D as well as genes involved in apoptosis and other relevant pathways. All findings will be tested in independent replication samples from the same population and further validated by comparison to healthy sibling controls. Because my studies are performed in a total population birth cohort, we will be able to make risk prediction suitable for the identification of targets for preventive strategies."
Summary
"The ambitious goal of this proposal is to identify causal mechanisms in schizophrenia, a devastating disease affecting about 1 percent of the population worldwide, and for which there is no current prevention or cure.
If my team and I are successful, we will discover etiological factors that can be targets for preventive interventions on the general population level and in high-risk groups, as well as inform the development of novel treatments.
I will use a truly unique population-based set of registers and biobanks, based upon a total national Danish birth cohort of more that 1.6 million individuals, and apply a novel combination of epidemiological design and methods and molecular biological techniques to the study of early risk factors for schizophrenia: I propose to combine cohort, nested case-control and case-sibling designs in studies of this total national birth cohort with detailed biological assessment of genetic and environmental risk factors operating during fetal life and around birth, in combination with detailed longitudinal information about the life course of cases, controls and their relatives.
Together with my team, I will for the first time in a human population empirically test a range of novel and specific hypotheses, tied together by a common theoretical framework of inflammatory and immune mechanisms interacting with individual genetic vulnerability during fetal life. Specifically the focus will be on infectious agents, markers of inflammation, effects of maternal auto-antibodies, and interactions with maternal vitamin D as well as genes involved in apoptosis and other relevant pathways. All findings will be tested in independent replication samples from the same population and further validated by comparison to healthy sibling controls. Because my studies are performed in a total population birth cohort, we will be able to make risk prediction suitable for the identification of targets for preventive strategies."
Max ERC Funding
2 471 736 €
Duration
Start date: 2012-05-01, End date: 2017-04-30
Project acronym ENVISION
Project Novel mechanisms of early defense against virus infections
Researcher (PI) Søren Riis PALUDAN
Host Institution (HI) AARHUS UNIVERSITET
Call Details Advanced Grant (AdG), LS6, ERC-2017-ADG
Summary Virus-induced type I interferons (IFN) have classically been considered to constitute the first line of defense against virus infections However, recent work by us and others has identified early antiviral actions that occur independently of inducible type I and III IFN expression and sometimes even prior to IFN action (e.g. Iversen,...., Paludan. Nature Immunology, 2016; Paludan. Trends in Immunology, 2016). These discoveries challenge the current thinking in the field that IFNs constitute the first line of defense. Hence, there is an urgent need for more detailed understanding of the immediate antiviral defense mechanisms. Most importantly, we remain to identify key players in IFN-independent antiviral responses, we completely lack insight into the mechanisms that govern these responses, and we also lack information on the importance of this layer of defense in mice and humans. In accord with this, my proposal follows four aims: (i) Identification of mechanisms of virus detection at epithelial surfaces, (ii) elucidation of the role of tonic IFN signaling in antiviral defense, (iii) identification and characterization of novel restriction factors, and (iv) deciphering the mechanisms that govern induction of the first wave of IFNs at epithelial surfaces. In addition, I will also explore the interactions between the early antiviral actions. To achieve the goals, I will combine unbiased genome-wide screens with hypothesis-driven approaches, and will integrate molecular biology/genetics/biochemistry with advanced cell culture systems, animal science and analysis of patient material. Strong preliminary data have been generated for all four aims, and world-leading collaborations are in place, hence minimizing the risks, and allowing fast progress. Our findings will (i) change the thinking in innate immunology by uncovering a novel layer of antiviral defense and (ii) provide new avenues for therapeutic modulation of immune responses.
Summary
Virus-induced type I interferons (IFN) have classically been considered to constitute the first line of defense against virus infections However, recent work by us and others has identified early antiviral actions that occur independently of inducible type I and III IFN expression and sometimes even prior to IFN action (e.g. Iversen,...., Paludan. Nature Immunology, 2016; Paludan. Trends in Immunology, 2016). These discoveries challenge the current thinking in the field that IFNs constitute the first line of defense. Hence, there is an urgent need for more detailed understanding of the immediate antiviral defense mechanisms. Most importantly, we remain to identify key players in IFN-independent antiviral responses, we completely lack insight into the mechanisms that govern these responses, and we also lack information on the importance of this layer of defense in mice and humans. In accord with this, my proposal follows four aims: (i) Identification of mechanisms of virus detection at epithelial surfaces, (ii) elucidation of the role of tonic IFN signaling in antiviral defense, (iii) identification and characterization of novel restriction factors, and (iv) deciphering the mechanisms that govern induction of the first wave of IFNs at epithelial surfaces. In addition, I will also explore the interactions between the early antiviral actions. To achieve the goals, I will combine unbiased genome-wide screens with hypothesis-driven approaches, and will integrate molecular biology/genetics/biochemistry with advanced cell culture systems, animal science and analysis of patient material. Strong preliminary data have been generated for all four aims, and world-leading collaborations are in place, hence minimizing the risks, and allowing fast progress. Our findings will (i) change the thinking in innate immunology by uncovering a novel layer of antiviral defense and (ii) provide new avenues for therapeutic modulation of immune responses.
Max ERC Funding
2 480 338 €
Duration
Start date: 2018-12-01, End date: 2023-11-30
Project acronym EU-rhythmy
Project Molecular strategies to treat inherited arrhythmias
Researcher (PI) Silvia Giuliana Priori
Host Institution (HI) UNIVERSITA DEGLI STUDI DI PAVIA
Call Details Advanced Grant (AdG), LS7, ERC-2014-ADG
Summary Sudden cardiac death (SCD) is a leading cause of death in western countries: coronary artery disease is the major cause of SCD in older subjects while inherited arrhythmogenic diseases are the leading cause of SCD in younger individuals. After 25 years dedicated to research of the molecular bases of heritable arrhythmias, the PI of this proposal now intends to pioneer gene therapy for prevention of SCD: a virtually unexplored field. The development of molecular therapies for rhythm disturbances is a high risk effort however, if successful, it will be highly rewarding. The PI has envisioned an ambitious and comprehensive project to target two severe inherited arrhythmogenic diseases: dominant catecholaminergic polymorphic ventricular tachycardia (CPVT) and Long QT syndrome type 8 (LQT8). The availability of a clinically relevant model is critical to ensure clinical translation of results: the team will exploit an existing CPVT model and will engineer a knock-in pig to model LQT8. The PI and her team will investigate innovative strategies of gene-delivery, gene-silencing and gene-editing to the heart comparing efficacy of different constructs and promoters. The team will also carefully engineer novel gene-therapy approaches to avoid the development of regional inhomogeneity in protein expression that may facilitate proarrhythmic events. Such a comprehensive approach will provide a most valuable core of knowledge on the comparative efficacy of a broad range of molecular strategies on the electrical milieu of the heart. It is expected that these results will not only benefit CPVT and LQT8 but rather they will foster development of gene therapy for other inherited and acquired arrhythmias.
Summary
Sudden cardiac death (SCD) is a leading cause of death in western countries: coronary artery disease is the major cause of SCD in older subjects while inherited arrhythmogenic diseases are the leading cause of SCD in younger individuals. After 25 years dedicated to research of the molecular bases of heritable arrhythmias, the PI of this proposal now intends to pioneer gene therapy for prevention of SCD: a virtually unexplored field. The development of molecular therapies for rhythm disturbances is a high risk effort however, if successful, it will be highly rewarding. The PI has envisioned an ambitious and comprehensive project to target two severe inherited arrhythmogenic diseases: dominant catecholaminergic polymorphic ventricular tachycardia (CPVT) and Long QT syndrome type 8 (LQT8). The availability of a clinically relevant model is critical to ensure clinical translation of results: the team will exploit an existing CPVT model and will engineer a knock-in pig to model LQT8. The PI and her team will investigate innovative strategies of gene-delivery, gene-silencing and gene-editing to the heart comparing efficacy of different constructs and promoters. The team will also carefully engineer novel gene-therapy approaches to avoid the development of regional inhomogeneity in protein expression that may facilitate proarrhythmic events. Such a comprehensive approach will provide a most valuable core of knowledge on the comparative efficacy of a broad range of molecular strategies on the electrical milieu of the heart. It is expected that these results will not only benefit CPVT and LQT8 but rather they will foster development of gene therapy for other inherited and acquired arrhythmias.
Max ERC Funding
2 314 029 €
Duration
Start date: 2015-11-01, End date: 2020-10-31
Project acronym EURECA
Project Eukaryotic Regulated RNA Catabolism
Researcher (PI) Torben Heick Jensen
Host Institution (HI) AARHUS UNIVERSITET
Call Details Advanced Grant (AdG), LS1, ERC-2013-ADG
Summary "Regulation and fidelity of gene expression is fundamental to the differentiation and maintenance of all living organisms. While historically attention has been focused on the process of transcriptional activation, we predict that RNA turnover pathways are equally important for gene expression regulation. This has been implied for selected protein-coding RNAs (mRNAs) but is virtually unexplored for non-protein-coding RNAs (ncRNAs).
The intention of the EURECA proposal is to establish cutting-edge research to characterize mammalian nuclear RNA turnover; its factor utility, substrate specificity and regulatory capacity. We foresee that RNA turnover is at the core of gene expression regulation - forming intricate connection to RNA productive systems – thus, being centrally placed to determine RNA fate. EURECA seeks to dramatically improve our understanding of cellular decision processes impacting RNA levels and to establish models for how regulated RNA turnover helps control key biological processes.
The realization that the number of ncRNA producing genes was previously grossly underestimated foretells that ncRNA regulation will impact on most aspects of cell biology. Consistently, aberrant ncRNA levels correlate with human disease phenotypes and RNA turnover complexes are linked to disease biology. Still, solid models for how ncRNA turnover regulate biological processes in higher eukaryotes are not available. Moreover, which ncRNAs retain function and which are merely transcriptional by-products remain a major challenge to sort out. The circumstances and kinetics of ncRNA turnover are therefore important to delineate as these will ultimately relate to the likelihood of molecular function. A fundamental challenge here is to also discern which protein complements of non-coding ribonucleoprotein particles (ncRNPs) are (in)compatible with function. Balancing single transcript/factor analysis with high-throughput methodology, EURECA will address these questions."
Summary
"Regulation and fidelity of gene expression is fundamental to the differentiation and maintenance of all living organisms. While historically attention has been focused on the process of transcriptional activation, we predict that RNA turnover pathways are equally important for gene expression regulation. This has been implied for selected protein-coding RNAs (mRNAs) but is virtually unexplored for non-protein-coding RNAs (ncRNAs).
The intention of the EURECA proposal is to establish cutting-edge research to characterize mammalian nuclear RNA turnover; its factor utility, substrate specificity and regulatory capacity. We foresee that RNA turnover is at the core of gene expression regulation - forming intricate connection to RNA productive systems – thus, being centrally placed to determine RNA fate. EURECA seeks to dramatically improve our understanding of cellular decision processes impacting RNA levels and to establish models for how regulated RNA turnover helps control key biological processes.
The realization that the number of ncRNA producing genes was previously grossly underestimated foretells that ncRNA regulation will impact on most aspects of cell biology. Consistently, aberrant ncRNA levels correlate with human disease phenotypes and RNA turnover complexes are linked to disease biology. Still, solid models for how ncRNA turnover regulate biological processes in higher eukaryotes are not available. Moreover, which ncRNAs retain function and which are merely transcriptional by-products remain a major challenge to sort out. The circumstances and kinetics of ncRNA turnover are therefore important to delineate as these will ultimately relate to the likelihood of molecular function. A fundamental challenge here is to also discern which protein complements of non-coding ribonucleoprotein particles (ncRNPs) are (in)compatible with function. Balancing single transcript/factor analysis with high-throughput methodology, EURECA will address these questions."
Max ERC Funding
2 497 960 €
Duration
Start date: 2014-04-01, End date: 2019-03-31
Project acronym EVOLNA
Project Evolution of LNA Aptamers
Researcher (PI) Jesper Thagaard Wengel
Host Institution (HI) SYDDANSK UNIVERSITET
Call Details Advanced Grant (AdG), LS9, ERC-2010-AdG_20100317
Summary Aptamers are single-stranded oligonucleotides which are able to target peptides, proteins, small molecules or live cells by virtue of their well-defined three-dimensional shapes. Aptamers are typically generated by evolution of specific sequences against a given target by in vitro evolution using the process known as SELEX. Progress of this field with respect to drug development has so far been hampered by the relative large size and poor biostability of evolved aptamers composed of unmodified nucleotides, necessitating tedious and extensive post-SELEX truncation and modification approaches. LNA (locked nucleic acid) is a prominent nucleotide modification which is in the process of revolutionizing gene silencing and RNA detection. LNA however has never been included in de novo aptamer evolution. EVOLNA is an ambitious but coherent research program with the objective of transforming the field of aptamer technology. The vision is to enable evolution of aptamers that per se possess most of the desired properties, thereby alleviating the need for extensive post-SELEX procedures. This will be realized by combining the unique properties of LNA with innovative methods for LNA aptamer evolution. LNA aptamer technology is envisioned to enable evolution of aptamers displaying maximum chemical diversity, minimum size and high biostability. The developed strategies will be applicable not only towards evolution of therapeutic aptamers, which will be the main subject of this program, but also towards evolution of aptamers for biosensing, diagnostic and imaging applications. The program is at the very frontier of biotechnology research and spans the areas of chemistry, molecular biology and drug research.
Summary
Aptamers are single-stranded oligonucleotides which are able to target peptides, proteins, small molecules or live cells by virtue of their well-defined three-dimensional shapes. Aptamers are typically generated by evolution of specific sequences against a given target by in vitro evolution using the process known as SELEX. Progress of this field with respect to drug development has so far been hampered by the relative large size and poor biostability of evolved aptamers composed of unmodified nucleotides, necessitating tedious and extensive post-SELEX truncation and modification approaches. LNA (locked nucleic acid) is a prominent nucleotide modification which is in the process of revolutionizing gene silencing and RNA detection. LNA however has never been included in de novo aptamer evolution. EVOLNA is an ambitious but coherent research program with the objective of transforming the field of aptamer technology. The vision is to enable evolution of aptamers that per se possess most of the desired properties, thereby alleviating the need for extensive post-SELEX procedures. This will be realized by combining the unique properties of LNA with innovative methods for LNA aptamer evolution. LNA aptamer technology is envisioned to enable evolution of aptamers displaying maximum chemical diversity, minimum size and high biostability. The developed strategies will be applicable not only towards evolution of therapeutic aptamers, which will be the main subject of this program, but also towards evolution of aptamers for biosensing, diagnostic and imaging applications. The program is at the very frontier of biotechnology research and spans the areas of chemistry, molecular biology and drug research.
Max ERC Funding
2 497 720 €
Duration
Start date: 2011-04-01, End date: 2016-03-31
Project acronym EYEGET
Project Gene therapy of inherited retinal diseases
Researcher (PI) Alberto AURICCHIO
Host Institution (HI) FONDAZIONE TELETHON
Call Details Advanced Grant (AdG), LS7, ERC-2015-AdG
Summary Inherited retinal degenerations (IRDs) are a major cause of blindness worldwide. IRD patients witness inexorable progressive vision loss as no therapy is currently available. In the last decade my group has significantly contributed to a change of this scenario by developing efficient adeno-associated viral (AAV) vectors for retinal gene therapy that are safe and effective in humans. The objective of EYEGET (EYE GEne Therapy) is to overcome some of the current major limitations in the field of retinal gene therapy to expand initial therapeutic successes to a larger number of IRDs. To achieve this, we propose to use four parallel, highly innovative and complementary approaches: i. expansion of the limited AAV cargo capacity by a novel methodology based on co-administration of multiple AAVs that reassemble in target retinal cells and reconstitute large genes; ii. targeting of frequent dominant gain-of-function mutations that cause RP using state-of-the-art AAV-mediated genome editing technologies; iii. induction of retinal cells clearance of toxic IRD products by AAV-mediated activation of autophagy and lysosomal function; iv. development of methodologies to directly convert fibroblasts to photoreceptors that can be transplanted in retinas from IRD patients with advanced PR loss and for whom in vivo gene therapy is no longer an option. We will use a combination of in vitro and in vivo state-of-the-art technologies including novel AAV vector design, high content screening of drugs that enhance AAV transduction, genome editing, and advanced in vivo retinal phenotyping to obtain proof-of-concept for each of these therapeutic strategies. The results from this study may impact the quality of life of millions of people worldwide by providing a cure based on gene and/or cell therapy for a large group of IRDs.
Summary
Inherited retinal degenerations (IRDs) are a major cause of blindness worldwide. IRD patients witness inexorable progressive vision loss as no therapy is currently available. In the last decade my group has significantly contributed to a change of this scenario by developing efficient adeno-associated viral (AAV) vectors for retinal gene therapy that are safe and effective in humans. The objective of EYEGET (EYE GEne Therapy) is to overcome some of the current major limitations in the field of retinal gene therapy to expand initial therapeutic successes to a larger number of IRDs. To achieve this, we propose to use four parallel, highly innovative and complementary approaches: i. expansion of the limited AAV cargo capacity by a novel methodology based on co-administration of multiple AAVs that reassemble in target retinal cells and reconstitute large genes; ii. targeting of frequent dominant gain-of-function mutations that cause RP using state-of-the-art AAV-mediated genome editing technologies; iii. induction of retinal cells clearance of toxic IRD products by AAV-mediated activation of autophagy and lysosomal function; iv. development of methodologies to directly convert fibroblasts to photoreceptors that can be transplanted in retinas from IRD patients with advanced PR loss and for whom in vivo gene therapy is no longer an option. We will use a combination of in vitro and in vivo state-of-the-art technologies including novel AAV vector design, high content screening of drugs that enhance AAV transduction, genome editing, and advanced in vivo retinal phenotyping to obtain proof-of-concept for each of these therapeutic strategies. The results from this study may impact the quality of life of millions of people worldwide by providing a cure based on gene and/or cell therapy for a large group of IRDs.
Max ERC Funding
2 499 564 €
Duration
Start date: 2017-01-01, End date: 2021-12-31
Project acronym FAST
Project Investigating new therapeutic approaches to Friedreich's Ataxia
Researcher (PI) Roberto Testi
Host Institution (HI) UNIVERSITA DEGLI STUDI DI ROMA TOR VERGATA
Call Details Advanced Grant (AdG), LS7, ERC-2011-ADG_20110310
Summary Friedreich’s Ataxia (FRDA) is a devastating degenerative disease with no specific therapy. It is passed by autosomal recessive inheritance and affects 1:30,000 individuals in Caucasian populations. Symptoms appear in the first decade of life and include progressive and unremitting lack of movement coordination, leading to complete inability, and dilated cardiomyopathy leading to congestive heart failure, the most common cause of premature death. FRDA is due to the insufficient transcription of the gene coding for the mitochondrial protein frataxin. Reduced cellular levels of frataxin cause impaired mitochondrial function and increased sensitivity to oxidative stress, leading to accelerated cell death in critical tissues.
Severity of the disease critically depends on residual frataxin levels. Therapeutic efforts are mostly focused on increasing cellular frataxin . We found that frataxin is normally degraded by the ubiquitin-proteasome system. We identified the lysine responsible for the ubiquitination of frataxin and, by computational screening followed by experimental validation, we identified and validated a series of small molecules, called ubiquitin-competing molecules (UCM), that prevent frataxin ubiquitination and induce frataxin accumulation in cells derived from FRDA patients. Moreover, treatment with UCM partially rescues aconitase and ATP production defects in cells derived from FRDA patients.
Our goal is two fold: 1) submit a set of leads we already identified, as well as their new and more complex derivatives, to preclinical testing in FRDA mice 2) identify the E3 ligase that is responsible for frataxin ubiquitination, and investigate the possibility to use it as a druggable target for small molecules to prevent frataxin degradation.
Summary
Friedreich’s Ataxia (FRDA) is a devastating degenerative disease with no specific therapy. It is passed by autosomal recessive inheritance and affects 1:30,000 individuals in Caucasian populations. Symptoms appear in the first decade of life and include progressive and unremitting lack of movement coordination, leading to complete inability, and dilated cardiomyopathy leading to congestive heart failure, the most common cause of premature death. FRDA is due to the insufficient transcription of the gene coding for the mitochondrial protein frataxin. Reduced cellular levels of frataxin cause impaired mitochondrial function and increased sensitivity to oxidative stress, leading to accelerated cell death in critical tissues.
Severity of the disease critically depends on residual frataxin levels. Therapeutic efforts are mostly focused on increasing cellular frataxin . We found that frataxin is normally degraded by the ubiquitin-proteasome system. We identified the lysine responsible for the ubiquitination of frataxin and, by computational screening followed by experimental validation, we identified and validated a series of small molecules, called ubiquitin-competing molecules (UCM), that prevent frataxin ubiquitination and induce frataxin accumulation in cells derived from FRDA patients. Moreover, treatment with UCM partially rescues aconitase and ATP production defects in cells derived from FRDA patients.
Our goal is two fold: 1) submit a set of leads we already identified, as well as their new and more complex derivatives, to preclinical testing in FRDA mice 2) identify the E3 ligase that is responsible for frataxin ubiquitination, and investigate the possibility to use it as a druggable target for small molecules to prevent frataxin degradation.
Max ERC Funding
1 496 200 €
Duration
Start date: 2012-03-01, End date: 2015-02-28
