Project acronym DeFiNER
Project Nucleotide Excision Repair: Decoding its Functional Role in Mammals
Researcher (PI) Georgios Garinis
Host Institution (HI) IDRYMA TECHNOLOGIAS KAI EREVNAS
Call Details Consolidator Grant (CoG), LS4, ERC-2014-CoG
Summary Genome maintenance, chromatin remodelling and transcription are tightly linked biological processes that are currently poorly understood and vastly unexplored. Nucleotide excision repair (NER) is a major DNA repair pathway that mammalian cells employ to maintain their genome intact and faithfully transmit it into their progeny. Besides cancer and aging, however, defects in NER give rise to developmental disorders whose clinical heterogeneity and varying severity can only insufficiently be explained by the DNA repair defect. Recent work reveals that NER factors play a role, in addition to DNA repair, in transcription and the three-dimensional organization of our genome. Indeed, NER factors are now known to function in the regulation of gene expression, the transcriptional reprogramming of pluripotent stem cells and the fine-tuning of growth hormones during mammalian development. In this regard, the non-random organization of our genome, chromatin and the process of transcription itself are expected to play paramount roles in how NER factors coordinate, prioritize and execute their distinct tasks during development and disease progression. At present, however, no solid evidence exists as to how NER is functionally involved in such complex processes, what are the NER-associated protein complexes and underlying gene networks or how NER factors operate within the complex chromatin architecture. This is primarily due to our difficulties in dissecting the diverse functional contributions of NER proteins in an intact organism. Here, we propose to use a unique series of knock-in, transgenic and NER progeroid mice to decode the functional role of NER in mammals, thus paving the way for understanding how genome maintenance pathways are connected to developmental defects and disease mechanisms in vivo.
Summary
Genome maintenance, chromatin remodelling and transcription are tightly linked biological processes that are currently poorly understood and vastly unexplored. Nucleotide excision repair (NER) is a major DNA repair pathway that mammalian cells employ to maintain their genome intact and faithfully transmit it into their progeny. Besides cancer and aging, however, defects in NER give rise to developmental disorders whose clinical heterogeneity and varying severity can only insufficiently be explained by the DNA repair defect. Recent work reveals that NER factors play a role, in addition to DNA repair, in transcription and the three-dimensional organization of our genome. Indeed, NER factors are now known to function in the regulation of gene expression, the transcriptional reprogramming of pluripotent stem cells and the fine-tuning of growth hormones during mammalian development. In this regard, the non-random organization of our genome, chromatin and the process of transcription itself are expected to play paramount roles in how NER factors coordinate, prioritize and execute their distinct tasks during development and disease progression. At present, however, no solid evidence exists as to how NER is functionally involved in such complex processes, what are the NER-associated protein complexes and underlying gene networks or how NER factors operate within the complex chromatin architecture. This is primarily due to our difficulties in dissecting the diverse functional contributions of NER proteins in an intact organism. Here, we propose to use a unique series of knock-in, transgenic and NER progeroid mice to decode the functional role of NER in mammals, thus paving the way for understanding how genome maintenance pathways are connected to developmental defects and disease mechanisms in vivo.
Max ERC Funding
1 995 000 €
Duration
Start date: 2016-01-01, End date: 2020-12-31
Project acronym KRASHIMPE
Project KRas mutation interactions with host immunity in malignant pleural effusion
Researcher (PI) Georgios Stathopoulos
Host Institution (HI) PANEPISTIMIO PATRON
Call Details Starting Grant (StG), LS4, ERC-2010-StG_20091118
Summary Malignant pleural effusion (MPE) is a significant problem most commonly caused by adenocarcinomas. Although tumors involving the pleura vary in their ability to produce MPE, pathways critical for MPE formation are poorly defined. We have found that mouse tumors harboring mutant (”)KRas produce MPE in mice while tumors without ”KRas do not. LLC and MC38 lung and colon adenocarcinomas, potent inducers of MPE in syngeneic mice, harbor ”KRas that drives constitutive Ras and alternative nuclear factor (NF)-ºB signaling, inflammatory gene expression, and recruitment of specific myeloid cells to the pleural space. In contrast, mouse B16 melanoma and AE17 mesothelioma have wtKRas, lack constitutive Ras/alternative NF-º’ signaling, and are incapable of forming MPE. RNAi-mediated silencing of KRas in MC38 tumors abrogated MPE formation and Ras/alternative NF-º’ activation, while these phenomena were reconstituted in B16 tumors after KRas overexpression. We hypothesize that Ras-activating mutations drive the inflammatory phenotype of adenocarcinomas critical for MPE formation, which is characterized by Ras/alternative NF-ºB activation, inflammatory signalling to host vasculature/immune system, and recruitment of specific myeloid cells, and results in endothelial proliferation/leakiness. To test this hypothesis, we propose to: 1) define the relationship between Ras-activating mutations (RAM) and MPE formation; 2) identify tumor cell Ras-dependent signalling pathways and gene expression signature critical for MPE formation; 3) investigate the host response to tumor cells with RAM that results in MPE; and 4) target Ras and dependent signalling pathways as potential therapy for MPE. Studies will be performed using delivery of mouse/human tumors with/without RAM into the pleura of syngeneic/immunocompromized mice and are likely to yield new insights into the mechanisms of pleural tumor progression and to identify novel approaches to treatment of cancer patients with MPE.
Summary
Malignant pleural effusion (MPE) is a significant problem most commonly caused by adenocarcinomas. Although tumors involving the pleura vary in their ability to produce MPE, pathways critical for MPE formation are poorly defined. We have found that mouse tumors harboring mutant (”)KRas produce MPE in mice while tumors without ”KRas do not. LLC and MC38 lung and colon adenocarcinomas, potent inducers of MPE in syngeneic mice, harbor ”KRas that drives constitutive Ras and alternative nuclear factor (NF)-ºB signaling, inflammatory gene expression, and recruitment of specific myeloid cells to the pleural space. In contrast, mouse B16 melanoma and AE17 mesothelioma have wtKRas, lack constitutive Ras/alternative NF-º’ signaling, and are incapable of forming MPE. RNAi-mediated silencing of KRas in MC38 tumors abrogated MPE formation and Ras/alternative NF-º’ activation, while these phenomena were reconstituted in B16 tumors after KRas overexpression. We hypothesize that Ras-activating mutations drive the inflammatory phenotype of adenocarcinomas critical for MPE formation, which is characterized by Ras/alternative NF-ºB activation, inflammatory signalling to host vasculature/immune system, and recruitment of specific myeloid cells, and results in endothelial proliferation/leakiness. To test this hypothesis, we propose to: 1) define the relationship between Ras-activating mutations (RAM) and MPE formation; 2) identify tumor cell Ras-dependent signalling pathways and gene expression signature critical for MPE formation; 3) investigate the host response to tumor cells with RAM that results in MPE; and 4) target Ras and dependent signalling pathways as potential therapy for MPE. Studies will be performed using delivery of mouse/human tumors with/without RAM into the pleura of syngeneic/immunocompromized mice and are likely to yield new insights into the mechanisms of pleural tumor progression and to identify novel approaches to treatment of cancer patients with MPE.
Max ERC Funding
1 995 000 €
Duration
Start date: 2011-04-01, End date: 2016-03-31
Project acronym MANNA
Project MacroAutophagy and Necrotic Neurodegeneration in Ageing
Researcher (PI) Nektarios TAVERNARAKIS
Host Institution (HI) IDRYMA TECHNOLOGIAS KAI EREVNAS
Call Details Advanced Grant (AdG), LS4, ERC-2015-AdG
Summary Necrosis contributes critically in devastating human pathologies such as stroke, ischemia, and age-associated neurodegenerative disorders. Ageing increases susceptibility to neurodegeneration, in diverse species ranging from the lowly nematode Caenorhabditis elegans to humans. The mechanisms that govern necrotic neurodegeneration and its modulation by ageing are poorly understood. Autophagy has been implicated in necrosis and neurodegeneration, both with pro-survival and a pro-death roles. Autophagic flux declines with age, while induction of autophagy enhances longevity under conditions such as low insulin/IGF1 signalling and dietary restriction, which extend lifespan across diverse taxa. Our recent findings indicate that organelle-specific autophagy, including mitophagy, pexophagy and nucleophagy, is an important, evolutionarily conserved, determinant of longevity. We propose to dissect the molecular underpinnings of neuron vulnerability to necrosis during ageing, focusing on cargo-specific macroautophagy. To this end, we will implement a multifaceted approach that combines the power and versatility of C. elegans genetics with advanced, in vivo neuronal imaging and microfluidics technology. Our objectives are fourfold. First, we will monitor autophagic flux of organellar cargo, during neurodegeneration, under conditions that alter lifespan and identify mediators of organelle-specific autophagy in neurons. Second, we will conduct genome-wide screens for modifiers of age-inflicted neurodegeneration. Third, we will interrogate nematode models of human neurodegenerative disorders for organelle-specific autophagy and susceptibility to necrosis, upon manipulations that alter lifespan. Fourth, we will investigate the functional conservation of key mechanisms in mammalian models of neuronal necrosis. Together, these studies will deepen our understanding of age-related neurodegeneration and provide critical insights with broad relevance to human health and quality of life.
Summary
Necrosis contributes critically in devastating human pathologies such as stroke, ischemia, and age-associated neurodegenerative disorders. Ageing increases susceptibility to neurodegeneration, in diverse species ranging from the lowly nematode Caenorhabditis elegans to humans. The mechanisms that govern necrotic neurodegeneration and its modulation by ageing are poorly understood. Autophagy has been implicated in necrosis and neurodegeneration, both with pro-survival and a pro-death roles. Autophagic flux declines with age, while induction of autophagy enhances longevity under conditions such as low insulin/IGF1 signalling and dietary restriction, which extend lifespan across diverse taxa. Our recent findings indicate that organelle-specific autophagy, including mitophagy, pexophagy and nucleophagy, is an important, evolutionarily conserved, determinant of longevity. We propose to dissect the molecular underpinnings of neuron vulnerability to necrosis during ageing, focusing on cargo-specific macroautophagy. To this end, we will implement a multifaceted approach that combines the power and versatility of C. elegans genetics with advanced, in vivo neuronal imaging and microfluidics technology. Our objectives are fourfold. First, we will monitor autophagic flux of organellar cargo, during neurodegeneration, under conditions that alter lifespan and identify mediators of organelle-specific autophagy in neurons. Second, we will conduct genome-wide screens for modifiers of age-inflicted neurodegeneration. Third, we will interrogate nematode models of human neurodegenerative disorders for organelle-specific autophagy and susceptibility to necrosis, upon manipulations that alter lifespan. Fourth, we will investigate the functional conservation of key mechanisms in mammalian models of neuronal necrosis. Together, these studies will deepen our understanding of age-related neurodegeneration and provide critical insights with broad relevance to human health and quality of life.
Max ERC Funding
2 254 109 €
Duration
Start date: 2017-01-01, End date: 2021-12-31
Project acronym NEURONAGE
Project Molecular Basis of Neuronal Ageing
Researcher (PI) Nektarios Tavernarakis
Host Institution (HI) IDRYMA TECHNOLOGIAS KAI EREVNAS
Call Details Advanced Grant (AdG), LS4, ERC-2008-AdG
Summary Ageing is associated with marked decrease of neuronal function and increased susceptibility to neurodegeneration, in organisms as diverse as the lowly worm Caenorhabditis elegans and humans. Although, age-related deterioration of the nervous system is a universal phenomenon, its cellular and molecular underpinnings remain obscure. What mechanisms are responsible for the detrimental effects of ageing on neuronal function? The aim of the proposed research programme is to address this fundamental problem. We will implement an interdisciplinary approach, combining the power of C. elegans, a highly malleable genetic model which offers a precisely defined nervous system, with state-of-the-art microfluidics and optical imaging technologies, to manipulate and monitor neuronal activity during ageing, in vivo. Our objectives are four-fold. First, develop a microfluidics platform for high-throughput manipulation and imaging of specific neurons in individual animals, in vivo. Second, use the platform to monitor neuronal function during ageing in isogenic populations of wild type animals, long-lived mutants and animals under caloric restriction, a condition known to extend lifespan from yeast to primates. Third, examine how ageing modulates susceptibility to neuronal damage in nematode models of human neurodegenerative disorders. Fourth, conduct both forward and reverse genetic screens for modifiers of resistance to ageing-inflicted neuronal function decline. We will seek to identify and thoroughly characterize genes and molecular pathways involved in neuron deterioration during ageing. Ultimately, we will investigate the functional conservation of key isolated factors in more complex ageing models such as Drosophila and the mouse. Together, these studies will lead to an unprecedented understanding of age-related breakdown of neuronal function and will provide critical insights with broad relevance to human health and quality of life.
Summary
Ageing is associated with marked decrease of neuronal function and increased susceptibility to neurodegeneration, in organisms as diverse as the lowly worm Caenorhabditis elegans and humans. Although, age-related deterioration of the nervous system is a universal phenomenon, its cellular and molecular underpinnings remain obscure. What mechanisms are responsible for the detrimental effects of ageing on neuronal function? The aim of the proposed research programme is to address this fundamental problem. We will implement an interdisciplinary approach, combining the power of C. elegans, a highly malleable genetic model which offers a precisely defined nervous system, with state-of-the-art microfluidics and optical imaging technologies, to manipulate and monitor neuronal activity during ageing, in vivo. Our objectives are four-fold. First, develop a microfluidics platform for high-throughput manipulation and imaging of specific neurons in individual animals, in vivo. Second, use the platform to monitor neuronal function during ageing in isogenic populations of wild type animals, long-lived mutants and animals under caloric restriction, a condition known to extend lifespan from yeast to primates. Third, examine how ageing modulates susceptibility to neuronal damage in nematode models of human neurodegenerative disorders. Fourth, conduct both forward and reverse genetic screens for modifiers of resistance to ageing-inflicted neuronal function decline. We will seek to identify and thoroughly characterize genes and molecular pathways involved in neuron deterioration during ageing. Ultimately, we will investigate the functional conservation of key isolated factors in more complex ageing models such as Drosophila and the mouse. Together, these studies will lead to an unprecedented understanding of age-related breakdown of neuronal function and will provide critical insights with broad relevance to human health and quality of life.
Max ERC Funding
2 376 000 €
Duration
Start date: 2009-05-01, End date: 2015-04-30
Project acronym SET-NET
Project Enzymatic and genomic targets of histone modifying enzymes and their role in liver metabolism and hepatocarcinogenesis
Researcher (PI) Ioannis Talianidis
Host Institution (HI) BIOMEDICAL SCIENCES RESEARCH CENTER ALEXANDER FLEMING
Call Details Advanced Grant (AdG), LS4, ERC-2011-ADG_20110310
Summary "In this proposal we will study the role of histone methytransferases Set9, PR-SET7, Smyd2, Smyd3 and the demethylase LSD1 in hepatocarcinogenesis and in the regulation of hepatic metabolic pathways.
The hypothesis raised here suggests that the function of histone modifying enzymes is realized through 4 overlapping regulatory layers: i. via modifications of chromatin, ii. via modifications of recently identified transcription factor substrates, iii. via influencing the hepatic transcription factor crossregulatory circuitry, and iv. via modification of each other.
To dissect the role of these regulatory layers and determine their contribution in the control of hepatic metabolic pathways, and in the development of hepatocellular carcinoma, our activities will involve: i. Generation of relevant KO and transgenic mouse models, ii. Functional characterization of novel non-histone and histone substrates, iii. Analysis of novel cross-regulatory protein modifications affecting the activity of the enzymes and iv. the identification of their genomic targets and associated chromatin modifications using global approaches.
The work is expected to provide important insights into a previously unanticipated network of protein methylation-directed regulatory modules, potentially operating in multiple biological pathways such as liver development, metabolism, apoptosis and carcinogenesis. The functioning of such network would be of high biological importance, with far-reaching implications in drug development, rivaling those of phosphorylation or acetylation regulated processes."
Summary
"In this proposal we will study the role of histone methytransferases Set9, PR-SET7, Smyd2, Smyd3 and the demethylase LSD1 in hepatocarcinogenesis and in the regulation of hepatic metabolic pathways.
The hypothesis raised here suggests that the function of histone modifying enzymes is realized through 4 overlapping regulatory layers: i. via modifications of chromatin, ii. via modifications of recently identified transcription factor substrates, iii. via influencing the hepatic transcription factor crossregulatory circuitry, and iv. via modification of each other.
To dissect the role of these regulatory layers and determine their contribution in the control of hepatic metabolic pathways, and in the development of hepatocellular carcinoma, our activities will involve: i. Generation of relevant KO and transgenic mouse models, ii. Functional characterization of novel non-histone and histone substrates, iii. Analysis of novel cross-regulatory protein modifications affecting the activity of the enzymes and iv. the identification of their genomic targets and associated chromatin modifications using global approaches.
The work is expected to provide important insights into a previously unanticipated network of protein methylation-directed regulatory modules, potentially operating in multiple biological pathways such as liver development, metabolism, apoptosis and carcinogenesis. The functioning of such network would be of high biological importance, with far-reaching implications in drug development, rivaling those of phosphorylation or acetylation regulated processes."
Max ERC Funding
2 499 600 €
Duration
Start date: 2012-01-01, End date: 2016-12-31
