Project acronym ImmunoFit
Project Harnessing tumor metabolism to overcome immunosupression
Researcher (PI) Massimiliano MAZZONE
Host Institution (HI) VIB
Call Details Consolidator Grant (CoG), LS4, ERC-2017-COG
Summary Anti-cancer immunotherapy has provided patients with a promising treatment. Yet, it has also unveiled that the immunosuppressive tumor microenvironment (TME) hampers the efficiency of this therapeutic option and limits its success. The concept that metabolism is able to shape the immune response has gained general acceptance. Nonetheless, little is known on how the metabolic crosstalk between different tumor compartments contributes to the harsh TME and ultimately impairs T cell fitness within the tumor.
This proposal aims to decipher which metabolic changes in the TME impede proper anti-tumor immunity. Starting from the meta-analysis of public human datasets, corroborated by metabolomics and transcriptomics data from several mouse tumors, we ranked clinically relevant and altered metabolic pathways that correlate with resistance to immunotherapy. Using a CRISPR/Cas9 platform for their functional in vivo selection, we want to identify cancer cell intrinsic metabolic mediators and, indirectly, distinguish those belonging specifically to the stroma. By means of genetic tools and small molecules, we will modify promising metabolic pathways in cancer cells and stromal cells (particularly in tumor-associated macrophages) to harness tumor immunosuppression. In a mirroring approach, we will apply a similar screening tool on cytotoxic T cells to identify metabolic targets that enhance their fitness under adverse growth conditions. This will allow us to manipulate T cells ex vivo and to therapeutically intervene via adoptive T cell transfer. By analyzing the metabolic network and crosstalk within the tumor, this project will shed light on how metabolism contributes to the immunosuppressive TME and T cell maladaptation. The overall goal is to identify druggable metabolic targets that i) reinforce the intrinsic anti-tumor immune response by breaking immunosuppression and ii) promote T cell function in immunotherapeutic settings by rewiring either the TME or the T cell itself.
Summary
Anti-cancer immunotherapy has provided patients with a promising treatment. Yet, it has also unveiled that the immunosuppressive tumor microenvironment (TME) hampers the efficiency of this therapeutic option and limits its success. The concept that metabolism is able to shape the immune response has gained general acceptance. Nonetheless, little is known on how the metabolic crosstalk between different tumor compartments contributes to the harsh TME and ultimately impairs T cell fitness within the tumor.
This proposal aims to decipher which metabolic changes in the TME impede proper anti-tumor immunity. Starting from the meta-analysis of public human datasets, corroborated by metabolomics and transcriptomics data from several mouse tumors, we ranked clinically relevant and altered metabolic pathways that correlate with resistance to immunotherapy. Using a CRISPR/Cas9 platform for their functional in vivo selection, we want to identify cancer cell intrinsic metabolic mediators and, indirectly, distinguish those belonging specifically to the stroma. By means of genetic tools and small molecules, we will modify promising metabolic pathways in cancer cells and stromal cells (particularly in tumor-associated macrophages) to harness tumor immunosuppression. In a mirroring approach, we will apply a similar screening tool on cytotoxic T cells to identify metabolic targets that enhance their fitness under adverse growth conditions. This will allow us to manipulate T cells ex vivo and to therapeutically intervene via adoptive T cell transfer. By analyzing the metabolic network and crosstalk within the tumor, this project will shed light on how metabolism contributes to the immunosuppressive TME and T cell maladaptation. The overall goal is to identify druggable metabolic targets that i) reinforce the intrinsic anti-tumor immune response by breaking immunosuppression and ii) promote T cell function in immunotherapeutic settings by rewiring either the TME or the T cell itself.
Max ERC Funding
1 999 721 €
Duration
Start date: 2018-07-01, End date: 2023-06-30
Project acronym ImmunoStem
Project Dissecting and Overcoming Innate Immune Barriers for Therapeutically Efficient Hematopoietic Stem Cell Gene Engineering
Researcher (PI) Anna Christina Kajaste-Rudnitski
Host Institution (HI) OSPEDALE SAN RAFFAELE SRL
Call Details Consolidator Grant (CoG), LS7, ERC-2018-COG
Summary The low gene manipulation efficiency of human hematopoietic stem cells (HSC) remains a major hurdle for sustainable and broad clinical application of innovative therapies for a wide range of disorders. Indeed, high vector doses and prolonged ex vivo culture are still required for clinically relevant levels of gene transfer even with the most established lentiviral vector-based delivery platforms.
Current and emerging gene transfer and editing technologies expose HSC to components potentially recognized by host antiviral factors and nucleic acid sensors that likely restrict their genetic engineering and contribute to broad individual variability in clinical outcomes observed in recent gene therapy trials. Nevertheless, specific effectors are yet to be identified in HSC. We have recently identified an antiviral factor that potently blocks gene transfer in HSC and have discovered small molecules that efficiently counteract it. This is the first example of how manipulating a single host factor can significantly impact gene transfer efficiencies in HSC but likely represents the mere tip of the iceberg of the plethora of innate sensing mechanisms potentially hampering genetic manipulation of this primitive cell compartment.
This proposal aims to identify the antiviral factors and innate sensing pathways that prevent efficient modification of HSC and to mitigate their effects using methods developed through a thorough understanding of their mechanisms of action. My approach builds on the innovative concept that understanding the crosstalk between HSC and viral vectors will instruct us on which immune sensors and effectors to avoid and how, with direct implications for all gene engineering technologies. Successful completion of this project will deliver broadly exportable novel paradigms of innate pathogen recognition that will allow ground-breaking progress in the development of cutting-edge cell and gene therapies and to fight infectious and autoimmune diseases.
Summary
The low gene manipulation efficiency of human hematopoietic stem cells (HSC) remains a major hurdle for sustainable and broad clinical application of innovative therapies for a wide range of disorders. Indeed, high vector doses and prolonged ex vivo culture are still required for clinically relevant levels of gene transfer even with the most established lentiviral vector-based delivery platforms.
Current and emerging gene transfer and editing technologies expose HSC to components potentially recognized by host antiviral factors and nucleic acid sensors that likely restrict their genetic engineering and contribute to broad individual variability in clinical outcomes observed in recent gene therapy trials. Nevertheless, specific effectors are yet to be identified in HSC. We have recently identified an antiviral factor that potently blocks gene transfer in HSC and have discovered small molecules that efficiently counteract it. This is the first example of how manipulating a single host factor can significantly impact gene transfer efficiencies in HSC but likely represents the mere tip of the iceberg of the plethora of innate sensing mechanisms potentially hampering genetic manipulation of this primitive cell compartment.
This proposal aims to identify the antiviral factors and innate sensing pathways that prevent efficient modification of HSC and to mitigate their effects using methods developed through a thorough understanding of their mechanisms of action. My approach builds on the innovative concept that understanding the crosstalk between HSC and viral vectors will instruct us on which immune sensors and effectors to avoid and how, with direct implications for all gene engineering technologies. Successful completion of this project will deliver broadly exportable novel paradigms of innate pathogen recognition that will allow ground-breaking progress in the development of cutting-edge cell and gene therapies and to fight infectious and autoimmune diseases.
Max ERC Funding
1 994 375 €
Duration
Start date: 2019-03-01, End date: 2024-02-29
Project acronym InMec
Project Inside mechanisms sustaining cancer stem cells
Researcher (PI) Pier Giuseppe Pelicci
Host Institution (HI) ISTITUTO EUROPEO DI ONCOLOGIA SRL
Call Details Advanced Grant (AdG), LS4, ERC-2013-ADG
Summary The “Cancer Stem Cell (CSC) Hypothesis” postulates that the capacity to maintain tumour growth is owned by rare cancer cells, the CSCs, endowed with self-renewal properties. This hypothesis implies that CSCs must be eliminated to achieve cancer cure. Nevertheless, direct proof is still lacking, and recent findings challenge our concepts of CSCs, showing the limits of the CSC-defining assay (transplantation) and suggesting that CSC-identity might be context-dependent. We found two properties of CSCs self-renewal that are indispensable for the maintenance of an expanding CSC-pool and tumour growth: increased frequency of symmetric divisions, due to inactivation of the p53 tumour suppressor, and increased replicative potential, due to up-regulation of the cell-cycle inhibitor p21. We will now investigate: i) How loss of p53 in tumours leads to expansion of the CSC pool, by testing the hypothesis that p53-loss activates the Myc oncogene which induces CSC-reprogramming of differentiated cancer cells. ii) Whether p53-independent pathways are also implicated, by in vivo shRNA screens of primary tumours or normal progenitors to identify pathways involved, respectively, in CSC self-renewal or inhibition of SC-reprogramming. iii) How p21-induced cell-cycle arrest protects CSCs from self-renewal exhaustion, by investigating regulation of cell-cycle recruitment of quiescent CSCs. iv) Whether activation of p21 in CSCs induces a mutator phenotype, due to its ability to activate DNA repair, by investigating mechanisms of DNA-damage, mutation rates, and relevance of CSC mutations for development of chemoresistance. We will test self-renewal functions in a transplantation-independent assay, based on tumour re-growth in vivo after cytotoxic treatments and “clonal tracking” of re-growing tumours (using barcoded lentiviral libraries). Our long-term goal is the identification of CSC-specific targets that could be used to create the basis for CSC-specific pharmacological intervention.
Summary
The “Cancer Stem Cell (CSC) Hypothesis” postulates that the capacity to maintain tumour growth is owned by rare cancer cells, the CSCs, endowed with self-renewal properties. This hypothesis implies that CSCs must be eliminated to achieve cancer cure. Nevertheless, direct proof is still lacking, and recent findings challenge our concepts of CSCs, showing the limits of the CSC-defining assay (transplantation) and suggesting that CSC-identity might be context-dependent. We found two properties of CSCs self-renewal that are indispensable for the maintenance of an expanding CSC-pool and tumour growth: increased frequency of symmetric divisions, due to inactivation of the p53 tumour suppressor, and increased replicative potential, due to up-regulation of the cell-cycle inhibitor p21. We will now investigate: i) How loss of p53 in tumours leads to expansion of the CSC pool, by testing the hypothesis that p53-loss activates the Myc oncogene which induces CSC-reprogramming of differentiated cancer cells. ii) Whether p53-independent pathways are also implicated, by in vivo shRNA screens of primary tumours or normal progenitors to identify pathways involved, respectively, in CSC self-renewal or inhibition of SC-reprogramming. iii) How p21-induced cell-cycle arrest protects CSCs from self-renewal exhaustion, by investigating regulation of cell-cycle recruitment of quiescent CSCs. iv) Whether activation of p21 in CSCs induces a mutator phenotype, due to its ability to activate DNA repair, by investigating mechanisms of DNA-damage, mutation rates, and relevance of CSC mutations for development of chemoresistance. We will test self-renewal functions in a transplantation-independent assay, based on tumour re-growth in vivo after cytotoxic treatments and “clonal tracking” of re-growing tumours (using barcoded lentiviral libraries). Our long-term goal is the identification of CSC-specific targets that could be used to create the basis for CSC-specific pharmacological intervention.
Max ERC Funding
2 500 000 €
Duration
Start date: 2014-07-01, End date: 2019-06-30
Project acronym INTERACT
Project Counteracting psychosis by optimizing interaction
Researcher (PI) Inez Yvonne Ronald Germeys
Host Institution (HI) KATHOLIEKE UNIVERSITEIT LEUVEN
Call Details Starting Grant (StG), LS7, ERC-2012-StG_20111109
Summary Psychotic disorders are amongst the most severe mental disorders. However, current treatments have failed to reduce disability or change the prospects for recovery for patients with a psychotic disorder. In this project, I will investigate an entirely novel therapy, targeting the core vulnerability profile of altered person-environment interactions underlying psychosis, specifically increased stress-reactivity and reduced motivated and goal-directed behaviour. My colleagues and I have developed a digital apparatus, the ‘PsyMate’, allowing real-time interventions for patients with severe mental illness. In this project, the PsyMate will be used to (1)reduce psychotic and emotional reactivity to stress with “detachment and acceptance” exercises in real life situations, and (2)improve motivated and goal-directed behaviour with real-time behavioural activation therapy. In a randomized controlled trial, I will investigate whether this self-management therapy, conducted outside the office in the patient’s real life, is capable of reducing psychotic reactivity to stress and of improving motivated behaviour in participants with an at-risk mental state for psychosis.
In order to understand the impact of this intervention in terms of brain plasticity and prediction of response, I will use an experimental medicine approach to investigate the neural effects of the intervention. I will focus particularly on prefrontal dopamine-reactivity as the brain mechanism mediating altered person-environment interactions. In the current study, I will examine prefrontal dopamine reactivity towards positive as well as stressful negative events as the biological process mediating underlying motivated behaviour and environmental reactivity. Furthermore, I will investigate whether a self-management therapy specifically focused at aberrant person-environment interactions alters brain plasticity at the level of prefrontal dopaminergic neurotransmission in persons at risk for psychosis.
Summary
Psychotic disorders are amongst the most severe mental disorders. However, current treatments have failed to reduce disability or change the prospects for recovery for patients with a psychotic disorder. In this project, I will investigate an entirely novel therapy, targeting the core vulnerability profile of altered person-environment interactions underlying psychosis, specifically increased stress-reactivity and reduced motivated and goal-directed behaviour. My colleagues and I have developed a digital apparatus, the ‘PsyMate’, allowing real-time interventions for patients with severe mental illness. In this project, the PsyMate will be used to (1)reduce psychotic and emotional reactivity to stress with “detachment and acceptance” exercises in real life situations, and (2)improve motivated and goal-directed behaviour with real-time behavioural activation therapy. In a randomized controlled trial, I will investigate whether this self-management therapy, conducted outside the office in the patient’s real life, is capable of reducing psychotic reactivity to stress and of improving motivated behaviour in participants with an at-risk mental state for psychosis.
In order to understand the impact of this intervention in terms of brain plasticity and prediction of response, I will use an experimental medicine approach to investigate the neural effects of the intervention. I will focus particularly on prefrontal dopamine-reactivity as the brain mechanism mediating altered person-environment interactions. In the current study, I will examine prefrontal dopamine reactivity towards positive as well as stressful negative events as the biological process mediating underlying motivated behaviour and environmental reactivity. Furthermore, I will investigate whether a self-management therapy specifically focused at aberrant person-environment interactions alters brain plasticity at the level of prefrontal dopaminergic neurotransmission in persons at risk for psychosis.
Max ERC Funding
1 498 896 €
Duration
Start date: 2013-04-01, End date: 2018-03-31
Project acronym INTERRUPTB
Project "Estimating the effective reproductive rate of M. tuberculosis from changes in molecular clustering rates, to measure the impact of public health interventions on TB transmission"
Researcher (PI) Bouke Catherine De Jong
Host Institution (HI) PRINS LEOPOLD INSTITUUT VOOR TROPISCHE GENEESKUNDE
Call Details Starting Grant (StG), LS7, ERC-2012-StG_20111109
Summary "Excessive delays in treatment onset limit current tuberculosis (TB) control programs, presenting a major obstacle to the control of the TB epidemic. Increasing case detection, both quantitatively and temporally, is considered a priority, benefiting the patient (reduced morbidity and mortality) and the society (shortened period of infectiousness). These improvements in patient care have a common goal: to reduce transmission and eventually contain the spread of TB within the population. However, assessing reduced transmission of TB proofs to be difficult, as to date molecular tools have not been integrated in mathematical models or in field trials of public health interventions. Therefore, I aim to develop a model that incorporates bacterial genotyping to follow TB transmission within the human host population, hypothesizing that an effective Enhanced-Case-Finding (ECF) method can interrupt TB transmission. Integration of routine epidemiological and genotyping data with bioinformatics and mathematical modelling provides a novel and powerful approach to understand the key determinants of the TB epidemic, such as the Effective Reproductive Number, and predict the dynamics of TB transmission. I have the unique opportunity to position the present proposal as an added-value study that builds on 3-year Cluster Randomized Trial of ECF that I designed, which is about to be launched in The Gambia in 2012. By applying molecular genotyping methods to bacterial isolates collected from both the ECF intervention- and control arm, I will develop a method to measure and model the impact of ECF on the transmission of TB. This will be the first study of its kind in integrating molecular genotyping data in a TB transmission model as applied to a population level interventional study. The identification of significant transmission parameters will be important both for basic TB research and also for health experts that design and evaluate Public Health TB interventions in the future."
Summary
"Excessive delays in treatment onset limit current tuberculosis (TB) control programs, presenting a major obstacle to the control of the TB epidemic. Increasing case detection, both quantitatively and temporally, is considered a priority, benefiting the patient (reduced morbidity and mortality) and the society (shortened period of infectiousness). These improvements in patient care have a common goal: to reduce transmission and eventually contain the spread of TB within the population. However, assessing reduced transmission of TB proofs to be difficult, as to date molecular tools have not been integrated in mathematical models or in field trials of public health interventions. Therefore, I aim to develop a model that incorporates bacterial genotyping to follow TB transmission within the human host population, hypothesizing that an effective Enhanced-Case-Finding (ECF) method can interrupt TB transmission. Integration of routine epidemiological and genotyping data with bioinformatics and mathematical modelling provides a novel and powerful approach to understand the key determinants of the TB epidemic, such as the Effective Reproductive Number, and predict the dynamics of TB transmission. I have the unique opportunity to position the present proposal as an added-value study that builds on 3-year Cluster Randomized Trial of ECF that I designed, which is about to be launched in The Gambia in 2012. By applying molecular genotyping methods to bacterial isolates collected from both the ECF intervention- and control arm, I will develop a method to measure and model the impact of ECF on the transmission of TB. This will be the first study of its kind in integrating molecular genotyping data in a TB transmission model as applied to a population level interventional study. The identification of significant transmission parameters will be important both for basic TB research and also for health experts that design and evaluate Public Health TB interventions in the future."
Max ERC Funding
1 490 986 €
Duration
Start date: 2013-01-01, End date: 2017-12-31
Project acronym iPROTECTION
Project Molecular mechanisms of induced protection against sepsis by DNA damage responses
Researcher (PI) Luis Filipe Ferreira Moita
Host Institution (HI) FUNDACAO CALOUSTE GULBENKIAN
Call Details Consolidator Grant (CoG), LS4, ERC-2014-CoG
Summary Severe sepsis remains a poorly understood systemic inflammatory condition with high mortality rates and limited therapeutic options outside of infection control and organ support measures. Based on our recent discovery that anthracycline drugs prevent organ failure without affecting the bacterial burden in a model of severe sepsis, we propose that strategies aimed at target organ protection have extraordinary potential for the treatment of sepsis and possibly for other inflammation-driven conditions. However, the mechanisms of organ protection and disease tolerance are either unknown or poorly characterized.
The central goal of the current proposal is to identify and characterize novel cytoprotective mechanisms, with a focus on DNA damage response dependent protection activated by anthracyclines as a window into stress-induced genetic programs conferring disease tolerance. To that end, we will carry out a combination of candidate and unbiased approaches for the in vivo identification of ATM-dependent and independent mechanisms of tissue protection. We will validate the leading candidates through adenovirus-mediated delivery of constructs for overexpression (gain-of-function) or shRNA for gene silencing (loss-of-function) to the lung, based on our recent finding that rescuing this organ is essential and perhaps sufficient in anthracycline-induced protection against severe sepsis. The candidates showing the most promise will be characterized using a combination of in vitro and in vivo genetic, biochemical, cell biological and physiological methods.
The results arising from the current proposal are likely not only to inspire the design of transformative therapies for sepsis but also to open a completely new field of opportunity to molecularly understand core surveillance mechanisms of basic cellular processes with a critical role in the homeostasis of organ function and whose activation can ultimately promote quality of life during aging and increase lifespan.
Summary
Severe sepsis remains a poorly understood systemic inflammatory condition with high mortality rates and limited therapeutic options outside of infection control and organ support measures. Based on our recent discovery that anthracycline drugs prevent organ failure without affecting the bacterial burden in a model of severe sepsis, we propose that strategies aimed at target organ protection have extraordinary potential for the treatment of sepsis and possibly for other inflammation-driven conditions. However, the mechanisms of organ protection and disease tolerance are either unknown or poorly characterized.
The central goal of the current proposal is to identify and characterize novel cytoprotective mechanisms, with a focus on DNA damage response dependent protection activated by anthracyclines as a window into stress-induced genetic programs conferring disease tolerance. To that end, we will carry out a combination of candidate and unbiased approaches for the in vivo identification of ATM-dependent and independent mechanisms of tissue protection. We will validate the leading candidates through adenovirus-mediated delivery of constructs for overexpression (gain-of-function) or shRNA for gene silencing (loss-of-function) to the lung, based on our recent finding that rescuing this organ is essential and perhaps sufficient in anthracycline-induced protection against severe sepsis. The candidates showing the most promise will be characterized using a combination of in vitro and in vivo genetic, biochemical, cell biological and physiological methods.
The results arising from the current proposal are likely not only to inspire the design of transformative therapies for sepsis but also to open a completely new field of opportunity to molecularly understand core surveillance mechanisms of basic cellular processes with a critical role in the homeostasis of organ function and whose activation can ultimately promote quality of life during aging and increase lifespan.
Max ERC Funding
1 985 375 €
Duration
Start date: 2015-10-01, End date: 2020-09-30
Project acronym ISIFit
Project Individualised and self-adapting sound processing for cochlear implants
Researcher (PI) Tom Mark H. Francart
Host Institution (HI) KATHOLIEKE UNIVERSITEIT LEUVEN
Call Details Starting Grant (StG), LS7, ERC-2014-STG
Summary Cochlear implants (CIs) are successful auditory prostheses that enable people with deafness to hear through electrical stimulation of the auditory nerve. In a CI sound processor, a sound signal is converted into a sequence of electrical pulses. This conversion entails many parameters that should ideally be fine-tuned (fitted) for every individual patient, to account for various anatomical and physiological differences. In current clinical practice, devices are fitted during the initial rehabilitation and yearly thereafter. As fitting is very time consuming, only the bare minimum number of parameters is fitted individually. However, for many other parameters, for which currently the same default values are used for all patients, better speech understanding can be achieved with individual fitting. Apart from the fitting, CIs do not take into account the neural or perceptual effects of stimulation.
The objective of this project is to provide better fitting to individual patients by developing a closed-loop CI that automatically adjusts its fitting and sound processing based on the neural response to speech. To achieve this, we will (1) objectively measure speech understanding, by recording the electroencephalogram (EEG) in response to ecological speech signals, (2) automatically fit a wide array of sound processing parameters accordingly using a genetic algorithm, and (3) develop a wearable closed-loop CI that continuously records the EEG and adjusts the fitting in real-life situations.
This will lead to a better understanding of speech perception of people with a hearing impairment, an objective measure of speech intelligibility with many applications in diagnostics, a method to automatically fit CIs, and a novel closed-loop CI. For the patient this means improved speech intelligibility in noise and therefore better communication and quality of life. For the clinic this means improved efficiency and the ability to better fit devices.
Summary
Cochlear implants (CIs) are successful auditory prostheses that enable people with deafness to hear through electrical stimulation of the auditory nerve. In a CI sound processor, a sound signal is converted into a sequence of electrical pulses. This conversion entails many parameters that should ideally be fine-tuned (fitted) for every individual patient, to account for various anatomical and physiological differences. In current clinical practice, devices are fitted during the initial rehabilitation and yearly thereafter. As fitting is very time consuming, only the bare minimum number of parameters is fitted individually. However, for many other parameters, for which currently the same default values are used for all patients, better speech understanding can be achieved with individual fitting. Apart from the fitting, CIs do not take into account the neural or perceptual effects of stimulation.
The objective of this project is to provide better fitting to individual patients by developing a closed-loop CI that automatically adjusts its fitting and sound processing based on the neural response to speech. To achieve this, we will (1) objectively measure speech understanding, by recording the electroencephalogram (EEG) in response to ecological speech signals, (2) automatically fit a wide array of sound processing parameters accordingly using a genetic algorithm, and (3) develop a wearable closed-loop CI that continuously records the EEG and adjusts the fitting in real-life situations.
This will lead to a better understanding of speech perception of people with a hearing impairment, an objective measure of speech intelligibility with many applications in diagnostics, a method to automatically fit CIs, and a novel closed-loop CI. For the patient this means improved speech intelligibility in noise and therefore better communication and quality of life. For the clinic this means improved efficiency and the ability to better fit devices.
Max ERC Funding
1 734 360 €
Duration
Start date: 2015-11-01, End date: 2020-10-31
Project acronym IVM-VIRUS-NAB
Project In vivo dynamics of antibody responses to lymph-borne viruses
Researcher (PI) Matteo Iannacone
Host Institution (HI) UNIVERSITA VITA-SALUTE SAN RAFFAELE
Call Details Starting Grant (StG), LS6, ERC-2011-StG_20101109
Summary Objective. Our objective is to elucidate how neutralizing antibody (nAb) responses against live viruses are generated in vivo within lymph nodes (LNs). To this end we will make use of state-of-the-art imaging technology (i.e. multiphoton intravital microscopy [MP-IVM]), fluorescent replication-competent viruses and dedicated mouse models.
Background/Rationale. nAbs are critical for virus control, prevention of re-infection and protection conferred by available vaccines. Thanks to the recent advent of MP-IVM, several cellular and molecular events by which LNs orchestrate humoral immune responses have been clarified. As none of these studies employed live viruses, further work is required to extend these results to a more relevant natural setting. Also, the mechanisms by which cytopathic viruses (e.g. rabies virus in humans and vesicular stomatitis virus [VSV] in mice) induce early high affinity nAb responses while non-cytopathic viruses (e.g. hepatitis C virus in humans and lymphocytic choriomeningitis virus [LCMV] in mice) fail to do so remain poorly understood. Our rationale is based on the notion that, by bringing together unique reagents and advanced technology, we can - at last - address these issues experimentally.
Description of the project. The spatial and temporal constraints whereby virus-specific naïve B cells encounter viral antigen, interact with different LN cells and differentiate into plasma cells will be dynamically dissected in the various LN sub-compartments of mice infected with live cytopathic (VSV) and non-cytopathic (LCMV) viruses.
Anticipated output. We will provide the first complete in vivo imaging survey of virus-specific B cell activation, from the first minutes of viral entry into LNs to the generation of high affinity nAb-secreting cells. We will also identify virus-induced mechanisms interfering with nAb responses. This new knowledge will provide insight into aspects of viral immunity that may lead to novel rational vaccine strategies.
Summary
Objective. Our objective is to elucidate how neutralizing antibody (nAb) responses against live viruses are generated in vivo within lymph nodes (LNs). To this end we will make use of state-of-the-art imaging technology (i.e. multiphoton intravital microscopy [MP-IVM]), fluorescent replication-competent viruses and dedicated mouse models.
Background/Rationale. nAbs are critical for virus control, prevention of re-infection and protection conferred by available vaccines. Thanks to the recent advent of MP-IVM, several cellular and molecular events by which LNs orchestrate humoral immune responses have been clarified. As none of these studies employed live viruses, further work is required to extend these results to a more relevant natural setting. Also, the mechanisms by which cytopathic viruses (e.g. rabies virus in humans and vesicular stomatitis virus [VSV] in mice) induce early high affinity nAb responses while non-cytopathic viruses (e.g. hepatitis C virus in humans and lymphocytic choriomeningitis virus [LCMV] in mice) fail to do so remain poorly understood. Our rationale is based on the notion that, by bringing together unique reagents and advanced technology, we can - at last - address these issues experimentally.
Description of the project. The spatial and temporal constraints whereby virus-specific naïve B cells encounter viral antigen, interact with different LN cells and differentiate into plasma cells will be dynamically dissected in the various LN sub-compartments of mice infected with live cytopathic (VSV) and non-cytopathic (LCMV) viruses.
Anticipated output. We will provide the first complete in vivo imaging survey of virus-specific B cell activation, from the first minutes of viral entry into LNs to the generation of high affinity nAb-secreting cells. We will also identify virus-induced mechanisms interfering with nAb responses. This new knowledge will provide insight into aspects of viral immunity that may lead to novel rational vaccine strategies.
Max ERC Funding
1 934 200 €
Duration
Start date: 2012-02-01, End date: 2017-06-30
Project acronym KupfferCellNiche
Project Determining the instructive tissue signals and the master transcription factors driving Kupffer cell differentiation
Researcher (PI) Martin Wim V GUILLIAMS
Host Institution (HI) VIB
Call Details Consolidator Grant (CoG), LS6, ERC-2016-COG
Summary We have recently shown that contrary to common hypotheses, circulating monocytes can efficiently differentiate into Kupffer cells (KCs), the liver-resident macrophages. Using self-generated knock-in mice that allow specific KC depletion, we found that monocytes colonize the KC niche in a single wave upon KC depletion and rapidly differentiate into self-maintaining KCs that are transcriptionally and functionally identical to their embryonic counterparts. This implies that: (i) access to the KC niche is tightly regulated, ensuring that monocytes do not differentiate into KCs when the KC niche is full but differentiate very efficiently into KCs upon temporary niche availability, and (ii) imprinting by the KC niche is the dominant factor conferring KC identity. Understanding which cells represent the macrophage niche, which signals produced by these cells imprint the tissue-specific macrophage gene expression profile and through which transcription factors (TxFs) this is mediated is emerging as the next challenge in the field. We here propose an original strategy combining state-of-the-art in silico approaches and unique in vivo transgenic mouse models to tackle this challenge specifically for KCs, the most abundant macrophage in the body. We hypothesize that the liver sinusoidal endothelial cell (LSEC) to which the KC is attached represents the most likely candidate to sense KC loss, recruit new monocytes and drive their differentiation into KCs. Thus, this proposal aims to: (I) determine the TxFs through which the niche imprints KC identity, (II) map the LSEC-KC crosstalk during KC development, (III) generate LSEC-specific knock-in mice to study LSECs in vivo, (IV) demonstrate which LSEC factors influence KC development and function. Importantly, understanding how the KC-TxFs and the LSEC-KC crosstalk control KC development and function will be essential for the development of novel therapeutic interventions for hepatic disorders in which KCs play a central role.
Summary
We have recently shown that contrary to common hypotheses, circulating monocytes can efficiently differentiate into Kupffer cells (KCs), the liver-resident macrophages. Using self-generated knock-in mice that allow specific KC depletion, we found that monocytes colonize the KC niche in a single wave upon KC depletion and rapidly differentiate into self-maintaining KCs that are transcriptionally and functionally identical to their embryonic counterparts. This implies that: (i) access to the KC niche is tightly regulated, ensuring that monocytes do not differentiate into KCs when the KC niche is full but differentiate very efficiently into KCs upon temporary niche availability, and (ii) imprinting by the KC niche is the dominant factor conferring KC identity. Understanding which cells represent the macrophage niche, which signals produced by these cells imprint the tissue-specific macrophage gene expression profile and through which transcription factors (TxFs) this is mediated is emerging as the next challenge in the field. We here propose an original strategy combining state-of-the-art in silico approaches and unique in vivo transgenic mouse models to tackle this challenge specifically for KCs, the most abundant macrophage in the body. We hypothesize that the liver sinusoidal endothelial cell (LSEC) to which the KC is attached represents the most likely candidate to sense KC loss, recruit new monocytes and drive their differentiation into KCs. Thus, this proposal aims to: (I) determine the TxFs through which the niche imprints KC identity, (II) map the LSEC-KC crosstalk during KC development, (III) generate LSEC-specific knock-in mice to study LSECs in vivo, (IV) demonstrate which LSEC factors influence KC development and function. Importantly, understanding how the KC-TxFs and the LSEC-KC crosstalk control KC development and function will be essential for the development of novel therapeutic interventions for hepatic disorders in which KCs play a central role.
Max ERC Funding
1 996 705 €
Duration
Start date: 2017-07-01, End date: 2022-06-30
Project acronym LEAF-FALL
Project What makes leaves fall in autumn? A new process description for the timing of leaf senescence in temperate and boreal trees
Researcher (PI) Matteo CAMPIOLI
Host Institution (HI) UNIVERSITEIT ANTWERPEN
Call Details Starting Grant (StG), LS8, ERC-2016-STG
Summary Leaf phenology is a key component in the functioning of temperate and boreal deciduous forests. The environmental cues for bud-burst in spring are well known, but little is known about the cues controlling the timing of leaf fall in autumn. Leaf fall is the last stage of leaf senescence, a process which allows trees to recover leaf nutrients. We urgently need to understand the controls timing leaf senescence to improve our projections of forest growth and climate change. I propose a new general paradigm of the onset of leaf senescence, hypothesizing that leaf senescence is triggered by the cessation of tree growth in autumn. I expect that: (i) in the absence of growth-limiting environmental conditions, tree growth cessation directly controls leaf-senescence onset; and (ii) in the presence of growth-limiting conditions, photoperiod controls leaf-senescence onset – this prevents trees from starting to senesce too early. I will test these hypotheses with a combination of: (i) manipulative experiments on young trees - these will disentangle the impact of photoperiod from that of other factors affecting tree growth cessation, namely: temperature, drought and soil nutrient availability; (ii) monitoring leaf senescence and growth in mature forest stands; (iii) comparing the leaf senescence dynamics of four major tree species (Fagus sylvatica, Quercus robur, Betula pendula and Populus tremula) in four European locations spanning from 40º to 70º N; and (iv) integrating the new paradigm into a model of forest ecosystem dynamics and testing it for the major forested areas of Europe. The aim is to solve the conundrum of the timing of leaf senescence in temperate and boreal deciduous trees, provide a new interpretation of the relationship between leaf senescence, tree growth and environment, and deliver a modelling tool able to predict leaf senescence and tree growth, for projections of forest biomass production and climate change.
Summary
Leaf phenology is a key component in the functioning of temperate and boreal deciduous forests. The environmental cues for bud-burst in spring are well known, but little is known about the cues controlling the timing of leaf fall in autumn. Leaf fall is the last stage of leaf senescence, a process which allows trees to recover leaf nutrients. We urgently need to understand the controls timing leaf senescence to improve our projections of forest growth and climate change. I propose a new general paradigm of the onset of leaf senescence, hypothesizing that leaf senescence is triggered by the cessation of tree growth in autumn. I expect that: (i) in the absence of growth-limiting environmental conditions, tree growth cessation directly controls leaf-senescence onset; and (ii) in the presence of growth-limiting conditions, photoperiod controls leaf-senescence onset – this prevents trees from starting to senesce too early. I will test these hypotheses with a combination of: (i) manipulative experiments on young trees - these will disentangle the impact of photoperiod from that of other factors affecting tree growth cessation, namely: temperature, drought and soil nutrient availability; (ii) monitoring leaf senescence and growth in mature forest stands; (iii) comparing the leaf senescence dynamics of four major tree species (Fagus sylvatica, Quercus robur, Betula pendula and Populus tremula) in four European locations spanning from 40º to 70º N; and (iv) integrating the new paradigm into a model of forest ecosystem dynamics and testing it for the major forested areas of Europe. The aim is to solve the conundrum of the timing of leaf senescence in temperate and boreal deciduous trees, provide a new interpretation of the relationship between leaf senescence, tree growth and environment, and deliver a modelling tool able to predict leaf senescence and tree growth, for projections of forest biomass production and climate change.
Max ERC Funding
1 499 250 €
Duration
Start date: 2017-02-01, End date: 2022-01-31
Project acronym LEARN2SEE
Project Invariant visual object representations in the early postnatal and adult cortex: bridging theory, model and neurobiology
Researcher (PI) Davide Franco Zoccolan
Host Institution (HI) SCUOLA INTERNAZIONALE SUPERIORE DI STUDI AVANZATI DI TRIESTE
Call Details Consolidator Grant (CoG), LS5, ERC-2013-CoG
Summary Our visual system can effortlessly recognize hundreds of thousands of objects in spite of tremendous variation in their appearance, resulting, for instance, from changes in object position and pose. Achieving such an invariant representation of the visual world is an extremely challenging computational problem that even the most advanced artificial vision systems are not fully able to solve. This is why understanding the neuronal mechanisms underlying object vision is one of the major challenges of systems neuroscience and a crucial step towards developing artificial vision systems and visual prostheses.
Little is known yet about how the brain develops and maintains invariant object representations. The leading theory is that visual neurons exploit the spatiotemporal continuity of visual experience (i.e., the natural tendency of different object views to occur nearby in time) to learn to produce similar responses for temporally contiguous stimuli, so as to factorize object identity from other variables (such as position, size, etc.). This Unsupervised Temporal Learning (UTL) strategy has been instantiated in a number of computational frameworks, but its empirical investigation has received little attention. My proposal will use the visual system of the rat to address key questions about the nature of UTL and other learning theories, such as their impact on recognition behavior and object representations at both single-neuron and population level, and their role during early postnatal development. This will be achieved through a highly multidisciplinary approach, including high-throughput behavioral testing, in vivo neuronal recordings, immediate-early gene labeling, controlled-rearing in virtual visual environments, and computational modeling. This will lead to ground-breaking insights into the learning principles that sculpt the cortical representations of visual objects through unsupervised exposure to the spatiotemporal statistics of visual experience.
Summary
Our visual system can effortlessly recognize hundreds of thousands of objects in spite of tremendous variation in their appearance, resulting, for instance, from changes in object position and pose. Achieving such an invariant representation of the visual world is an extremely challenging computational problem that even the most advanced artificial vision systems are not fully able to solve. This is why understanding the neuronal mechanisms underlying object vision is one of the major challenges of systems neuroscience and a crucial step towards developing artificial vision systems and visual prostheses.
Little is known yet about how the brain develops and maintains invariant object representations. The leading theory is that visual neurons exploit the spatiotemporal continuity of visual experience (i.e., the natural tendency of different object views to occur nearby in time) to learn to produce similar responses for temporally contiguous stimuli, so as to factorize object identity from other variables (such as position, size, etc.). This Unsupervised Temporal Learning (UTL) strategy has been instantiated in a number of computational frameworks, but its empirical investigation has received little attention. My proposal will use the visual system of the rat to address key questions about the nature of UTL and other learning theories, such as their impact on recognition behavior and object representations at both single-neuron and population level, and their role during early postnatal development. This will be achieved through a highly multidisciplinary approach, including high-throughput behavioral testing, in vivo neuronal recordings, immediate-early gene labeling, controlled-rearing in virtual visual environments, and computational modeling. This will lead to ground-breaking insights into the learning principles that sculpt the cortical representations of visual objects through unsupervised exposure to the spatiotemporal statistics of visual experience.
Max ERC Funding
2 000 000 €
Duration
Start date: 2014-05-01, End date: 2019-04-30
Project acronym LEPTINMS
Project Leptin, metabolic state and natural regulatory T cells: cellular and molecular basis for a novel immune intervention in autoimmunity
Researcher (PI) Giuseppe Matarese
Host Institution (HI) CONSIGLIO NAZIONALE DELLE RICERCHE
Call Details Starting Grant (StG), LS3, ERC-2007-StG
Summary Our Group has been investigating the cellular and molecular mechanisms involving leptin, the adipocyte-derived hormone, in the pathogenesis of autoimmunity such as experimental autoimmune encephalomyelitis (EAE) and multiple sclerosis (MS).We analyzed the serum and cerebro-spinal fluid (CSF) leptin secretion and the interaction between serum leptin and naturally occurring Foxp3+CD4+CD25+ regulatory T cells (Tregs) in naïve-to-therapy multiple sclerosis (MS) patients. Leptin production was significantly increased in serum and CSF of MS patients and correlated with interferon-gamma (IFN-g) secretion in the CSF.T cell lines against human myelin basic protein (hMBP) produced leptin and upregulated the expression of the leptin receptor (ObR) after activation with hMBP; treatment with either anti-leptin or anti-leptin receptor neutralizing antibodies inhibited in vitro proliferation to hMBP.Interestingly, in the MS patients an inverse correlation between serum leptin and percentage of circulating Tregs was also observed. Moreover, treatment of EAE-susceptible mice with a leptin antagonist increased the percentage of Tregs and ameliorated disease clinical course and progression in proteolipid protein peptide (PLP139-151)-induced EAE.These findings show for the first time an inverse relationship between leptin secretion and the frequency of Tregs in EAE and MS.In the present project, we intend to analyze in vitro and in vivo, the relationship between leptin and Tregs in human and in animal models, studying at molecular and cellular level the effect of leptin and its neutralization on the survival, proliferation and cytokine secretion of Tregs.Despite recent advances, the precise requirements for the physiological development of Tregs such as the necessary milieu and their molecular/biochemical requirements, remain enigmatic.Understanding these events will be important for the generation of Tregs which could have potential implications for treatment of autoimmunity.
Summary
Our Group has been investigating the cellular and molecular mechanisms involving leptin, the adipocyte-derived hormone, in the pathogenesis of autoimmunity such as experimental autoimmune encephalomyelitis (EAE) and multiple sclerosis (MS).We analyzed the serum and cerebro-spinal fluid (CSF) leptin secretion and the interaction between serum leptin and naturally occurring Foxp3+CD4+CD25+ regulatory T cells (Tregs) in naïve-to-therapy multiple sclerosis (MS) patients. Leptin production was significantly increased in serum and CSF of MS patients and correlated with interferon-gamma (IFN-g) secretion in the CSF.T cell lines against human myelin basic protein (hMBP) produced leptin and upregulated the expression of the leptin receptor (ObR) after activation with hMBP; treatment with either anti-leptin or anti-leptin receptor neutralizing antibodies inhibited in vitro proliferation to hMBP.Interestingly, in the MS patients an inverse correlation between serum leptin and percentage of circulating Tregs was also observed. Moreover, treatment of EAE-susceptible mice with a leptin antagonist increased the percentage of Tregs and ameliorated disease clinical course and progression in proteolipid protein peptide (PLP139-151)-induced EAE.These findings show for the first time an inverse relationship between leptin secretion and the frequency of Tregs in EAE and MS.In the present project, we intend to analyze in vitro and in vivo, the relationship between leptin and Tregs in human and in animal models, studying at molecular and cellular level the effect of leptin and its neutralization on the survival, proliferation and cytokine secretion of Tregs.Despite recent advances, the precise requirements for the physiological development of Tregs such as the necessary milieu and their molecular/biochemical requirements, remain enigmatic.Understanding these events will be important for the generation of Tregs which could have potential implications for treatment of autoimmunity.
Max ERC Funding
880 000 €
Duration
Start date: 2008-07-01, End date: 2011-10-31
Project acronym LIMBo
Project Zooming the link between diet and brain health: how phenolic metabolites modulate brain inflammation
Researcher (PI) Cláudia NUNES DOS SANTOS
Host Institution (HI) UNIVERSIDADE NOVA DE LISBOA
Call Details Starting Grant (StG), LS9, ERC-2018-STG
Summary Currently a big concern of our aging society is to efficiently delay the onset of neurodegenerative diseases which are progressively rising in incidence. The paradigm that a diet rich in the phenolics, prevalent e.g. in fruits, is beneficial to brain health has reached the public. However their mechanistic actions in brain functions remain to be seen, particularly since the nature of those acting in the brain remains overlooked. I wish to address this gap by identifying candidate compounds that can support development of effective strategies to delay neurodegeneration.
Specifically, I will be analysing the potential of dietary phenolics in both prevention and treatment (i.e delay) of neuroinflammation – key process shared in neurodegenerative diseases. To break down the current indeterminate status of “cause vs effect”, my vision is to focus my research on metabolites derived from dietary phenolics that reach the brain. I will be investigating their effects in both established and unknown response pathways of microglia cells - the innate immune cells of the central nervous system, either alone or when communicating with other brain cells. Ultimately, to attain an integrated view of their effects I will establish nutrition trials in mice. LIMBo considers both pro- and anti- inflammatory processes to preliminary validate the action of any promising metabolite in prevention and/or therapeutics.
LIMBo provides valuable scientific insights for future implementation of healthy brain diets. My group is in a unique position to address LIMBo objectives due to multidisciplinary expertise in organic synthesis, metabolomics and molecular and cellular biology, together with our previous data on novel neuroactive metabolites.
LIMBo also creates far-reaching opportunities by generating knowledge that impacts our fundamental understanding on the diversity of phenolic metabolites and their specific influences in neuroinflammation and potential use as prodrugs.
Summary
Currently a big concern of our aging society is to efficiently delay the onset of neurodegenerative diseases which are progressively rising in incidence. The paradigm that a diet rich in the phenolics, prevalent e.g. in fruits, is beneficial to brain health has reached the public. However their mechanistic actions in brain functions remain to be seen, particularly since the nature of those acting in the brain remains overlooked. I wish to address this gap by identifying candidate compounds that can support development of effective strategies to delay neurodegeneration.
Specifically, I will be analysing the potential of dietary phenolics in both prevention and treatment (i.e delay) of neuroinflammation – key process shared in neurodegenerative diseases. To break down the current indeterminate status of “cause vs effect”, my vision is to focus my research on metabolites derived from dietary phenolics that reach the brain. I will be investigating their effects in both established and unknown response pathways of microglia cells - the innate immune cells of the central nervous system, either alone or when communicating with other brain cells. Ultimately, to attain an integrated view of their effects I will establish nutrition trials in mice. LIMBo considers both pro- and anti- inflammatory processes to preliminary validate the action of any promising metabolite in prevention and/or therapeutics.
LIMBo provides valuable scientific insights for future implementation of healthy brain diets. My group is in a unique position to address LIMBo objectives due to multidisciplinary expertise in organic synthesis, metabolomics and molecular and cellular biology, together with our previous data on novel neuroactive metabolites.
LIMBo also creates far-reaching opportunities by generating knowledge that impacts our fundamental understanding on the diversity of phenolic metabolites and their specific influences in neuroinflammation and potential use as prodrugs.
Max ERC Funding
1 496 022 €
Duration
Start date: 2019-04-01, End date: 2024-03-31
Project acronym LIVER IVM AND HBV
Project Imaging liver immunopathology by intravital microscopy (IVM): a new approach to study the pathogenesis of hepatitis B virus (HBV) infection
Researcher (PI) Luca Guidotti
Host Institution (HI) OSPEDALE SAN RAFFAELE SRL
Call Details Advanced Grant (AdG), LS6, ERC-2009-AdG
Summary Overall objective and Specific Aims. The overall objective of this proposal is to elucidate the pathogenesis of
HBV infection with the ultimate hope that this knowledge will lead to the development of new therapeutic
strategies to terminate persistent infection and its attendant costs and complications. Our approach is to dissect
poorly understood cellular and molecular pathways responsible for both liver disease and viral clearance taking
advantage of technological advances in the field of live imaging and unique mouse models of HBV infection.
Three specific aims will be pursued:
1. Visualize and characterize where and how naïve and effector CTL of different specificities adhere to
vessels and recognize/kill HBV-expressing hepatocytes within the “normal”, fibrotic/cirrhotic or
cancerous liver.
2. Characterize the role of platelets in HBV pathogenesis.
3. Characterize the role of Kupffer cells in HBV pathogenesis.
Summary
Overall objective and Specific Aims. The overall objective of this proposal is to elucidate the pathogenesis of
HBV infection with the ultimate hope that this knowledge will lead to the development of new therapeutic
strategies to terminate persistent infection and its attendant costs and complications. Our approach is to dissect
poorly understood cellular and molecular pathways responsible for both liver disease and viral clearance taking
advantage of technological advances in the field of live imaging and unique mouse models of HBV infection.
Three specific aims will be pursued:
1. Visualize and characterize where and how naïve and effector CTL of different specificities adhere to
vessels and recognize/kill HBV-expressing hepatocytes within the “normal”, fibrotic/cirrhotic or
cancerous liver.
2. Characterize the role of platelets in HBV pathogenesis.
3. Characterize the role of Kupffer cells in HBV pathogenesis.
Max ERC Funding
2 046 200 €
Duration
Start date: 2010-09-01, End date: 2016-03-31
Project acronym LOCOMOUSE
Project Cerebellar circuit mechanisms of coordinated locomotion in mice
Researcher (PI) Megan Rose Carey
Host Institution (HI) FUNDACAO D. ANNA SOMMER CHAMPALIMAUD E DR. CARLOS MONTEZ CHAMPALIMAUD
Call Details Starting Grant (StG), LS5, ERC-2014-STG
Summary A remarkable aspect of motor control is our seemingly effortless ability to generate coordinated movements. How is activity within neural circuits orchestrated to allow us to engage in complex activities like gymnastics, riding a bike, or walking down the street while drinking a cup of coffee? The cerebellum is critical for coordinated movement, and the well-described, stereotyped circuitry of the cerebellum has made it an attractive system for neural circuits research. Much is known about how activity and plasticity in its identified cell types contribute to simple forms of motor learning. In contrast, while gait ataxia, or uncoordinated walking, is a hallmark of cerebellar damage, the circuit mechanisms underlying cerebellar contributions to coordinated locomotion are not well understood. One limitation has been the difficulty in extracting quantitative measures of coordination from the complex, whole body action of locomotion. We have developed a custom-built system (LocoMouse) to analyze mouse locomotor coordination. It tracks continuous paw, snout, and tail trajectories in 3D with unprecedented spatiotemporal resolution and it has allowed us to identify specific, quantitative locomotor elements that depend on intact cerebellar function. Here we will combine this quantitative behavioral approach with electrophysiology and optogenetics to investigate circuit mechanisms of locomotor coordination. We will 1) Optogenetically silence the output of cerebellar subregions to understand their distinct contributions to locomotion. 2) Record from identified neurons and correlate their activity with specific locomotor parameters. 3) Optogenetically stimulate defined cell types to investigate circuit mechanisms of coordinated locomotion. These experiments will establish causal relationships between neural circuit activity and coordinated motor control, a problem with important implications for both health and disease.
Summary
A remarkable aspect of motor control is our seemingly effortless ability to generate coordinated movements. How is activity within neural circuits orchestrated to allow us to engage in complex activities like gymnastics, riding a bike, or walking down the street while drinking a cup of coffee? The cerebellum is critical for coordinated movement, and the well-described, stereotyped circuitry of the cerebellum has made it an attractive system for neural circuits research. Much is known about how activity and plasticity in its identified cell types contribute to simple forms of motor learning. In contrast, while gait ataxia, or uncoordinated walking, is a hallmark of cerebellar damage, the circuit mechanisms underlying cerebellar contributions to coordinated locomotion are not well understood. One limitation has been the difficulty in extracting quantitative measures of coordination from the complex, whole body action of locomotion. We have developed a custom-built system (LocoMouse) to analyze mouse locomotor coordination. It tracks continuous paw, snout, and tail trajectories in 3D with unprecedented spatiotemporal resolution and it has allowed us to identify specific, quantitative locomotor elements that depend on intact cerebellar function. Here we will combine this quantitative behavioral approach with electrophysiology and optogenetics to investigate circuit mechanisms of locomotor coordination. We will 1) Optogenetically silence the output of cerebellar subregions to understand their distinct contributions to locomotion. 2) Record from identified neurons and correlate their activity with specific locomotor parameters. 3) Optogenetically stimulate defined cell types to investigate circuit mechanisms of coordinated locomotion. These experiments will establish causal relationships between neural circuit activity and coordinated motor control, a problem with important implications for both health and disease.
Max ERC Funding
1 496 750 €
Duration
Start date: 2015-05-01, End date: 2020-04-30
Project acronym LUNELY
Project ALK as a common target for the pathogenesis and therapy in lymphoma, lung carcinoma and neuroblastoma
Researcher (PI) Roberto Chiarle
Host Institution (HI) UNIVERSITA DEGLI STUDI DI TORINO
Call Details Starting Grant (StG), LS4, ERC-2009-StG
Summary The Anaplastic Lymphoma Kinase (ALK) has been discovered as the result of chromosomal translocations in Anaplastic Large Cell Lymphomas (ALCL) (Chiarle et al Nat Rev Cancer. 2008, 8:11). In ALCL, the role of the ALK oncogenic translocations has been established in vitro and in transgenic mouse models. Recent findings have shown ALK translocations, mutations or amplifications in other types of solid cancers, such as lung carcinoma (Soda et al. Nature. 2007, 448:561) and neuroblastoma (Mossè et al. Nature 2008, 455: 930). However, the role of ALK gene mutations in these solid tumours remains largely undetermined. This lack of knowledge is even worse given the fact that a therapy that targets ALK in these tumours could be feasible. Aim 1. Targeting of ALK in ALCL lymphomas. ALCL ALK positive lymphomas will be tested for small molecule inhibitors of the activity of ALK. In addition, a combination of gene silencing, such as small interfering RNA (siRNA), and vaccination against ALK will be validated as selective ALK therapies. Aim 2. Characterization of the role of ALK in lung cancer through the generation of mouse models. We propose to characterize the pathogenetic role of ALK in lung cancer by in vitro studies and by generating mouse models for ALK positive lung cancers. These mouse models will be fundamental to validate the innovative therapies against ALK positive lung carcinoma. Aim 3. Validation of ALK as an oncogene and a therapeutic target in neuroblastoma. We plan to develop mouse models of neuroblastoma to investigate the pathogenetic role of ALK in the onset and maintenance of neuroblastoma in vivo. These mouse model of neuroblastoma will be used for the validation of ALK specific therapies. Overall, the proposed project will define the role of ALK in lymphoma, neuroblastoma and lungcancer and validate its potential use as a a target for therapy in those tumours. The impact of these novel therapies will be of great value in these deadly tumours.
Summary
The Anaplastic Lymphoma Kinase (ALK) has been discovered as the result of chromosomal translocations in Anaplastic Large Cell Lymphomas (ALCL) (Chiarle et al Nat Rev Cancer. 2008, 8:11). In ALCL, the role of the ALK oncogenic translocations has been established in vitro and in transgenic mouse models. Recent findings have shown ALK translocations, mutations or amplifications in other types of solid cancers, such as lung carcinoma (Soda et al. Nature. 2007, 448:561) and neuroblastoma (Mossè et al. Nature 2008, 455: 930). However, the role of ALK gene mutations in these solid tumours remains largely undetermined. This lack of knowledge is even worse given the fact that a therapy that targets ALK in these tumours could be feasible. Aim 1. Targeting of ALK in ALCL lymphomas. ALCL ALK positive lymphomas will be tested for small molecule inhibitors of the activity of ALK. In addition, a combination of gene silencing, such as small interfering RNA (siRNA), and vaccination against ALK will be validated as selective ALK therapies. Aim 2. Characterization of the role of ALK in lung cancer through the generation of mouse models. We propose to characterize the pathogenetic role of ALK in lung cancer by in vitro studies and by generating mouse models for ALK positive lung cancers. These mouse models will be fundamental to validate the innovative therapies against ALK positive lung carcinoma. Aim 3. Validation of ALK as an oncogene and a therapeutic target in neuroblastoma. We plan to develop mouse models of neuroblastoma to investigate the pathogenetic role of ALK in the onset and maintenance of neuroblastoma in vivo. These mouse model of neuroblastoma will be used for the validation of ALK specific therapies. Overall, the proposed project will define the role of ALK in lymphoma, neuroblastoma and lungcancer and validate its potential use as a a target for therapy in those tumours. The impact of these novel therapies will be of great value in these deadly tumours.
Max ERC Funding
1 010 000 €
Duration
Start date: 2009-11-01, End date: 2014-04-30
Project acronym LYSOSOMICS
Project Functional Genomics of the Lysosome
Researcher (PI) Andrea BALLABIO
Host Institution (HI) FONDAZIONE TELETHON
Call Details Advanced Grant (AdG), LS2, ERC-2015-AdG
Summary For a long time the lysosome has been viewed as a “static” organelle that performs “routine” work for the cell, mostly pertaining to degradation and recycling of cellular waste. My group has challenged this view and used a systems biology approach to discover that the lysosome is subject to a global transcriptional regulation, is able to adapt to environmental clues, and acts as a signalling hub to regulate cell homeostasis. Furthermore, an emerging role of the lysosome has been identified in many types of diseases, including the common neurodegenerative disorders Parkinson's and Alzheimer’s. These findings have opened entirely new fields of investigation on lysosomal biology, suggesting that there is a lot to be learned on the role of the lysosome in health and disease. The goal of LYSOSOMICS is to use “omics” approaches to study lysosomal function and its regulation in normal and pathological conditions. In this “organellar systems biology project” we plan to perform several types of genetic perturbations in three widely used cell lines and study their effects on lysosomal function using a set of newly developed cellular phenotypic assays. Moreover, we plan to identify lysosomal protein-protein interactions using a novel High Content FRET-based approach. Finally, we will use the CRISPR-Cas9 technology to generate a collection of cellular models for all lysosomal storage diseases, a group of severe inherited diseases often associated with early onset neurodegeneration. State-of-the-art computational approaches will be used to predict gene function and identify disease mechanisms potentially exploitable for therapeutic purposes. The physiological relevance of newly identified pathways will be validated by in vivo studies performed on selected genes by using medaka and mice as model systems. This study will allow us to gain a comprehensive understanding of lysosomal function and dysfunction and to use this knowledge to develop new therapeutic strategies.
Summary
For a long time the lysosome has been viewed as a “static” organelle that performs “routine” work for the cell, mostly pertaining to degradation and recycling of cellular waste. My group has challenged this view and used a systems biology approach to discover that the lysosome is subject to a global transcriptional regulation, is able to adapt to environmental clues, and acts as a signalling hub to regulate cell homeostasis. Furthermore, an emerging role of the lysosome has been identified in many types of diseases, including the common neurodegenerative disorders Parkinson's and Alzheimer’s. These findings have opened entirely new fields of investigation on lysosomal biology, suggesting that there is a lot to be learned on the role of the lysosome in health and disease. The goal of LYSOSOMICS is to use “omics” approaches to study lysosomal function and its regulation in normal and pathological conditions. In this “organellar systems biology project” we plan to perform several types of genetic perturbations in three widely used cell lines and study their effects on lysosomal function using a set of newly developed cellular phenotypic assays. Moreover, we plan to identify lysosomal protein-protein interactions using a novel High Content FRET-based approach. Finally, we will use the CRISPR-Cas9 technology to generate a collection of cellular models for all lysosomal storage diseases, a group of severe inherited diseases often associated with early onset neurodegeneration. State-of-the-art computational approaches will be used to predict gene function and identify disease mechanisms potentially exploitable for therapeutic purposes. The physiological relevance of newly identified pathways will be validated by in vivo studies performed on selected genes by using medaka and mice as model systems. This study will allow us to gain a comprehensive understanding of lysosomal function and dysfunction and to use this knowledge to develop new therapeutic strategies.
Max ERC Funding
2 362 563 €
Duration
Start date: 2016-10-01, End date: 2021-09-30
Project acronym MAMMASTEM
Project Molecular mechanisms of the regulation of mammary stem cell homeostasis and their subversion in cancer
Researcher (PI) Pier Paolo Di Fiore
Host Institution (HI) IFOM FONDAZIONE ISTITUTO FIRC DI ONCOLOGIA MOLECOLARE
Call Details Advanced Grant (AdG), LS3, ERC-2008-AdG
Summary Stem cells (SCs) are thought to be integral to the development and progression of cancer, and their eradication may be essential for the cure of cancer. Yet, direct proof is lacking due to our poor understanding of the molecular differences between normal and cancer SCs. We will investigate normal and cancer mammary stem cells (MSCs) by focusing on the role of the cell fate determinant Numb in two signaling axes: Numb:Notch and Numb:p53. Numb is a tumor suppressor in human breast cancer. Its expression is lost, through increased degradation, in ~50% of breast cancers. These Numbneg cancers display overall poorer prognosis. Mechanistically, loss of Numb causes increased Notch signaling and decreased p53 signaling. Thus, Numb controls both an oncogenic pathway (the Numb:Notch axis) and a tumor suppressor one (the Numb:p53 axis). We showed that Numb is asymmetrically partitioned at the first division of normal MSCs and hypothesize that loss of Numb affects the kinetics of division and MSC fate. Our specific aims are to: 1. Define the role of the Numb:Notch and Numb:p53 axes in normal and cancer MSCs. We will exploit our capacity to propagate and isolate MSCs to near-purity, for biological, biochemical and omics approaches. In this task, we will integrate knowledge derived from the analysis of real human cancers and of genetically-defined mouse models. 2. Define the broader biological context of Numb impact in stem cell biology, by analyzing the role of endocytosis in MSC fate determination. This is justified by the fact that Numb is an endocytic protein and that data in Drosophila indicate a complex role of endocytosis in cell fate specification. 3. Identify the E3 ligase responsible for Numb degradation in Numbneg breast tumors, in order to obtain druggable targets to restore Numb levels in these tumors. If successful, our work will elucidate major mechanisms of normal and cancer stem cell regulation, and provide tools for SC-specific therapeutic intervention.
Summary
Stem cells (SCs) are thought to be integral to the development and progression of cancer, and their eradication may be essential for the cure of cancer. Yet, direct proof is lacking due to our poor understanding of the molecular differences between normal and cancer SCs. We will investigate normal and cancer mammary stem cells (MSCs) by focusing on the role of the cell fate determinant Numb in two signaling axes: Numb:Notch and Numb:p53. Numb is a tumor suppressor in human breast cancer. Its expression is lost, through increased degradation, in ~50% of breast cancers. These Numbneg cancers display overall poorer prognosis. Mechanistically, loss of Numb causes increased Notch signaling and decreased p53 signaling. Thus, Numb controls both an oncogenic pathway (the Numb:Notch axis) and a tumor suppressor one (the Numb:p53 axis). We showed that Numb is asymmetrically partitioned at the first division of normal MSCs and hypothesize that loss of Numb affects the kinetics of division and MSC fate. Our specific aims are to: 1. Define the role of the Numb:Notch and Numb:p53 axes in normal and cancer MSCs. We will exploit our capacity to propagate and isolate MSCs to near-purity, for biological, biochemical and omics approaches. In this task, we will integrate knowledge derived from the analysis of real human cancers and of genetically-defined mouse models. 2. Define the broader biological context of Numb impact in stem cell biology, by analyzing the role of endocytosis in MSC fate determination. This is justified by the fact that Numb is an endocytic protein and that data in Drosophila indicate a complex role of endocytosis in cell fate specification. 3. Identify the E3 ligase responsible for Numb degradation in Numbneg breast tumors, in order to obtain druggable targets to restore Numb levels in these tumors. If successful, our work will elucidate major mechanisms of normal and cancer stem cell regulation, and provide tools for SC-specific therapeutic intervention.
Max ERC Funding
2 274 862 €
Duration
Start date: 2009-03-01, End date: 2014-02-28
Project acronym MANGO
Project The determinants of cross-seeding of protein aggregation: a Multiple TANGO
Researcher (PI) Joost Schymkowitz
Host Institution (HI) VIB
Call Details Consolidator Grant (CoG), LS2, ERC-2014-CoG
Summary Amyloid-like protein aggregation is a process of protein assembly via the formation of intermolecular β-structures by short aggregation prone sequence regions. This occurs as an unwanted side-reaction of impaired protein folding in disease, but also for the construction of natural nanomaterials. Aggregates appear to be strongly enriched in particular proteins, suggesting that the assembly process itself is specific, but the cross-seeding of the aggregation of one protein by aggregates of another protein has also been reported.
The key question that I aim to address in this proposal is how the beta-interactions of the amino acids in the aggregate spine determine the trade-off between the specificity of aggregation versus cross-seeding. To this end, I will determine the energy difference between homotypic versus heterotypic interactions and how differences in sequence translate into energy gaps. Moreover, I will analyse the sequence variations of aggregation prone stretches in natural proteomes to understand the danger of widespread co-aggregation.
To achieve these outcomes, I will study the interactions and cross-seeding of aggregating proteins and model peptides in vitro and in cells. I will extract the sequence and structural determinants of co-aggregation, and employ these to construct novel bioinformatics algorithm that can accurately predict co-aggregation and cross-seeding. I will use these to analyse co-aggregation cascades in natural proteomes looking for mechanisms that protect them from wide-spread cross-seeding.
This work will have a significant impact on the understanding of the downstream effects of protein aggregates and may reveal co-aggregation networks in human diseases such as the major neurodegenerative diseases or cancer, potentially opening up new research lines on the mechanisms underlying these pathologies and thus identify targets for novel therapies.
Summary
Amyloid-like protein aggregation is a process of protein assembly via the formation of intermolecular β-structures by short aggregation prone sequence regions. This occurs as an unwanted side-reaction of impaired protein folding in disease, but also for the construction of natural nanomaterials. Aggregates appear to be strongly enriched in particular proteins, suggesting that the assembly process itself is specific, but the cross-seeding of the aggregation of one protein by aggregates of another protein has also been reported.
The key question that I aim to address in this proposal is how the beta-interactions of the amino acids in the aggregate spine determine the trade-off between the specificity of aggregation versus cross-seeding. To this end, I will determine the energy difference between homotypic versus heterotypic interactions and how differences in sequence translate into energy gaps. Moreover, I will analyse the sequence variations of aggregation prone stretches in natural proteomes to understand the danger of widespread co-aggregation.
To achieve these outcomes, I will study the interactions and cross-seeding of aggregating proteins and model peptides in vitro and in cells. I will extract the sequence and structural determinants of co-aggregation, and employ these to construct novel bioinformatics algorithm that can accurately predict co-aggregation and cross-seeding. I will use these to analyse co-aggregation cascades in natural proteomes looking for mechanisms that protect them from wide-spread cross-seeding.
This work will have a significant impact on the understanding of the downstream effects of protein aggregates and may reveal co-aggregation networks in human diseases such as the major neurodegenerative diseases or cancer, potentially opening up new research lines on the mechanisms underlying these pathologies and thus identify targets for novel therapies.
Max ERC Funding
1 995 523 €
Duration
Start date: 2015-06-01, End date: 2020-05-31
Project acronym MEDICI
Project The inflammatory gene expression program in macrophages: An integrative approach for the systematic characterization of transcriptional co-regulators
Researcher (PI) gioacchino Natoli
Host Institution (HI) HUMANITAS UNIVERSITY
Call Details Advanced Grant (AdG), LS6, ERC-2015-AdG
Summary Tissue responses to microbial and endogenous danger signals involve the activation of both resident and monocyte-derived macrophages, as well as the coordinated inducible expression of hundreds of inflammatory genes. Gene transcription is controlled by the information contained in thousands of genomic regulatory elements (enhancers and promoters), which is first read by transcription factors (TFs) and then integrated and relayed to the transcriptional machinery via an array of co-regulators with disparate biochemical activities and functions. The recent work of several groups, including our own, has extensively characterized how in macrophages the genomic regulatory sequences controlling inflammatory gene expression are coordinately bound and activated by myeloid lineage-determining TFs and broadly expressed stimulus-activated TFs. However, we still have a very incomplete understanding of the necessary next step in the process, namely how distinct combinations of DNA-bound TFs regulate recruitment and function of the co-regulators and machineries that control gene transcription.
Here, I propose to systematically identify the complement of co-regulators that control the induction of inflammatory genes in macrophages, which will be then mechanistically and functionally characterized both in vitro and in vivo. By integrating cutting edge genomic and computational approaches with focused genetic screens and biochemical analyses, and eventually validating relevant results in mouse models, this project aims at obtaining an unprecedented level of understanding of the information flow linking genomic regulatory elements to inflammatory gene transcription.
Summary
Tissue responses to microbial and endogenous danger signals involve the activation of both resident and monocyte-derived macrophages, as well as the coordinated inducible expression of hundreds of inflammatory genes. Gene transcription is controlled by the information contained in thousands of genomic regulatory elements (enhancers and promoters), which is first read by transcription factors (TFs) and then integrated and relayed to the transcriptional machinery via an array of co-regulators with disparate biochemical activities and functions. The recent work of several groups, including our own, has extensively characterized how in macrophages the genomic regulatory sequences controlling inflammatory gene expression are coordinately bound and activated by myeloid lineage-determining TFs and broadly expressed stimulus-activated TFs. However, we still have a very incomplete understanding of the necessary next step in the process, namely how distinct combinations of DNA-bound TFs regulate recruitment and function of the co-regulators and machineries that control gene transcription.
Here, I propose to systematically identify the complement of co-regulators that control the induction of inflammatory genes in macrophages, which will be then mechanistically and functionally characterized both in vitro and in vivo. By integrating cutting edge genomic and computational approaches with focused genetic screens and biochemical analyses, and eventually validating relevant results in mouse models, this project aims at obtaining an unprecedented level of understanding of the information flow linking genomic regulatory elements to inflammatory gene transcription.
Max ERC Funding
2 500 000 €
Duration
Start date: 2016-11-01, End date: 2021-10-31
