Project acronym BrokenGenome
Project Breaking and rebuilding the genome: mechanistic rules for the dangerous game of sex.
Researcher (PI) Corentin CLAEYS BOUUAERT
Host Institution (HI) UNIVERSITE CATHOLIQUE DE LOUVAIN
Call Details Starting Grant (StG), LS1, ERC-2018-STG
Summary Sexual reproduction depends on the programmed induction of DNA double-strand breaks (DSBs) and their ensuing repair by homologous recombination. This complex process is essential for sexual reproduction because it ultimately allows the pairing and separation of homologous chromosomes during formation of haploid gametes. Although meiotic recombination has been investigated for decades, many of the underlying molecular processes remain unclear, largely due to the lack of biochemical studies. I have recently made important progress by, for the first time, successfully purifying proteins involved in two aspects of meiotic recombination: DSB formation and the final stage of formation of the crossovers that are a central raison-d’être of meiotic recombination. This has opened new avenues for future research that I intend to pursue in my own laboratory. Here, I propose a set of biochemical approaches, complemented by molecular genetics methods, to gain insights into four central problems: (i) How meiotic proteins collaborate to induce DSBs; (ii) How DSB proteins interact with components that form the axes of meiotic chromosomes; (iii) How proteins involved at later stages of recombination form crossovers; and (iv) How crossover proteins interact with components of synapsed chromosomes. For each problem, I will set up in vitro systems to probe the activities of the players involved, their interactions with DNA, and their assembly into macromolecular complexes. In addition, I propose to develop new methodology for identifying proteins that are associated with DNA that has undergone recombination-related DNA synthesis. My goal is to gain insights into the mechanisms that govern meiotic recombination. Importantly, these mechanisms are intimately linked not only to gamete formation, but also to the general recombination pathways that all cells use to maintain genome stability. In both contexts, our findings will be relevant to the development and avoidance of disease states.
Summary
Sexual reproduction depends on the programmed induction of DNA double-strand breaks (DSBs) and their ensuing repair by homologous recombination. This complex process is essential for sexual reproduction because it ultimately allows the pairing and separation of homologous chromosomes during formation of haploid gametes. Although meiotic recombination has been investigated for decades, many of the underlying molecular processes remain unclear, largely due to the lack of biochemical studies. I have recently made important progress by, for the first time, successfully purifying proteins involved in two aspects of meiotic recombination: DSB formation and the final stage of formation of the crossovers that are a central raison-d’être of meiotic recombination. This has opened new avenues for future research that I intend to pursue in my own laboratory. Here, I propose a set of biochemical approaches, complemented by molecular genetics methods, to gain insights into four central problems: (i) How meiotic proteins collaborate to induce DSBs; (ii) How DSB proteins interact with components that form the axes of meiotic chromosomes; (iii) How proteins involved at later stages of recombination form crossovers; and (iv) How crossover proteins interact with components of synapsed chromosomes. For each problem, I will set up in vitro systems to probe the activities of the players involved, their interactions with DNA, and their assembly into macromolecular complexes. In addition, I propose to develop new methodology for identifying proteins that are associated with DNA that has undergone recombination-related DNA synthesis. My goal is to gain insights into the mechanisms that govern meiotic recombination. Importantly, these mechanisms are intimately linked not only to gamete formation, but also to the general recombination pathways that all cells use to maintain genome stability. In both contexts, our findings will be relevant to the development and avoidance of disease states.
Max ERC Funding
1 499 075 €
Duration
Start date: 2019-07-01, End date: 2024-06-30
Project acronym CANCERSTEM
Project Stem cells in epithelial cancer initiation and growth
Researcher (PI) Cédric Blanpain
Host Institution (HI) UNIVERSITE LIBRE DE BRUXELLES
Call Details Starting Grant (StG), LS6, ERC-2007-StG
Summary Cancer is the result of a multi-step process requiring the accumulation of mutations in several genes. For most cancers, the target cells of oncogenic mutations are unknown. Adult stem cells (SCs) might be the initial target cells as they self-renew for extended periods of time, providing increased opportunity to accumulate the mutations required for cancer formation. Certain cancers contain cells characteristics of SC with high self-renewal capacities and the ability to reform the parental tumor upon transplantation. However, whether the initial oncogenic mutations arise in normal stem cells or in more differentiated cells that re-acquire stem cell-like properties remains to be determined. The demonstration that SCs are the target cells of the initial transforming events and that cancers contain cells with SC characteristics await the development of tools allowing for the isolation and characterization of normal adult SCs. In most epithelia from which cancers naturally arise, such tools are not yet available. We have recently developed novel methods to specifically mark and isolate multipotent epidermal slow-cycling SCs, making it now possible to determine the role of SC during epithelial cancer formation. In this project, we will use mice epidermis as a model to define the role of SC in epithelial cancer initiation and growth. Specifically, we will determine whether epithelial SCs are the initial target cells of oncogenic mutations during skin cancer formation, whether oncogenic mutations lead preferentially to skin cancer when they arise in SC rather than in more committed cells and whether cancer stem cells contribute to epithelial tumor growth and relapse after therapy.
Summary
Cancer is the result of a multi-step process requiring the accumulation of mutations in several genes. For most cancers, the target cells of oncogenic mutations are unknown. Adult stem cells (SCs) might be the initial target cells as they self-renew for extended periods of time, providing increased opportunity to accumulate the mutations required for cancer formation. Certain cancers contain cells characteristics of SC with high self-renewal capacities and the ability to reform the parental tumor upon transplantation. However, whether the initial oncogenic mutations arise in normal stem cells or in more differentiated cells that re-acquire stem cell-like properties remains to be determined. The demonstration that SCs are the target cells of the initial transforming events and that cancers contain cells with SC characteristics await the development of tools allowing for the isolation and characterization of normal adult SCs. In most epithelia from which cancers naturally arise, such tools are not yet available. We have recently developed novel methods to specifically mark and isolate multipotent epidermal slow-cycling SCs, making it now possible to determine the role of SC during epithelial cancer formation. In this project, we will use mice epidermis as a model to define the role of SC in epithelial cancer initiation and growth. Specifically, we will determine whether epithelial SCs are the initial target cells of oncogenic mutations during skin cancer formation, whether oncogenic mutations lead preferentially to skin cancer when they arise in SC rather than in more committed cells and whether cancer stem cells contribute to epithelial tumor growth and relapse after therapy.
Max ERC Funding
1 600 000 €
Duration
Start date: 2008-07-01, End date: 2013-12-31
Project acronym IM-ID
Project Defining the intrinsic transcriptional programs and the microenvironmental signals tailoring lung Interstitial Macrophage IDentity
Researcher (PI) Thomas MARICHAL
Host Institution (HI) UNIVERSITE DE LIEGE
Call Details Starting Grant (StG), LS6, ERC-2018-STG
Summary The mechanisms underlying lung homeostasis are of fundamental biological importance and have critical implications for the prevention of immune-mediated diseases such as asthma. We have demonstrated that lung Interstitial Macrophages (IM) exhibit a tolerogenic profile and are able to prevent and limit the development of aberrant immune responses against allergens, thus underscoring their role as crucial regulators of lung homeostasis. In addition, we have shown that IM could expand from monocyte precursors upon host exposure to bacterial unmethylated CpG-DNA, resulting in robust protection against allergic asthma. To date, however, IM have only been characterized as a bulk population in functional studies, and little is known about the tissue-instructive signals, specific transcription factors and differentiation programs which contribute to determining their identity (ID) and function, as proposed by the macrophage niche model. We have developed an innovative transgenic tool to selectively target IM which, in combination with high dimensional single cell technologies, will allow us to (1) define the precise ID of IM, i.e. their spatial organization, heterogeneity, molecular signature and the specific TF governing their differentiation and function; (2) investigate how IM ID is imprinted by the local niche to sustain lung homeostasis. Specifically, we aim to identify the epithelial cell-derived chemo-attractive signals controlling IM precursor recruitment and to elucidate the contribution of the lung cholinergic nervous system to IM ID and lung homeostasis. This research will increase our understanding of the basic mechanisms underlying the fine-tuning of tolerogenic IM and will thus provide robust foundations for novel IM-targeted approaches promoting health and preventing airway diseases in which IM (dys)functions have been implicated.
Summary
The mechanisms underlying lung homeostasis are of fundamental biological importance and have critical implications for the prevention of immune-mediated diseases such as asthma. We have demonstrated that lung Interstitial Macrophages (IM) exhibit a tolerogenic profile and are able to prevent and limit the development of aberrant immune responses against allergens, thus underscoring their role as crucial regulators of lung homeostasis. In addition, we have shown that IM could expand from monocyte precursors upon host exposure to bacterial unmethylated CpG-DNA, resulting in robust protection against allergic asthma. To date, however, IM have only been characterized as a bulk population in functional studies, and little is known about the tissue-instructive signals, specific transcription factors and differentiation programs which contribute to determining their identity (ID) and function, as proposed by the macrophage niche model. We have developed an innovative transgenic tool to selectively target IM which, in combination with high dimensional single cell technologies, will allow us to (1) define the precise ID of IM, i.e. their spatial organization, heterogeneity, molecular signature and the specific TF governing their differentiation and function; (2) investigate how IM ID is imprinted by the local niche to sustain lung homeostasis. Specifically, we aim to identify the epithelial cell-derived chemo-attractive signals controlling IM precursor recruitment and to elucidate the contribution of the lung cholinergic nervous system to IM ID and lung homeostasis. This research will increase our understanding of the basic mechanisms underlying the fine-tuning of tolerogenic IM and will thus provide robust foundations for novel IM-targeted approaches promoting health and preventing airway diseases in which IM (dys)functions have been implicated.
Max ERC Funding
1 500 000 €
Duration
Start date: 2019-01-01, End date: 2023-12-31
Project acronym IMAGINED
Project Integrated Multi-disciplinary Approach to Gain INsight into Endothelial Diversity
Researcher (PI) Aernout Luttun
Host Institution (HI) KATHOLIEKE UNIVERSITEIT LEUVEN
Call Details Starting Grant (StG), LS6, ERC-2007-StG
Summary Endothelial cells (EC) lining the inside of blood/lymphatic vessels in different organs show significant heterogeneity caused by cell-intrinsic and -extrinsic factors. While intrinsic properties are preserved in vitro, EC-extrinsic characteristics are lost upon isolation from the in vivo context. Thus, getting a grasp on EC diversity requires an approach that integrates EC-intrinsic and -extrinsic cues. EC heterogeneity likely forms the basis of vessel-type restricted disorders and may explain the side effects and limited success of ‘broad-spectrum’ (anti-)angiogenic therapies. Also, EC progenitor-based revascularization studies have not asked whether cells acquire the desired EC phenotype once engrafted in diseased tissue where appropriate environmental cues are lacking. Unraveling mechanisms of EC heterogeneity should allow designing tailor-made therapies, which remains the main challenge in curing vessel-related disease. This research program proposes to use an unprecedented integrated in vitro/in vivo multi-disciplinary approach based on stem/progenitor cells and small animal models to: (i) expand our knowledge of EC diversity; (ii) exploit that knowledge to design specialized vascular therapies for (lymph)vascular disorders. In phase 1, gene-profiles (‘blueprints’) will be obtained by micro-array on EC isolated from various organs and macrovessels of different species with (intrinsic blueprint) or without (extrinsic blueprint) further culture. In phase 2, (co-)culture techniques that simulate the in vivo context will be applied to generate EC with the desired blueprint and appropriate function/morphology, by EC differentiation from adult stem cells. In phase 3, information obtained from phase 1/2 will be validated in vivo by (i) testing the expression profile of selected blueprint-genes, (ii) by morpholino knock-down of these genes in zebrafish, (iii) by transplanting stem cells, pre-specialized or not, into models of vascular bed or organ-specific disorders.
Summary
Endothelial cells (EC) lining the inside of blood/lymphatic vessels in different organs show significant heterogeneity caused by cell-intrinsic and -extrinsic factors. While intrinsic properties are preserved in vitro, EC-extrinsic characteristics are lost upon isolation from the in vivo context. Thus, getting a grasp on EC diversity requires an approach that integrates EC-intrinsic and -extrinsic cues. EC heterogeneity likely forms the basis of vessel-type restricted disorders and may explain the side effects and limited success of ‘broad-spectrum’ (anti-)angiogenic therapies. Also, EC progenitor-based revascularization studies have not asked whether cells acquire the desired EC phenotype once engrafted in diseased tissue where appropriate environmental cues are lacking. Unraveling mechanisms of EC heterogeneity should allow designing tailor-made therapies, which remains the main challenge in curing vessel-related disease. This research program proposes to use an unprecedented integrated in vitro/in vivo multi-disciplinary approach based on stem/progenitor cells and small animal models to: (i) expand our knowledge of EC diversity; (ii) exploit that knowledge to design specialized vascular therapies for (lymph)vascular disorders. In phase 1, gene-profiles (‘blueprints’) will be obtained by micro-array on EC isolated from various organs and macrovessels of different species with (intrinsic blueprint) or without (extrinsic blueprint) further culture. In phase 2, (co-)culture techniques that simulate the in vivo context will be applied to generate EC with the desired blueprint and appropriate function/morphology, by EC differentiation from adult stem cells. In phase 3, information obtained from phase 1/2 will be validated in vivo by (i) testing the expression profile of selected blueprint-genes, (ii) by morpholino knock-down of these genes in zebrafish, (iii) by transplanting stem cells, pre-specialized or not, into models of vascular bed or organ-specific disorders.
Max ERC Funding
1 616 719 €
Duration
Start date: 2008-10-01, End date: 2013-09-30
Project acronym MOLTALL
Project Molecularly targeted therapy for T cell acute lymphoblastic leukemia
Researcher (PI) Jan Cools
Host Institution (HI) VIB
Call Details Starting Grant (StG), LS6, ERC-2007-StG
Summary T cell acute lymphoblastic leukemia (T-ALL) is an aggressive T cell malignancy that is most common in children and adolescents. Our current understanding of the molecular genetics of T-ALL indicates that leukemic transformation of thymocytes is caused by the cooperation of mutations that affect proliferation, survival, cell cycle, differentiation and self renewal. Molecular analysis has identified a large number of T-ALL specific oncogenes, but the genetic defects that are implicated in the aberrant proliferation and survival of the leukemic cells remain largely unknown. It is the aim of this project to continue the molecular characterization of T-ALL using genome wide analyses, focused RNAi screens, and drug library screens to identify oncogenes that specifically provide proliferation and survival advantages, as well as other targets for therapy in T-ALL. In addition, we will study the cooperation of these oncogenes with other oncogenic events using in vitro and in vivo mouse models, and use those models for the development and characterization of novel therapeutics. This project will generate novel insights in the molecular pathogenesis of T-ALL and aims at translating this information towards novel targeted therapies.
Summary
T cell acute lymphoblastic leukemia (T-ALL) is an aggressive T cell malignancy that is most common in children and adolescents. Our current understanding of the molecular genetics of T-ALL indicates that leukemic transformation of thymocytes is caused by the cooperation of mutations that affect proliferation, survival, cell cycle, differentiation and self renewal. Molecular analysis has identified a large number of T-ALL specific oncogenes, but the genetic defects that are implicated in the aberrant proliferation and survival of the leukemic cells remain largely unknown. It is the aim of this project to continue the molecular characterization of T-ALL using genome wide analyses, focused RNAi screens, and drug library screens to identify oncogenes that specifically provide proliferation and survival advantages, as well as other targets for therapy in T-ALL. In addition, we will study the cooperation of these oncogenes with other oncogenic events using in vitro and in vivo mouse models, and use those models for the development and characterization of novel therapeutics. This project will generate novel insights in the molecular pathogenesis of T-ALL and aims at translating this information towards novel targeted therapies.
Max ERC Funding
1 384 632 €
Duration
Start date: 2008-10-01, End date: 2013-09-30
Project acronym RESEAL
Project Epithelial Resealing
Researcher (PI) Antonio Alfredo Coelho Jacinto
Host Institution (HI) FUNDACAO CALOUSTE GULBENKIAN
Call Details Starting Grant (StG), LS1, ERC-2007-StG
Summary Epithelia have the essential role of acting as a barrier that protects living organisms and its organs from the surrounding milieu. Therefore, it is crucial for epithelial tissues to have robust ways of maintaining its integrity despite the frequent damage caused by normal cell turnover, inflammation and injury. All epithelia have some capacity to repair themselves, however, the wound-healing process differs dramatically between the developmental stage and type of tissue involved. In this project we will focus on investigating the capacity that several simple epithelial tissues have to reseal small discontinuities very rapidly and efficiently. This repair mechanism that we call epithelial resealing is based on the contraction of an actomyosin purse string in the leading edge cells around the wound margin. Epithelial resealing seems to be a fundamental repair mechanism, acting in several types of simple embryonic and adult epithelia, in both vertebrates and invertebrates. The cell biology of epithelial resealing has started to be understood but there are still many open questions and the signalling cascades that regulate this process are largely unknown. We propose to investigate epithelial resealing using a combination of genetics and high resolution live imaging. The Drosophila embryonic epithelium will be our primary model system and we will start by characterizing in detail novel genes involved in resealing that have been identified in a pilot screen previously performed in the laboratory. We will also perform a new RNAi genetic screen based on a very large collections of transgenic lines to completely unravel the signalling network that controls epithelial resealing. In order to investigate how conserved in vertebrates are the epithelial resealing mechanisms, we will establish epithelial wounding assays in zebrafish simple epithelial tissues and we will study, in this vertebrate model system, the molecular mechanisms that we will uncover using Drosophila.
Summary
Epithelia have the essential role of acting as a barrier that protects living organisms and its organs from the surrounding milieu. Therefore, it is crucial for epithelial tissues to have robust ways of maintaining its integrity despite the frequent damage caused by normal cell turnover, inflammation and injury. All epithelia have some capacity to repair themselves, however, the wound-healing process differs dramatically between the developmental stage and type of tissue involved. In this project we will focus on investigating the capacity that several simple epithelial tissues have to reseal small discontinuities very rapidly and efficiently. This repair mechanism that we call epithelial resealing is based on the contraction of an actomyosin purse string in the leading edge cells around the wound margin. Epithelial resealing seems to be a fundamental repair mechanism, acting in several types of simple embryonic and adult epithelia, in both vertebrates and invertebrates. The cell biology of epithelial resealing has started to be understood but there are still many open questions and the signalling cascades that regulate this process are largely unknown. We propose to investigate epithelial resealing using a combination of genetics and high resolution live imaging. The Drosophila embryonic epithelium will be our primary model system and we will start by characterizing in detail novel genes involved in resealing that have been identified in a pilot screen previously performed in the laboratory. We will also perform a new RNAi genetic screen based on a very large collections of transgenic lines to completely unravel the signalling network that controls epithelial resealing. In order to investigate how conserved in vertebrates are the epithelial resealing mechanisms, we will establish epithelial wounding assays in zebrafish simple epithelial tissues and we will study, in this vertebrate model system, the molecular mechanisms that we will uncover using Drosophila.
Max ERC Funding
1 150 000 €
Duration
Start date: 2008-11-01, End date: 2014-10-31
