Project acronym CAVEHEART
Project Heart regeneration in the Mexican cavefish: The difference between healing and scarring
Researcher (PI) Mathilda MOMMERSTEEG
Host Institution (HI) THE CHANCELLOR, MASTERS AND SCHOLARS OF THE UNIVERSITY OF OXFORD
Call Details Starting Grant (StG), LS4, ERC-2016-STG
Summary Whereas the human heart cannot regenerate cardiac muscle after myocardial infarction, certain fish efficiently repair their hearts. Astyanax mexicanus, a close relative of the zebrafish, is a single fish species comprising cave-dwelling and surface river populations. Remarkably, while surface fish regenerate their heart after injury, cavefish cannot and form a permanent fibrotic scar, similar to the human heart. Using transcriptomics analysis and immunohistochemistry, we have identified key differences in the scarring and inflammatory response between the surface and cavefish heart after injury. These differences include extracellular matrix (ECM) proteins, growth factors and macrophage populations present in one, but not the other population, suggesting properties unique to the surface fish scar that promote heart regeneration. The objective of the proposed project is to characterise and utilise these findings to identify therapeutic targets to heal the human heart after myocardial infarction. First, we will analyse the identified differences in scarring and immune response between the fish in detail, before testing the role of the most interesting proteins and macrophage populations during regeneration using CRISPR mutagenesis and clodronate liposomes. Next, we will link the key scarring and inflammatory differences directly to both the genome and the ability for heart regeneration using new and prior Quantitative Trait Loci analyses. This will allow to find the most fundamental molecular mechanisms directing the wound healing process towards regeneration versus scarring. Together with an in vitro and in vivo small molecule screen directed specifically at influencing scarring towards a more ‘fish-like’ regenerative phenotype in the cavefish and mouse heart after injury, this will provide targets for therapeutic strategies to maximise the endogenous regenerative potential of the mammalian heart, with the aim to find a cure for myocardial infarction.
Summary
Whereas the human heart cannot regenerate cardiac muscle after myocardial infarction, certain fish efficiently repair their hearts. Astyanax mexicanus, a close relative of the zebrafish, is a single fish species comprising cave-dwelling and surface river populations. Remarkably, while surface fish regenerate their heart after injury, cavefish cannot and form a permanent fibrotic scar, similar to the human heart. Using transcriptomics analysis and immunohistochemistry, we have identified key differences in the scarring and inflammatory response between the surface and cavefish heart after injury. These differences include extracellular matrix (ECM) proteins, growth factors and macrophage populations present in one, but not the other population, suggesting properties unique to the surface fish scar that promote heart regeneration. The objective of the proposed project is to characterise and utilise these findings to identify therapeutic targets to heal the human heart after myocardial infarction. First, we will analyse the identified differences in scarring and immune response between the fish in detail, before testing the role of the most interesting proteins and macrophage populations during regeneration using CRISPR mutagenesis and clodronate liposomes. Next, we will link the key scarring and inflammatory differences directly to both the genome and the ability for heart regeneration using new and prior Quantitative Trait Loci analyses. This will allow to find the most fundamental molecular mechanisms directing the wound healing process towards regeneration versus scarring. Together with an in vitro and in vivo small molecule screen directed specifically at influencing scarring towards a more ‘fish-like’ regenerative phenotype in the cavefish and mouse heart after injury, this will provide targets for therapeutic strategies to maximise the endogenous regenerative potential of the mammalian heart, with the aim to find a cure for myocardial infarction.
Max ERC Funding
1 499 429 €
Duration
Start date: 2017-03-01, End date: 2022-02-28
Project acronym COLGENES
Project Defining novel mechanisms critical for colorectal tumourigenesis
Researcher (PI) Kevin Brian MYANT
Host Institution (HI) THE UNIVERSITY OF EDINBURGH
Call Details Starting Grant (StG), LS4, ERC-2016-STG
Summary Cancer genome sequencing has led to a paradigm shift in our understanding of oncogenesis. It has identified thousands of genetic alterations that segregate into two groups, a small number of frequently mutated genes and a much larger number of infrequently mutated genes. The causative role of frequently mutated genes is often clear and are the focus of concerted therapeutic development efforts. The role of those infrequently mutated is often unclear and can be difficult to separate from ‘mutational noise’. Determining the relevance of low frequency mutations is important for providing a full understanding of processes driving tumourigenesis and if functionally relevant may have broader implications on the applicability of targeted therapies.
This project aims to begin addressing this by defining the function of all genes mutated in colorectal cancer (CRC) in the earliest stages of tumour formation. I have performed a whole genome screen in a 3D organoid CRC initiation model identifying several potentially important mediators of this process. Crucially, some of these genes are mutated in CRC at low frequency but not described as cancer driver genes. Thus, I hypothesize that rather than ‘mutational noise’ infrequently mutated genes contribute to CRC initiation. I will test this by addressing two aims:
1) Determine the role of genes mutated in CRC during tumour initiation
2) Validate and determine the function of a subset of identified genes potentially defining novel cancer mechanisms
I will use a combination of CRISPR genetic disruption in state-of-the-art 3D mouse and human organoid cultures and advanced mouse models to address these aims. This comprehensive approach will provide a foundation for understanding the importance of the entire spectrum of mutations in CRC and open new avenues of research into the function of these genes. More broadly, it has the potential to make a profound impact on how we think about tumourigenic mechanisms and cancer therapeutics.
Summary
Cancer genome sequencing has led to a paradigm shift in our understanding of oncogenesis. It has identified thousands of genetic alterations that segregate into two groups, a small number of frequently mutated genes and a much larger number of infrequently mutated genes. The causative role of frequently mutated genes is often clear and are the focus of concerted therapeutic development efforts. The role of those infrequently mutated is often unclear and can be difficult to separate from ‘mutational noise’. Determining the relevance of low frequency mutations is important for providing a full understanding of processes driving tumourigenesis and if functionally relevant may have broader implications on the applicability of targeted therapies.
This project aims to begin addressing this by defining the function of all genes mutated in colorectal cancer (CRC) in the earliest stages of tumour formation. I have performed a whole genome screen in a 3D organoid CRC initiation model identifying several potentially important mediators of this process. Crucially, some of these genes are mutated in CRC at low frequency but not described as cancer driver genes. Thus, I hypothesize that rather than ‘mutational noise’ infrequently mutated genes contribute to CRC initiation. I will test this by addressing two aims:
1) Determine the role of genes mutated in CRC during tumour initiation
2) Validate and determine the function of a subset of identified genes potentially defining novel cancer mechanisms
I will use a combination of CRISPR genetic disruption in state-of-the-art 3D mouse and human organoid cultures and advanced mouse models to address these aims. This comprehensive approach will provide a foundation for understanding the importance of the entire spectrum of mutations in CRC and open new avenues of research into the function of these genes. More broadly, it has the potential to make a profound impact on how we think about tumourigenic mechanisms and cancer therapeutics.
Max ERC Funding
1 498 618 €
Duration
Start date: 2017-08-01, End date: 2022-07-31
Project acronym EnteroBariatric
Project Investigating Host-Microbial Interactions after Bariatric Surgery
Researcher (PI) Jia LI
Host Institution (HI) IMPERIAL COLLEGE OF SCIENCE TECHNOLOGY AND MEDICINE
Call Details Starting Grant (StG), LS4, ERC-2016-STG
Summary Obesity and related co-morbidities give rise to severe health and socioeconomic problems. Surgical treatment for obesity (bariatric surgery) is remarkably effective in the control of morbid obesity and rapid resolution of Type 2 Diabetes, and the number of such procedures is increasing rapidly in many obesity-prevalent countries. We, and others, have demonstrated that surgical interventions such as Roux-en-Y Gastric Bypass (RYGB) modulates gut hormone levels, induces systemic metabolic changes and results in the shift of the microbiome from Firmicutes to the Proteobacteria phylum. Although the gut microbiota have been implicated in the reduction of adiposity post-surgery, the long-term effect of altered gut microbiota on patients who have undergone RYGB, remains to be studied. Our recent data suggested that microbial activities are highly associated with inflammation and cancer. My research programme aims to investigate the RYGB-specific gut microbiota impacts on host physiology and colon cancer risk. To achieve this goal, I will employ a multidisciplinary approach that combines systems biology techniques with a bottom-up approach. This work will deliver phenotypic and mechanistic characterisation of the interplay between the host and the gut microbiota. The research findings will significantly contribute towards the understanding of fundamental molecular and cellular processes that are key in host and gut microbiota interactions. This will provide knowledge-based evidence of the gut microbial impact on human physiology, and has the potential to unravel novel prevention targets and promote a more thorough healthcare strategy for bariatric patients.
Summary
Obesity and related co-morbidities give rise to severe health and socioeconomic problems. Surgical treatment for obesity (bariatric surgery) is remarkably effective in the control of morbid obesity and rapid resolution of Type 2 Diabetes, and the number of such procedures is increasing rapidly in many obesity-prevalent countries. We, and others, have demonstrated that surgical interventions such as Roux-en-Y Gastric Bypass (RYGB) modulates gut hormone levels, induces systemic metabolic changes and results in the shift of the microbiome from Firmicutes to the Proteobacteria phylum. Although the gut microbiota have been implicated in the reduction of adiposity post-surgery, the long-term effect of altered gut microbiota on patients who have undergone RYGB, remains to be studied. Our recent data suggested that microbial activities are highly associated with inflammation and cancer. My research programme aims to investigate the RYGB-specific gut microbiota impacts on host physiology and colon cancer risk. To achieve this goal, I will employ a multidisciplinary approach that combines systems biology techniques with a bottom-up approach. This work will deliver phenotypic and mechanistic characterisation of the interplay between the host and the gut microbiota. The research findings will significantly contribute towards the understanding of fundamental molecular and cellular processes that are key in host and gut microbiota interactions. This will provide knowledge-based evidence of the gut microbial impact on human physiology, and has the potential to unravel novel prevention targets and promote a more thorough healthcare strategy for bariatric patients.
Max ERC Funding
1 499 091 €
Duration
Start date: 2017-08-01, End date: 2022-07-31
Project acronym GasPlaNt
Project Gas sensing in plants:Oxygen- and nitric oxide-regulated chromatin modification via a targeted protein degradation mechanism
Researcher (PI) Daniel James GIBBS
Host Institution (HI) THE UNIVERSITY OF BIRMINGHAM
Call Details Starting Grant (StG), LS3, ERC-2016-STG
Summary Oxygen (O2) and nitric oxide (NO) are gases that function as key developmental and stress-associated signals in plants. Investigating the molecular basis of their perception has the potential to identify new targets for crop improvement. In previous ground breaking work I showed that the direct transcriptional response to O2/NO is mediated by controlled degradation of specialised ‘gas-sensing’ transcription factors. We have now linked this degradation mechanism to a new functional class of ‘sensor’, a chromatin modifying protein that regulates the epigenetic silencing of genes. Here we will investigate the hypothesis that this protein acts as a previously undiscovered link between O2/NO and chromatin dynamics, and that plants have evolved a unique system for transducing gaseous signals into rapid transcriptional responses, and longer term epigenetic changes, through targeting different types of protein to the same degradation pathway.
Using multidisciplinary genetic, biochemical and omics approaches we will investigate the molecular basis of this novel gas perception system, which appears to be a plant-specific innovation. We will identify its global gene targets (the ‘gas-responsive epigenome’), and uncover its growth and stress-associated functions in Arabidopsis and barley. We will also investigate how manipulating this pathway using genome editing and synthetic biology techniques alters plant performance, focusing on traits of agronomic significance. This ambitious and timely research will take our knowledge of O2/NO-signaling and the control of chromatin dynamics beyond the current state of the art by offering insight into a completely novel signaling mechanism operating at the interface of gas-perception, protein degradation, and epigenetics. GasPlaNt will therefore provide a step-change in our understanding of how plants synchronise their gene expression in response to signals to optimise growth and development within a dynamic environment.
Summary
Oxygen (O2) and nitric oxide (NO) are gases that function as key developmental and stress-associated signals in plants. Investigating the molecular basis of their perception has the potential to identify new targets for crop improvement. In previous ground breaking work I showed that the direct transcriptional response to O2/NO is mediated by controlled degradation of specialised ‘gas-sensing’ transcription factors. We have now linked this degradation mechanism to a new functional class of ‘sensor’, a chromatin modifying protein that regulates the epigenetic silencing of genes. Here we will investigate the hypothesis that this protein acts as a previously undiscovered link between O2/NO and chromatin dynamics, and that plants have evolved a unique system for transducing gaseous signals into rapid transcriptional responses, and longer term epigenetic changes, through targeting different types of protein to the same degradation pathway.
Using multidisciplinary genetic, biochemical and omics approaches we will investigate the molecular basis of this novel gas perception system, which appears to be a plant-specific innovation. We will identify its global gene targets (the ‘gas-responsive epigenome’), and uncover its growth and stress-associated functions in Arabidopsis and barley. We will also investigate how manipulating this pathway using genome editing and synthetic biology techniques alters plant performance, focusing on traits of agronomic significance. This ambitious and timely research will take our knowledge of O2/NO-signaling and the control of chromatin dynamics beyond the current state of the art by offering insight into a completely novel signaling mechanism operating at the interface of gas-perception, protein degradation, and epigenetics. GasPlaNt will therefore provide a step-change in our understanding of how plants synchronise their gene expression in response to signals to optimise growth and development within a dynamic environment.
Max ERC Funding
1 495 341 €
Duration
Start date: 2017-03-01, End date: 2022-02-28
Project acronym IniReg
Project Mechanisms of Regeneration Initiation
Researcher (PI) Kerstin BARTSCHERER
Host Institution (HI) KONINKLIJKE NEDERLANDSE AKADEMIE VAN WETENSCHAPPEN - KNAW
Call Details Starting Grant (StG), LS3, ERC-2016-STG
Summary Injury poses a key threat to all multicellular organisms. However, while some animals can fully restore lost body parts, others can only prevent further damage by mere wound healing. Which molecular mechanisms determine whether regeneration is induced or not is an unsettled fundamental question. I will use whole body regeneration, one of the most fascinating biological processes, as an experimental paradigm to identify the mechanisms of regeneration initiation. As a model organism I will employ planarians, flatworms with extraordinary plasticity that regenerate every piece of their body within a few days. I will mechanistically dissect how these animals rapidly induce an efficient regeneration program in response to tissue loss and define the key switches that determine whether a wound regenerates. Combining the astonishing regenerative abilities of planarians with new technologies I will first comprehensively describe the molecular changes occurring during the amputation response. Second, with a powerful novel assay developed in my lab - dormant fragments - that allows for the first time the separation of wounding from tissue loss in a single planarian, I will analyze the dynamics of the earliest regenerative events. Third, I will functionally characterize the regeneration-initiating signals and their target pathways combining in vivo RNAi and phenotypic assays. Fourth, with a regeneration-deficient planarian species, I will test whether the identified key regulators act as network nodes that can be utilized to rescue regeneration. Importantly, using vertebrate paradigms, such as the regenerating zebrafish fin, I will investigate conserved roles of these network nodes and validate general principles of regeneration initiation. This project will not only uncover conserved mechanisms of regeneration initiation but will also identify the switches that must be levered to induce regeneration in non-regenerating animals.
Summary
Injury poses a key threat to all multicellular organisms. However, while some animals can fully restore lost body parts, others can only prevent further damage by mere wound healing. Which molecular mechanisms determine whether regeneration is induced or not is an unsettled fundamental question. I will use whole body regeneration, one of the most fascinating biological processes, as an experimental paradigm to identify the mechanisms of regeneration initiation. As a model organism I will employ planarians, flatworms with extraordinary plasticity that regenerate every piece of their body within a few days. I will mechanistically dissect how these animals rapidly induce an efficient regeneration program in response to tissue loss and define the key switches that determine whether a wound regenerates. Combining the astonishing regenerative abilities of planarians with new technologies I will first comprehensively describe the molecular changes occurring during the amputation response. Second, with a powerful novel assay developed in my lab - dormant fragments - that allows for the first time the separation of wounding from tissue loss in a single planarian, I will analyze the dynamics of the earliest regenerative events. Third, I will functionally characterize the regeneration-initiating signals and their target pathways combining in vivo RNAi and phenotypic assays. Fourth, with a regeneration-deficient planarian species, I will test whether the identified key regulators act as network nodes that can be utilized to rescue regeneration. Importantly, using vertebrate paradigms, such as the regenerating zebrafish fin, I will investigate conserved roles of these network nodes and validate general principles of regeneration initiation. This project will not only uncover conserved mechanisms of regeneration initiation but will also identify the switches that must be levered to induce regeneration in non-regenerating animals.
Max ERC Funding
1 500 000 €
Duration
Start date: 2017-04-01, End date: 2022-03-31
Project acronym LogNeuroDev
Project The molecular and cellular logic of vertebrate neural development
Researcher (PI) James BRISCOE
Host Institution (HI) THE FRANCIS CRICK INSTITUTE LIMITED
Call Details Advanced Grant (AdG), LS3, ERC-2016-ADG
Summary A central problem in biology and key to realising the potential of regenerative medicine is understanding the mechanisms that produce and organize cells in the complex tissues of an embryo. In broad terms, initially uncommitted progenitors acquire their fate in response to signals that control transcriptional programmes. These programmes drive cells through spatial and temporal successions of states that gradually refine cell identity. How these states are established and cell fate decisions implemented is poorly understood. To address this we use an experimentally tractable system – the formation of defined populations of progenitors in the vertebrate spinal cord. We take an interdisciplinary approach that combines our in vivo expertise with three recent advances in our group. First, we have developed in vitro differentiation systems and microfluidic devices that use embryonic stem cells to recapitulate development processes. Second, we have embraced new technologies that provide unprecedented ability to manipulate and assay single cells. Finally, we have established interdisciplinary collaborations to develop computational tools and construct data driven mathematical models. Using these approaches, alongside established embryological methods, we will establish a platform for manipulating and analysing mechanisms by which the multipotent progenitors that form the spinal cord acquire specific identities. We will identify the rules by which cells make decisions and we will define the design logic and network architectures that lead to distinct cell fate choices. The ability to: (i) follow the trajectory of a cell as it transitions to a specific neuronal subtype in vivo; (ii) manipulate the process in vitro and in vivo; and (iii) model it in silico, offers a unique system for understanding organogenesis. Together these approaches will provide the knowledge and technical foundations for rational, predictive tissue engineering of the spinal cord.
Summary
A central problem in biology and key to realising the potential of regenerative medicine is understanding the mechanisms that produce and organize cells in the complex tissues of an embryo. In broad terms, initially uncommitted progenitors acquire their fate in response to signals that control transcriptional programmes. These programmes drive cells through spatial and temporal successions of states that gradually refine cell identity. How these states are established and cell fate decisions implemented is poorly understood. To address this we use an experimentally tractable system – the formation of defined populations of progenitors in the vertebrate spinal cord. We take an interdisciplinary approach that combines our in vivo expertise with three recent advances in our group. First, we have developed in vitro differentiation systems and microfluidic devices that use embryonic stem cells to recapitulate development processes. Second, we have embraced new technologies that provide unprecedented ability to manipulate and assay single cells. Finally, we have established interdisciplinary collaborations to develop computational tools and construct data driven mathematical models. Using these approaches, alongside established embryological methods, we will establish a platform for manipulating and analysing mechanisms by which the multipotent progenitors that form the spinal cord acquire specific identities. We will identify the rules by which cells make decisions and we will define the design logic and network architectures that lead to distinct cell fate choices. The ability to: (i) follow the trajectory of a cell as it transitions to a specific neuronal subtype in vivo; (ii) manipulate the process in vitro and in vivo; and (iii) model it in silico, offers a unique system for understanding organogenesis. Together these approaches will provide the knowledge and technical foundations for rational, predictive tissue engineering of the spinal cord.
Max ERC Funding
2 357 000 €
Duration
Start date: 2018-01-01, End date: 2022-12-31
Project acronym MetResistance
Project The role of tumour microenvironment in metastatic hormone-refractory prostate cancer
Researcher (PI) Binzhi QIAN
Host Institution (HI) THE UNIVERSITY OF EDINBURGH
Call Details Starting Grant (StG), LS4, ERC-2016-STG
Summary The goal of this proposal is to investigate the role of tumor microenvironment in metastatic hormone-refractory prostate cancer (mHRPC). Prostate Cancer (PC) is the most common malignancy in men in Europe while mHRPC is the most lethal form of the disease, causing over 95% of PC related deaths. Extensive clinical and preclinical research using state-of-the-art tumour models has led to the development of several new therapeutics that, unfortunately, provide only marginal patient benefit. One key element missing in standard preclinical models is the relevant metastasis microenvironment associated with mHRPC that may dramatically affect disease outcome. Here, I plan to significantly advance our understanding in mHRPC associated microenvironment with the first androgen dependent PC bone metastasis model I developed that mimics both the pathology and disease progression in patients. My preliminary data indicate that metastasis associated stromal cells may form a unique bone metastasis microenvironment that promotes mHRPC. I aim to identify the underlying molecular mechanisms using a multidisciplinary approach combining intra-vital microscopy, dynamic ADT resistance reporter system, innovative adoptive transfer approach and genetic tools of lineage specific knockout. This work is also designed to translate findings made in mouse models into human disease using innovative humanized in vivo models of mHRPC. The findings generated in this project will lead to innovative therapeutic approaches that can effectively treat mHRPC thus relieve this lethal threat on European societies. MetResistance will make a step change in the field of cancer medicine research by providing new standards to study therapy resistance of metastatic cancer an area representing the number one challenge in cancer research and patient care.
Summary
The goal of this proposal is to investigate the role of tumor microenvironment in metastatic hormone-refractory prostate cancer (mHRPC). Prostate Cancer (PC) is the most common malignancy in men in Europe while mHRPC is the most lethal form of the disease, causing over 95% of PC related deaths. Extensive clinical and preclinical research using state-of-the-art tumour models has led to the development of several new therapeutics that, unfortunately, provide only marginal patient benefit. One key element missing in standard preclinical models is the relevant metastasis microenvironment associated with mHRPC that may dramatically affect disease outcome. Here, I plan to significantly advance our understanding in mHRPC associated microenvironment with the first androgen dependent PC bone metastasis model I developed that mimics both the pathology and disease progression in patients. My preliminary data indicate that metastasis associated stromal cells may form a unique bone metastasis microenvironment that promotes mHRPC. I aim to identify the underlying molecular mechanisms using a multidisciplinary approach combining intra-vital microscopy, dynamic ADT resistance reporter system, innovative adoptive transfer approach and genetic tools of lineage specific knockout. This work is also designed to translate findings made in mouse models into human disease using innovative humanized in vivo models of mHRPC. The findings generated in this project will lead to innovative therapeutic approaches that can effectively treat mHRPC thus relieve this lethal threat on European societies. MetResistance will make a step change in the field of cancer medicine research by providing new standards to study therapy resistance of metastatic cancer an area representing the number one challenge in cancer research and patient care.
Max ERC Funding
1 498 176 €
Duration
Start date: 2017-04-01, End date: 2022-03-31
Project acronym OptoBETA
Project Multicellular regulation of insulin secretion from pancreatic islets
Researcher (PI) David HODSON
Host Institution (HI) THE UNIVERSITY OF BIRMINGHAM
Call Details Starting Grant (StG), LS4, ERC-2016-STG
Summary Type 2 diabetes mellitus, one of the major healthcare challenges of our time, is characterized by failure of beta cells to functionally adapt to increased peripheral insulin resistance. The resulting chronic elevations in blood glucose concentration are associated with heart, kidney, liver, nerve and retinal disease, as well as cancer. Here, by combining novel optogenetic, photopharmacological and innovative imaging approaches, we aim to unravel the complexity underlying the multicellular regulation of insulin secretion from islets of Langerhans during health and disease. In particular, we will examine a role for privileged pacemakers/hubs in orchestrating population responses to stimuli, identify what makes these specialized cells unique at the RNA/protein level, and understand how they contribute to islet development and failure. Furthermore, we will address whether the intraislet regulation of insulin secretion operates in vivo to determine glucose homeostasis, focusing on the neural-endocrine interface. Lastly, the mechanisms underlying islet cross-talk will be investigated directly in situ within the pancreas of living mice, paying close attention to the roles of the vasculature and secreted factors. As such, these studies should unveil a new route for restoration of insulin secretion in man, as well as provide the foundation for the de novo construction of islets for transplantation.
Summary
Type 2 diabetes mellitus, one of the major healthcare challenges of our time, is characterized by failure of beta cells to functionally adapt to increased peripheral insulin resistance. The resulting chronic elevations in blood glucose concentration are associated with heart, kidney, liver, nerve and retinal disease, as well as cancer. Here, by combining novel optogenetic, photopharmacological and innovative imaging approaches, we aim to unravel the complexity underlying the multicellular regulation of insulin secretion from islets of Langerhans during health and disease. In particular, we will examine a role for privileged pacemakers/hubs in orchestrating population responses to stimuli, identify what makes these specialized cells unique at the RNA/protein level, and understand how they contribute to islet development and failure. Furthermore, we will address whether the intraislet regulation of insulin secretion operates in vivo to determine glucose homeostasis, focusing on the neural-endocrine interface. Lastly, the mechanisms underlying islet cross-talk will be investigated directly in situ within the pancreas of living mice, paying close attention to the roles of the vasculature and secreted factors. As such, these studies should unveil a new route for restoration of insulin secretion in man, as well as provide the foundation for the de novo construction of islets for transplantation.
Max ERC Funding
1 681 468 €
Duration
Start date: 2017-06-01, End date: 2022-05-31
Project acronym PHYSBIOHSC
Project Understanding the physical biology of adult blood stem cells
Researcher (PI) David KENT
Host Institution (HI) THE CHANCELLOR MASTERS AND SCHOLARS OF THE UNIVERSITY OF CAMBRIDGE
Call Details Starting Grant (StG), LS3, ERC-2016-STG
Summary The discovery of functional heterogeneity in normal and malignant stem cells has shifted our understanding of how single cells are subverted to drive cancer. To design therapies for diseases of stem cell origin and to better provide cell populations for clinical applications, it is critical to understand this diversity at the single cell level. This proposal focuses on understanding the complex biology of normal and malignant stem cells and the impact of individual mutations on clonal evolution by studying the physical and quantitative aspects of single blood stem cells.
This proposal aims to study single blood stem cell biomechanics and clonal evolution by leveraging new inter-disciplinary technologies and approaches and applying them to functionally defined mouse and human blood stem cell populations. It will combine in vitro and in vivo biological assays with mathematical modelling and microfluidic technology in an iterative manner across both human and mouse stem cell populations.
Summary
The discovery of functional heterogeneity in normal and malignant stem cells has shifted our understanding of how single cells are subverted to drive cancer. To design therapies for diseases of stem cell origin and to better provide cell populations for clinical applications, it is critical to understand this diversity at the single cell level. This proposal focuses on understanding the complex biology of normal and malignant stem cells and the impact of individual mutations on clonal evolution by studying the physical and quantitative aspects of single blood stem cells.
This proposal aims to study single blood stem cell biomechanics and clonal evolution by leveraging new inter-disciplinary technologies and approaches and applying them to functionally defined mouse and human blood stem cell populations. It will combine in vitro and in vivo biological assays with mathematical modelling and microfluidic technology in an iterative manner across both human and mouse stem cell populations.
Max ERC Funding
1 500 000 €
Duration
Start date: 2017-05-01, End date: 2022-04-30
Project acronym RepTime
Project Molecular control of DNA replication timing in mammalian cells
Researcher (PI) Sara Cristiana Barbara BUONOMO
Host Institution (HI) THE UNIVERSITY OF EDINBURGH
Call Details Consolidator Grant (CoG), LS3, ERC-2016-COG
Summary DNA replication is an essential process ensuring the transmission of genetic information and is highly regulated. Specifically, the DNA replication-timing program ensures that the sites of initiation of DNA replication, termed origins, are not all activated simultaneously but follow a cell-type specific schedule. This pathway is conserved throughout eukaryotic evolution, however its molecular control and biological role are not fully understood. In this proposal I aim to understand key aspects of replication-timing program by employing a combination of advanced mouse genetics, genomics, cell biology and proteomics. Currently one of the major limitations in the mammalian DNA replication field is the elusive identity of origins. I aim to comprehensively map origins in a variety of mouse cells/tissues and relate the regulation of origin firing to the control of gene expression and three-dimensional nuclear architecture. I have discovered that Rif1 controls replication timing and links it to nuclear three-dimensional organization. I have also revealed the existence of a novel Rif1-independent pathway that controls the timing of a significant fraction of the late-replicating genome, identified by constitutive association with a key nuclear architecture component, Lamin B1. Here, I propose complementary approaches to understand the molecular mechanism by which Rif1 coordinates replication timing and nuclear organization as well as the molecular underpinnings of the novel pathway instructing late-replication in Lamin B1-associated regions. Finally, my goal is to understand the in vivo biological role of the replication-timing program. Our preliminary data identify mammalian X inactivation as a process where replication timing may play a fundamental part. My ultimate objective is to contribute to the realization of a comprehensive understanding of nuclear function, integrating the co-regulation of DNA replication with gene expression, epigenetic inheritance and DNA repair.
Summary
DNA replication is an essential process ensuring the transmission of genetic information and is highly regulated. Specifically, the DNA replication-timing program ensures that the sites of initiation of DNA replication, termed origins, are not all activated simultaneously but follow a cell-type specific schedule. This pathway is conserved throughout eukaryotic evolution, however its molecular control and biological role are not fully understood. In this proposal I aim to understand key aspects of replication-timing program by employing a combination of advanced mouse genetics, genomics, cell biology and proteomics. Currently one of the major limitations in the mammalian DNA replication field is the elusive identity of origins. I aim to comprehensively map origins in a variety of mouse cells/tissues and relate the regulation of origin firing to the control of gene expression and three-dimensional nuclear architecture. I have discovered that Rif1 controls replication timing and links it to nuclear three-dimensional organization. I have also revealed the existence of a novel Rif1-independent pathway that controls the timing of a significant fraction of the late-replicating genome, identified by constitutive association with a key nuclear architecture component, Lamin B1. Here, I propose complementary approaches to understand the molecular mechanism by which Rif1 coordinates replication timing and nuclear organization as well as the molecular underpinnings of the novel pathway instructing late-replication in Lamin B1-associated regions. Finally, my goal is to understand the in vivo biological role of the replication-timing program. Our preliminary data identify mammalian X inactivation as a process where replication timing may play a fundamental part. My ultimate objective is to contribute to the realization of a comprehensive understanding of nuclear function, integrating the co-regulation of DNA replication with gene expression, epigenetic inheritance and DNA repair.
Max ERC Funding
1 999 785 €
Duration
Start date: 2017-10-01, End date: 2022-09-30
Project acronym Secret Surface
Project The cell surface tetraspanin web drives tumour development and alters metabolic signalling
Researcher (PI) Annemiek van Spriel
Host Institution (HI) STICHTING KATHOLIEKE UNIVERSITEIT
Call Details Consolidator Grant (CoG), LS4, ERC-2016-COG
Summary Cancer development is characterized by uncontrolled proliferation, cell survival and metabolic reprogramming. Tumour cells are surrounded by a fluid-mosaic membrane that contains tetraspanins (Tspans) which are evolutionary conserved proteins important in the formation of multiprotein complexes at the cell surface (‘tetraspanin web’). Increasing evidence indicates that Tspans are involved in cancer, still the architecture of the Tspan web in native tumour membranes and its (patho)physiological functions have not been resolved. Based on my preliminary data, I hypothesize that tumour cells contain a disrupted Tspan web in which Tspan interactions are modified leading to aberrant metabolic signalling and tumour development. This is supported by my discovery that loss of Tspan CD37 leads to spontaneous lymphomagenesis due to activation of the Akt survival pathway. The overall aim of Secret Surface is to unravel the composition, physiological functions and molecular mechanisms of the Tspan web on tumour development and clinical outcome. To achieve this, I will focus on studying lymphomas using a multidisciplinary approach: I. Detailed analyses of Tspan web composition in lymphoma to select clinically relevant Tspans (high-throughput tissue microarray technology, multispectral imaging). II. Resolve the endogenous Tspan web on lymphoma cells (super-resolution microscopy), and generation and analysis of lymphoma cells that have a complete deficiency of multiple Tspans (CRISPR/Cas9 technology). III. Decipher molecular mechanisms underlying Tspan web function in lymphoma cells (membrane organization, membrane-proximal signalling, metabolic reprogramming). With my unique toolbox of Tspan knock-outs coupled to advanced microscopy and metabolic studies, I expect that Secret Surface will lead to a new concept in cellular physiology in which cell surface organization by the Tspan web drives tumour development, which may open new horizons for the generation of new cancer therapies.
Summary
Cancer development is characterized by uncontrolled proliferation, cell survival and metabolic reprogramming. Tumour cells are surrounded by a fluid-mosaic membrane that contains tetraspanins (Tspans) which are evolutionary conserved proteins important in the formation of multiprotein complexes at the cell surface (‘tetraspanin web’). Increasing evidence indicates that Tspans are involved in cancer, still the architecture of the Tspan web in native tumour membranes and its (patho)physiological functions have not been resolved. Based on my preliminary data, I hypothesize that tumour cells contain a disrupted Tspan web in which Tspan interactions are modified leading to aberrant metabolic signalling and tumour development. This is supported by my discovery that loss of Tspan CD37 leads to spontaneous lymphomagenesis due to activation of the Akt survival pathway. The overall aim of Secret Surface is to unravel the composition, physiological functions and molecular mechanisms of the Tspan web on tumour development and clinical outcome. To achieve this, I will focus on studying lymphomas using a multidisciplinary approach: I. Detailed analyses of Tspan web composition in lymphoma to select clinically relevant Tspans (high-throughput tissue microarray technology, multispectral imaging). II. Resolve the endogenous Tspan web on lymphoma cells (super-resolution microscopy), and generation and analysis of lymphoma cells that have a complete deficiency of multiple Tspans (CRISPR/Cas9 technology). III. Decipher molecular mechanisms underlying Tspan web function in lymphoma cells (membrane organization, membrane-proximal signalling, metabolic reprogramming). With my unique toolbox of Tspan knock-outs coupled to advanced microscopy and metabolic studies, I expect that Secret Surface will lead to a new concept in cellular physiology in which cell surface organization by the Tspan web drives tumour development, which may open new horizons for the generation of new cancer therapies.
Max ERC Funding
2 000 000 €
Duration
Start date: 2017-10-01, End date: 2022-09-30
Project acronym Survive
Project Surviving metabolism: acid handling and signalling
Researcher (PI) Pawel Dominik SWIETACH
Host Institution (HI) THE CHANCELLOR, MASTERS AND SCHOLARS OF THE UNIVERSITY OF OXFORD
Call Details Consolidator Grant (CoG), LS4, ERC-2016-COG
Summary Metabolism generates vast quantities of acid, which exerts broad-spectrum biological effects because protein protonation is a powerful post-translational modification. Regulation of intracellular pH (pHi) is therefore a homeostatic priority, but carefully orchestrated proton dynamics are a versatile signal.
Extracellular acidity is an established chemical signature of tumours and has recently been proposed to convey a signal that shapes the phenotypic landscape of cancer. Cancer’s genetic instability yields diversity in acid handling and signalling, forming a substrate for selection under acid-stress. This is a plausible mechanism for disease progression and an analogy can be drawn to experimentally-verified hypoxic selection.
Current models of acid handling in cancer are, however, based on population-averages of observations made at the cell level. This fails to appreciate diversity and the complexity inherent in tissues. We will produce a more complete understanding of acid handling that accounts for diffusive transport across tissue compartments and the role of the tumour stroma. A systems-approach of characterising pH-regulatory processes cell-by-cell will identify which components are liable to vary, and thus are a substrate for acid-driven somatic evolution.
The long-term effects of proton signals on gene expression have not been tested, despite evidence for proton-sensing transcription factors. To address the mechanism for adaptation to acid-stress, proton-sensing transcription factors will be characterised from studies of gene expression under chemically and optogenetically operated pH stimuli.
The definition of a cell’s fitness to survive at a particular microenvironment pH and its relationship with stemness remain unclear. Phenotyping pHi-gated subpopulations in terms of growth, stemness and tumourigenicity will define pH-fitness and its role in aggressiveness. In evolving to survive metabolism, cancer cells may acquire the ability to thrive in new niches.
Summary
Metabolism generates vast quantities of acid, which exerts broad-spectrum biological effects because protein protonation is a powerful post-translational modification. Regulation of intracellular pH (pHi) is therefore a homeostatic priority, but carefully orchestrated proton dynamics are a versatile signal.
Extracellular acidity is an established chemical signature of tumours and has recently been proposed to convey a signal that shapes the phenotypic landscape of cancer. Cancer’s genetic instability yields diversity in acid handling and signalling, forming a substrate for selection under acid-stress. This is a plausible mechanism for disease progression and an analogy can be drawn to experimentally-verified hypoxic selection.
Current models of acid handling in cancer are, however, based on population-averages of observations made at the cell level. This fails to appreciate diversity and the complexity inherent in tissues. We will produce a more complete understanding of acid handling that accounts for diffusive transport across tissue compartments and the role of the tumour stroma. A systems-approach of characterising pH-regulatory processes cell-by-cell will identify which components are liable to vary, and thus are a substrate for acid-driven somatic evolution.
The long-term effects of proton signals on gene expression have not been tested, despite evidence for proton-sensing transcription factors. To address the mechanism for adaptation to acid-stress, proton-sensing transcription factors will be characterised from studies of gene expression under chemically and optogenetically operated pH stimuli.
The definition of a cell’s fitness to survive at a particular microenvironment pH and its relationship with stemness remain unclear. Phenotyping pHi-gated subpopulations in terms of growth, stemness and tumourigenicity will define pH-fitness and its role in aggressiveness. In evolving to survive metabolism, cancer cells may acquire the ability to thrive in new niches.
Max ERC Funding
1 922 575 €
Duration
Start date: 2017-06-01, End date: 2022-05-31
Project acronym WHOLENICHE
Project Hold it or let it go: a niche decision on cancer growth
Researcher (PI) Ilaria MALANCHI
Host Institution (HI) THE FRANCIS CRICK INSTITUTE LIMITED
Call Details Consolidator Grant (CoG), LS4, ERC-2016-COG
Summary The tumour microenvironment or niche is the vital non-cancerous compartment of the tumour structure. Thus, targeting its tissue-derived cells represents a promising avenue to better therapeutic interventions. However, knowledge about the tissue cells taking part of the tumour niche during early cancer development and later progression is lagging behind due to the difficulty of analysing and following early tissue changes in the surrounding of cancer cells in vivo. In our research proposal we will use a combination of original tools developed in the lab and state of the art technologies to overcome some of these constraints and expand our understanding of which cells in the niche support early cancer cell growth. We also aim to reveal their mechanism of action and identify approaches to block the niche supportive activity. Our five-year plan has three main objectives (I, II, III), which we will meet using two original strategies. With the first strategy we will visualize the early tumourigenic niche in vivo. This will allow us (I) to identify and characterize novel cellular components during dynamic niche evolution both in the context of metastatic colonization as well as during primary tumour onset. We will also use this original approach (II) to deepen our understanding of neutrophils in cancer, a particularly crucial emerging component of the cancer niche, whose role is still debated.
After dissemination, cancer cells may encounter an unfavourable niche, failing to start colonization and remaining dormant within the tissue. However, the quiescent-permissive tissue can change, cancer cells reactivate and form metastases even a long period after tumour resection. Little is known about the changes in the niche of dormant cells capable of triggering their reactivation. With the second strategy we will generate an in vivo a controllable, dormant-permissive tissue (III) to screen for potential signals triggering dormant cells reactivation.
Summary
The tumour microenvironment or niche is the vital non-cancerous compartment of the tumour structure. Thus, targeting its tissue-derived cells represents a promising avenue to better therapeutic interventions. However, knowledge about the tissue cells taking part of the tumour niche during early cancer development and later progression is lagging behind due to the difficulty of analysing and following early tissue changes in the surrounding of cancer cells in vivo. In our research proposal we will use a combination of original tools developed in the lab and state of the art technologies to overcome some of these constraints and expand our understanding of which cells in the niche support early cancer cell growth. We also aim to reveal their mechanism of action and identify approaches to block the niche supportive activity. Our five-year plan has three main objectives (I, II, III), which we will meet using two original strategies. With the first strategy we will visualize the early tumourigenic niche in vivo. This will allow us (I) to identify and characterize novel cellular components during dynamic niche evolution both in the context of metastatic colonization as well as during primary tumour onset. We will also use this original approach (II) to deepen our understanding of neutrophils in cancer, a particularly crucial emerging component of the cancer niche, whose role is still debated.
After dissemination, cancer cells may encounter an unfavourable niche, failing to start colonization and remaining dormant within the tissue. However, the quiescent-permissive tissue can change, cancer cells reactivate and form metastases even a long period after tumour resection. Little is known about the changes in the niche of dormant cells capable of triggering their reactivation. With the second strategy we will generate an in vivo a controllable, dormant-permissive tissue (III) to screen for potential signals triggering dormant cells reactivation.
Max ERC Funding
2 000 000 €
Duration
Start date: 2017-04-01, End date: 2022-03-31
