Project acronym ATG9_SOLVES_IT
Project In vitro high resolution reconstitution of autophagosome nucleation and expansion catalyzed byATG9
Researcher (PI) Sharon TOOZE
Host Institution (HI) THE FRANCIS CRICK INSTITUTE LIMITED
Call Details Advanced Grant (AdG), LS1, ERC-2017-ADG
Summary Autophagy is a conserved, lysosomal-mediated pathway required for cell homeostasis and survival. It is controlled by the master regulators of energy (AMPK) and growth (TORC1) and mediated by the ATG (autophagy) proteins. Deregulation of autophagy is implicated in cancer, immunity, infection, aging and neurodegeneration. Autophagosomes form and expand using membranes from the secretory and endocytic pathways but how this occurs is not understood. ATG9, the only transmembrane ATG protein traffics through the cell in vesicles, and is essential for rapid initiation and expansion of the membranes which form the autophagosome. Crucially, how ATG9 functions is unknown. I will determine how ATG9 initiates the formation and expansion of the autophagosome by amino acid starvation through a molecular dissection of proteins resident in ATG9 vesicles which modulate the composition and property of the initiating membrane. I will employ high resolution light and electron microscopy to characterize the nucleation of the autophagosome, proximity-specific biotinylation and quantitative Mass Spectrometry to uncover the proteome required for the function of the ATG9, and optogenetic tools to acutely regulate signaling lipids. Lastly, with our tools and knowledge I will develop an in vitro reconstitution system to define at a molecular level how ATG9 vesicle proteins, membranes that interact with ATG9 vesicles, and other accessory ATG components nucleate and form an autophagosome. In vitro reconstitution of autophagosomes will be assayed biochemically, and by correlative light and cryo-EM and cryo-EM tomography, while functional reconstitution of autophagy will be tested by selective cargo recruitment. The development of a reconstituted system and identification proteins and lipids which are key components for autophagosome formation will provide a means to identify a new generation of targets for translational work leading to manipulation of autophagy for disease related therapies.
Summary
Autophagy is a conserved, lysosomal-mediated pathway required for cell homeostasis and survival. It is controlled by the master regulators of energy (AMPK) and growth (TORC1) and mediated by the ATG (autophagy) proteins. Deregulation of autophagy is implicated in cancer, immunity, infection, aging and neurodegeneration. Autophagosomes form and expand using membranes from the secretory and endocytic pathways but how this occurs is not understood. ATG9, the only transmembrane ATG protein traffics through the cell in vesicles, and is essential for rapid initiation and expansion of the membranes which form the autophagosome. Crucially, how ATG9 functions is unknown. I will determine how ATG9 initiates the formation and expansion of the autophagosome by amino acid starvation through a molecular dissection of proteins resident in ATG9 vesicles which modulate the composition and property of the initiating membrane. I will employ high resolution light and electron microscopy to characterize the nucleation of the autophagosome, proximity-specific biotinylation and quantitative Mass Spectrometry to uncover the proteome required for the function of the ATG9, and optogenetic tools to acutely regulate signaling lipids. Lastly, with our tools and knowledge I will develop an in vitro reconstitution system to define at a molecular level how ATG9 vesicle proteins, membranes that interact with ATG9 vesicles, and other accessory ATG components nucleate and form an autophagosome. In vitro reconstitution of autophagosomes will be assayed biochemically, and by correlative light and cryo-EM and cryo-EM tomography, while functional reconstitution of autophagy will be tested by selective cargo recruitment. The development of a reconstituted system and identification proteins and lipids which are key components for autophagosome formation will provide a means to identify a new generation of targets for translational work leading to manipulation of autophagy for disease related therapies.
Max ERC Funding
2 121 055 €
Duration
Start date: 2018-07-01, End date: 2023-06-30
Project acronym C-POS
Project Children's Palliative care Outcome Scale
Researcher (PI) RICHARD HARDING-SWALE
Host Institution (HI) KING'S COLLEGE LONDON
Call Details Consolidator Grant (CoG), LS7, ERC-2017-COG
Summary Person-centred care is a core health value of modern health care. The overarching aim of C-POS (Children's Palliative care Outcome Scale) is to develop and validate a person-centred outcome measure for children, young people (CYP) and their families affected by life-limiting & life-threatening conditions (LLLTC). International systematic reviews, and clinical guides have highlighted that currently none exists. This novel study will draw together a unique multidisciplinary collaboration to pioneer new methods, enabling engagement in outcome measurement by a population currently neglected in research.
C-POS builds on an international program of work. The sequential mixed methods will collect substantive data through objectives to determine i) the primary concerns of CYP and their families affected by LLLTC & preferences to enable participation in ethical person-centred measurement (n=50); ii) view of clinicians and commissioners on optimal implementation methods (national Delphi study); iii) a systematic review of current data collection tools for CYP regardless of condition; iv) integration of objectives i-iii to develop a tool (C-POS) with face and content validity; v) cognitive interviews to determine interpretability (n=40); vi) longitudinal cohort of CYP and families to determine test-retest reliability, internal consistency, construct validity and responsiveness (n=151); vii) development of resources for routine implementation viii) translation and interpretation protocols for international adoption.
C-POS is an ambitious study that, for the first time, will enable measurement of person-centred outcomes of care. This will be a turning point in the scientific study of a hitherto neglected group.
Summary
Person-centred care is a core health value of modern health care. The overarching aim of C-POS (Children's Palliative care Outcome Scale) is to develop and validate a person-centred outcome measure for children, young people (CYP) and their families affected by life-limiting & life-threatening conditions (LLLTC). International systematic reviews, and clinical guides have highlighted that currently none exists. This novel study will draw together a unique multidisciplinary collaboration to pioneer new methods, enabling engagement in outcome measurement by a population currently neglected in research.
C-POS builds on an international program of work. The sequential mixed methods will collect substantive data through objectives to determine i) the primary concerns of CYP and their families affected by LLLTC & preferences to enable participation in ethical person-centred measurement (n=50); ii) view of clinicians and commissioners on optimal implementation methods (national Delphi study); iii) a systematic review of current data collection tools for CYP regardless of condition; iv) integration of objectives i-iii to develop a tool (C-POS) with face and content validity; v) cognitive interviews to determine interpretability (n=40); vi) longitudinal cohort of CYP and families to determine test-retest reliability, internal consistency, construct validity and responsiveness (n=151); vii) development of resources for routine implementation viii) translation and interpretation protocols for international adoption.
C-POS is an ambitious study that, for the first time, will enable measurement of person-centred outcomes of care. This will be a turning point in the scientific study of a hitherto neglected group.
Max ERC Funding
1 799 820 €
Duration
Start date: 2018-09-01, End date: 2023-02-28
Project acronym CellFateTech
Project Biotechnology for investigating cell fate choice
Researcher (PI) Kevin CHALUT
Host Institution (HI) THE CHANCELLOR MASTERS AND SCHOLARS OF THE UNIVERSITY OF CAMBRIDGE
Call Details Consolidator Grant (CoG), LS9, ERC-2017-COG
Summary The evolution from a stem cell to differentiated progeny underpins tissue development and homeostasis, which are driven by a multitude of cell fate choices. The transitions underlying these choices are not well understood. There are a number of challenges that must be overcome to achieve this understanding. In the proposed research we will tackle two of the challenges: first, the dynamics of fate choices, i.e. the dependence of transitions on time and inductive signals, remains cryptic; second, mechanical signalling regulates instructive cues for transitions but its role in the process is uncertain. One of the primary reasons these important aspects of cell fate choice remain a mystery is because the biology has not been coupled to the biotechnology appropriate to unravel it. This is the purpose of the proposed research: we will develop tools based in microfluidics, microfabrication and hydrogels and integrate them with our stem cell biology expertise to illuminate the process of cell fate choice. We will develop single cell microfluidic technology that possesses unprecedented temporal resolution and control over the signalling environment to study cell fate dynamics. We will also synthesize hydrogel substrates to exert complete control over the mechanical microenvironment of stem cells. Finally, we will advance tools to apply reproducible and defined forces to cells in order to study the role mechanical signalling in cell fate choice. Developing the proposed technology kit hand-in-hand with its biological applications will allow us to delve into the mechanisms of biological transitions in multiple stem cell systems, allowing us to uncover universal phenomena governing cell fate choice.
Summary
The evolution from a stem cell to differentiated progeny underpins tissue development and homeostasis, which are driven by a multitude of cell fate choices. The transitions underlying these choices are not well understood. There are a number of challenges that must be overcome to achieve this understanding. In the proposed research we will tackle two of the challenges: first, the dynamics of fate choices, i.e. the dependence of transitions on time and inductive signals, remains cryptic; second, mechanical signalling regulates instructive cues for transitions but its role in the process is uncertain. One of the primary reasons these important aspects of cell fate choice remain a mystery is because the biology has not been coupled to the biotechnology appropriate to unravel it. This is the purpose of the proposed research: we will develop tools based in microfluidics, microfabrication and hydrogels and integrate them with our stem cell biology expertise to illuminate the process of cell fate choice. We will develop single cell microfluidic technology that possesses unprecedented temporal resolution and control over the signalling environment to study cell fate dynamics. We will also synthesize hydrogel substrates to exert complete control over the mechanical microenvironment of stem cells. Finally, we will advance tools to apply reproducible and defined forces to cells in order to study the role mechanical signalling in cell fate choice. Developing the proposed technology kit hand-in-hand with its biological applications will allow us to delve into the mechanisms of biological transitions in multiple stem cell systems, allowing us to uncover universal phenomena governing cell fate choice.
Max ERC Funding
1 876 618 €
Duration
Start date: 2018-04-01, End date: 2023-03-31
Project acronym CharFL
Project Characterizing the fitness landscape on population and global scales
Researcher (PI) Fyodor Kondrashov
Host Institution (HI) INSTITUTE OF SCIENCE AND TECHNOLOGYAUSTRIA
Call Details Consolidator Grant (CoG), LS2, ERC-2017-COG
Summary The fitness landscape, the representation of how the genotype manifests at the phenotypic (fitness) levels, may be among the most useful concepts in biology with impact on diverse fields, including quantitative genetics, emergence of pathogen resistance, synthetic biology and protein engineering. While progress in characterizing fitness landscapes has been made, three directions of research in the field remain virtually unexplored: the nature of the genotype to phenotype of standing variation (variation found in a natural population), the shape of the fitness landscape encompassing many genotypes and the modelling of complex genetic interactions in protein sequences.
The current proposal is designed to advance the study of fitness landscapes in these three directions using large-scale genomic experiments and experimental data from a model protein and theoretical work. The study of the fitness landscape of standing variation is aimed at the resolution of an outstanding question in quantitative genetics: the extent to which epistasis, non-additive genetic interactions, is shaping the phenotype. The second aim of characterizing the global fitness landscape will give us an understanding of how evolution proceeds along long evolutionary timescales, which can be directly applied to protein engineering and synthetic biology for the design of novel phenotypes. Finally, the third aim of modelling complex interactions will improve our ability to predict phenotypes from genotypes, such as the prediction of human disease mutations. In summary, the proposed study presents an opportunity to provide a unifying understanding of how phenotypes are shaped through genetic interactions. The consolidation of our empirical and theoretical work on different scales of the genotype to phenotype relationship will provide empirical data and novel context for several fields of biology.
Summary
The fitness landscape, the representation of how the genotype manifests at the phenotypic (fitness) levels, may be among the most useful concepts in biology with impact on diverse fields, including quantitative genetics, emergence of pathogen resistance, synthetic biology and protein engineering. While progress in characterizing fitness landscapes has been made, three directions of research in the field remain virtually unexplored: the nature of the genotype to phenotype of standing variation (variation found in a natural population), the shape of the fitness landscape encompassing many genotypes and the modelling of complex genetic interactions in protein sequences.
The current proposal is designed to advance the study of fitness landscapes in these three directions using large-scale genomic experiments and experimental data from a model protein and theoretical work. The study of the fitness landscape of standing variation is aimed at the resolution of an outstanding question in quantitative genetics: the extent to which epistasis, non-additive genetic interactions, is shaping the phenotype. The second aim of characterizing the global fitness landscape will give us an understanding of how evolution proceeds along long evolutionary timescales, which can be directly applied to protein engineering and synthetic biology for the design of novel phenotypes. Finally, the third aim of modelling complex interactions will improve our ability to predict phenotypes from genotypes, such as the prediction of human disease mutations. In summary, the proposed study presents an opportunity to provide a unifying understanding of how phenotypes are shaped through genetic interactions. The consolidation of our empirical and theoretical work on different scales of the genotype to phenotype relationship will provide empirical data and novel context for several fields of biology.
Max ERC Funding
1 998 280 €
Duration
Start date: 2019-01-01, End date: 2023-12-31
Project acronym CombaTCancer
Project Rational combination therapies for metastatic cancer
Researcher (PI) Anna Obenauf
Host Institution (HI) FORSCHUNGSINSTITUT FUR MOLEKULARE PATHOLOGIE GESELLSCHAFT MBH
Call Details Starting Grant (StG), LS4, ERC-2017-STG
Summary Targeted therapy (TT) is frequently used to treat metastatic cancer. Although TT can achieve effective tumor control for several months, durable treatment responses are rare, due to emergence of aggressive, drug-resistant clones (RCs) with high metastatic competence. Tumor heterogeneity and plasticity result in multifaceted resistance mechanisms and targeting RCs poses a daunting challenge.
To better understand the clinical emergence of RCs, my work focuses on the poorly understood events during TT-induced tumor regression. We recently reported that during this phase drug-responsive cancer cells release a therapy-induced secretome, which remodels the tumor microenvironment (TME) and propagates disease relapse by promoting the survival of drug-sensitive cells and stimulating the outgrowth of RCs. Consequently, intervening with combination therapies during the tumor regression period has the potential to prevent the clinical emergence of RCs in the first place.
Here, we outline strategies to (1) understand how RCs emerge and (2) to leverage our findings on the TME remodeling for combination therapies. First, we will develop a novel and innovative parental clone-lookup method, that will allow us to identify and isolate treatment-naïve, parental clones (PCs) that gave rise to RCs. In functional experiments, we will assess (i) whether PCs were already resistant before or developed resistance during TT, (ii) whether PCs have a higher susceptibility to develop resistance than random clones, and (iii) the mechanistic basis for metastatic competence in different clones. Second, we will study the TT-induced TME remodeling, focusing on the effects on tumor vasculature and immune cells. We will utilize our results to target PCs and RCs by combining TT in the phase of tumor regression with other therapies, such as immunotherapies. Our study will provide new mechanistic insights into the biological processes during tumor regression and aims for novel therapeutic strategies.
Summary
Targeted therapy (TT) is frequently used to treat metastatic cancer. Although TT can achieve effective tumor control for several months, durable treatment responses are rare, due to emergence of aggressive, drug-resistant clones (RCs) with high metastatic competence. Tumor heterogeneity and plasticity result in multifaceted resistance mechanisms and targeting RCs poses a daunting challenge.
To better understand the clinical emergence of RCs, my work focuses on the poorly understood events during TT-induced tumor regression. We recently reported that during this phase drug-responsive cancer cells release a therapy-induced secretome, which remodels the tumor microenvironment (TME) and propagates disease relapse by promoting the survival of drug-sensitive cells and stimulating the outgrowth of RCs. Consequently, intervening with combination therapies during the tumor regression period has the potential to prevent the clinical emergence of RCs in the first place.
Here, we outline strategies to (1) understand how RCs emerge and (2) to leverage our findings on the TME remodeling for combination therapies. First, we will develop a novel and innovative parental clone-lookup method, that will allow us to identify and isolate treatment-naïve, parental clones (PCs) that gave rise to RCs. In functional experiments, we will assess (i) whether PCs were already resistant before or developed resistance during TT, (ii) whether PCs have a higher susceptibility to develop resistance than random clones, and (iii) the mechanistic basis for metastatic competence in different clones. Second, we will study the TT-induced TME remodeling, focusing on the effects on tumor vasculature and immune cells. We will utilize our results to target PCs and RCs by combining TT in the phase of tumor regression with other therapies, such as immunotherapies. Our study will provide new mechanistic insights into the biological processes during tumor regression and aims for novel therapeutic strategies.
Max ERC Funding
1 500 000 €
Duration
Start date: 2018-03-01, End date: 2023-02-28
Project acronym CuRE
Project Cardiac REgeneration from within
Researcher (PI) Mauro GIACCA
Host Institution (HI) KING'S COLLEGE LONDON
Call Details Advanced Grant (AdG), LS4, ERC-2017-ADG
Summary Biotechnological therapies for patients with myocardial infarction and heart failure are urgently needed, in light of the breadth of these diseases and a lack of curative treatments. CuRE is an ambitious project aimed at identifying novel factors (cytokines, growth factors, microRNAs) that promote cardiomyocyte proliferation and can thus be transformed into innovative therapeutics to stimulate cardiac regeneration. The Project leads from two concepts: first, that cardiac regeneration can be obtained by stimulating the endogenous capacity of cardiomyocytes to proliferate, second that effective biotherapeutics might be identified through systematic screenings both in vivo and ex vivo. In the mouse, CuRE will take advantage of two unique arrayed libraries cloned in adeno-associated virus (AAV) vectors, one corresponding to the secretome (1200 factors) and the other to the miRNAome (800 pri-miRNA genes). Both libraries will be functionally screened in mice to search for factors that enhance cardiac regeneration. This in vivo selection approach will be complemented by a series of high throughput screenings on primary cardiomyocytes ex vivo, aimed at systematically assessing the involvement of all components of the ubiquitin/proteasome pathway, the cytoskeleton and the sarcomere on cell proliferation. Cytokines and miRNAs can both be developed to become therapeutic molecules, in the form of recombinant proteins and synthetic nucleic acids, respectively. Therefore, a key aim of CuRE will be to establish procedures for their production and administration in vivo, and to assess their efficacy in both small and large animal models of myocardial damage. In addition to this translational goal, the project will entail the successful achievement of several intermediate objectives, each of which possesses intrinsic validity in terms of basic discovery and is thus expected to extend technology and knowledge in the cardiovascular field beyond state-of-the art.
Summary
Biotechnological therapies for patients with myocardial infarction and heart failure are urgently needed, in light of the breadth of these diseases and a lack of curative treatments. CuRE is an ambitious project aimed at identifying novel factors (cytokines, growth factors, microRNAs) that promote cardiomyocyte proliferation and can thus be transformed into innovative therapeutics to stimulate cardiac regeneration. The Project leads from two concepts: first, that cardiac regeneration can be obtained by stimulating the endogenous capacity of cardiomyocytes to proliferate, second that effective biotherapeutics might be identified through systematic screenings both in vivo and ex vivo. In the mouse, CuRE will take advantage of two unique arrayed libraries cloned in adeno-associated virus (AAV) vectors, one corresponding to the secretome (1200 factors) and the other to the miRNAome (800 pri-miRNA genes). Both libraries will be functionally screened in mice to search for factors that enhance cardiac regeneration. This in vivo selection approach will be complemented by a series of high throughput screenings on primary cardiomyocytes ex vivo, aimed at systematically assessing the involvement of all components of the ubiquitin/proteasome pathway, the cytoskeleton and the sarcomere on cell proliferation. Cytokines and miRNAs can both be developed to become therapeutic molecules, in the form of recombinant proteins and synthetic nucleic acids, respectively. Therefore, a key aim of CuRE will be to establish procedures for their production and administration in vivo, and to assess their efficacy in both small and large animal models of myocardial damage. In addition to this translational goal, the project will entail the successful achievement of several intermediate objectives, each of which possesses intrinsic validity in terms of basic discovery and is thus expected to extend technology and knowledge in the cardiovascular field beyond state-of-the art.
Max ERC Funding
2 428 492 €
Duration
Start date: 2019-01-01, End date: 2023-12-31
Project acronym DiSect
Project The Tumour Stroma as a Driver of Clonal Selection
Researcher (PI) Claus JORGENSEN
Host Institution (HI) THE UNIVERSITY OF MANCHESTER
Call Details Consolidator Grant (CoG), LS4, ERC-2017-COG
Summary Pancreatic ductal adenocarcinomas (PDA) are complex heterocellular tumours characterised by extensive desmoplasia. Tumour and stromal host cells actively engage to establish reciprocal signalling loops, which drive cancer progression, resistance to treatment and evasion of immune surveillance. However, the specificity and directionality of these interactions are incompletely characterised.
We have previously shown that tumour cells expressing the main oncogenic driver (KRASG12D) co-opt stromal fibroblasts to elicit a reciprocal signal, which activate tumour cell IGF-1R and AXL receptor tyrosine kinases. Importantly, these signals enable tumour cells to engage additional signalling pathways not activated when oncogenic KRAS is expressed in homogeneous tumour cell cultures. Therefore, to fully appreciate tumour cell signalling, studies should be undertaken within the context of the tumour stroma.
Early stages of PDA display a gradual accumulation of mutations where activated KRAS is accompanied by loss of tumour suppressors CDKN2A, TP53 and SMAD4. Simultaneously, there is an accumulation of infiltrating stromal cells. To address how PDA cells differ in their interaction with the infiltrating stroma, we will use in vitro co-cultures to study how PDA cells with frequent genetic aberrations recruit and interact with host stromal cells. We will combine our unique methodologies for cell-specific labelling with global proteomics and phosphoproteomics analysis to discern cell-specific signalling between tumour and stroma cells. Following, we will analyse the impact of the tumour stroma on clonal selection and use computational modelling to identify which cell autonomous and non-cell autonomous signals drive progression. Delineating how reciprocal signalling regulates early tumour cell signalling and clonal selection is critical to define pro-tumorigenic from restrictive stromal elements in order to improve combination therapies.
Summary
Pancreatic ductal adenocarcinomas (PDA) are complex heterocellular tumours characterised by extensive desmoplasia. Tumour and stromal host cells actively engage to establish reciprocal signalling loops, which drive cancer progression, resistance to treatment and evasion of immune surveillance. However, the specificity and directionality of these interactions are incompletely characterised.
We have previously shown that tumour cells expressing the main oncogenic driver (KRASG12D) co-opt stromal fibroblasts to elicit a reciprocal signal, which activate tumour cell IGF-1R and AXL receptor tyrosine kinases. Importantly, these signals enable tumour cells to engage additional signalling pathways not activated when oncogenic KRAS is expressed in homogeneous tumour cell cultures. Therefore, to fully appreciate tumour cell signalling, studies should be undertaken within the context of the tumour stroma.
Early stages of PDA display a gradual accumulation of mutations where activated KRAS is accompanied by loss of tumour suppressors CDKN2A, TP53 and SMAD4. Simultaneously, there is an accumulation of infiltrating stromal cells. To address how PDA cells differ in their interaction with the infiltrating stroma, we will use in vitro co-cultures to study how PDA cells with frequent genetic aberrations recruit and interact with host stromal cells. We will combine our unique methodologies for cell-specific labelling with global proteomics and phosphoproteomics analysis to discern cell-specific signalling between tumour and stroma cells. Following, we will analyse the impact of the tumour stroma on clonal selection and use computational modelling to identify which cell autonomous and non-cell autonomous signals drive progression. Delineating how reciprocal signalling regulates early tumour cell signalling and clonal selection is critical to define pro-tumorigenic from restrictive stromal elements in order to improve combination therapies.
Max ERC Funding
1 969 768 €
Duration
Start date: 2018-06-01, End date: 2023-05-31
Project acronym EPIC
Project Enabling Precision Immuno-oncology in Colorectal cancer
Researcher (PI) Zlatko TRAJANOSKI
Host Institution (HI) MEDIZINISCHE UNIVERSITAT INNSBRUCK
Call Details Advanced Grant (AdG), LS7, ERC-2017-ADG
Summary Immunotherapy with checkpoints blockers is transforming the treatment of advanced cancers. Colorectal cancer (CRC), a cancer with 1.4 million new cases diagnosed annually worldwide, is refractory to immunotherapy (with the exception of a minority of tumors with microsatellite instability). This is somehow paradoxical as CRC is a cancer for which we have shown that it is under immunological control and that tumor infiltrating lymphocytes represent a strong independent predictor of survival. Thus, there is an urgent need to broaden the clinical benefits of immune checkpoint blockers to CRC by combining agents with synergistic mechanisms of action. An attractive approach to sensitize tumors to immunotherapy is to harness immunogenic effects induced by approved conventional or targeted agents.
Here I propose a new paradigm to identify molecular determinants of resistance to immunotherapy and develop personalized in silico and in vitro models for predicting response to combination therapy in CRC. The EPIC concept is based on three pillars: 1) emphasis on antitumor T cell activity; 2) systematic interrogation of tumor-immune cell interactions using data-driven modeling and knowledge-based mechanistic modeling, and 3) generation of key quantitative data to train and validate algorithms using perturbation experiments with patient-derived tumor organoids and cutting-edge technologies for multidimensional profiling. We will investigate three immunomodulatory processes: 1) immunostimulatory effects of chemotherapeutics, 2) rewiring of signaling networks induced by targeted drugs and their interference with immunity, and 3) metabolic reprogramming of T cells to enhance antitumor immunity.
The anticipated outcome of EPIC is a precision immuno-oncology platform that integrates tumor organoids with high-throughput and high-content data for testing drug combinations, and machine learning for making therapeutic recommendations for individual patients.
Summary
Immunotherapy with checkpoints blockers is transforming the treatment of advanced cancers. Colorectal cancer (CRC), a cancer with 1.4 million new cases diagnosed annually worldwide, is refractory to immunotherapy (with the exception of a minority of tumors with microsatellite instability). This is somehow paradoxical as CRC is a cancer for which we have shown that it is under immunological control and that tumor infiltrating lymphocytes represent a strong independent predictor of survival. Thus, there is an urgent need to broaden the clinical benefits of immune checkpoint blockers to CRC by combining agents with synergistic mechanisms of action. An attractive approach to sensitize tumors to immunotherapy is to harness immunogenic effects induced by approved conventional or targeted agents.
Here I propose a new paradigm to identify molecular determinants of resistance to immunotherapy and develop personalized in silico and in vitro models for predicting response to combination therapy in CRC. The EPIC concept is based on three pillars: 1) emphasis on antitumor T cell activity; 2) systematic interrogation of tumor-immune cell interactions using data-driven modeling and knowledge-based mechanistic modeling, and 3) generation of key quantitative data to train and validate algorithms using perturbation experiments with patient-derived tumor organoids and cutting-edge technologies for multidimensional profiling. We will investigate three immunomodulatory processes: 1) immunostimulatory effects of chemotherapeutics, 2) rewiring of signaling networks induced by targeted drugs and their interference with immunity, and 3) metabolic reprogramming of T cells to enhance antitumor immunity.
The anticipated outcome of EPIC is a precision immuno-oncology platform that integrates tumor organoids with high-throughput and high-content data for testing drug combinations, and machine learning for making therapeutic recommendations for individual patients.
Max ERC Funding
2 460 500 €
Duration
Start date: 2018-10-01, End date: 2023-09-30
Project acronym EPICLINES
Project Elucidating the causes and consequences of the global pattern of epigenetic variation in Arabidopsis thaliana
Researcher (PI) Lars Magnus Henrik NORDBORG
Host Institution (HI) GREGOR MENDEL INSTITUT FUR MOLEKULARE PFLANZENBIOLOGIE GMBH
Call Details Advanced Grant (AdG), LS8, ERC-2017-ADG
Summary Epigenetics continues to fascinate, especially the notion that it blurs the line between “nature and nurture” and could make Lamarckian adaptation via the inheritance of acquired characteristics possible. That this is in principle possible is clear: in the model plant Arabidopsis thaliana (Thale cress), experimentally induced DNA methylation variation can be inherited and affect important traits. The question is whether this is important in nature. Recent studies of A. thaliana have revealed a pattern of correlation between levels of methylation and climate variables that strongly suggests that methylation is important in adaptation. However, somewhat paradoxically, the experiments also showed that much of the variation for this epigenetic trait appears to have a genetic rather than an epigenetic basis. This suggest that epigenetics may indeed be important for adaptation, but as part of a genetic mechanism that is currently not understood. The goal of this project is to determine whether the global pattern of methylation has a genetic or an epigenetic basis, and to use this information to elucidate the ultimate basis for the global pattern of variation: natural selection.
Summary
Epigenetics continues to fascinate, especially the notion that it blurs the line between “nature and nurture” and could make Lamarckian adaptation via the inheritance of acquired characteristics possible. That this is in principle possible is clear: in the model plant Arabidopsis thaliana (Thale cress), experimentally induced DNA methylation variation can be inherited and affect important traits. The question is whether this is important in nature. Recent studies of A. thaliana have revealed a pattern of correlation between levels of methylation and climate variables that strongly suggests that methylation is important in adaptation. However, somewhat paradoxically, the experiments also showed that much of the variation for this epigenetic trait appears to have a genetic rather than an epigenetic basis. This suggest that epigenetics may indeed be important for adaptation, but as part of a genetic mechanism that is currently not understood. The goal of this project is to determine whether the global pattern of methylation has a genetic or an epigenetic basis, and to use this information to elucidate the ultimate basis for the global pattern of variation: natural selection.
Max ERC Funding
2 498 468 €
Duration
Start date: 2018-06-01, End date: 2023-05-31
Project acronym EPICut
Project Molecular mechanisms, evolutionary impacts and applications of prokaryotic epigenetic-targeted immune systems
Researcher (PI) Mark Dominik SZCZELKUN
Host Institution (HI) UNIVERSITY OF BRISTOL
Call Details Advanced Grant (AdG), LS1, ERC-2017-ADG
Summary Interactions between bacteria and their viruses (bacteriophages) have led to the evolution of a wide range of bacterial mechanisms to resist viral infection. The exploitation of such systems has produced true revolutions in biotechnology; firstly, the restriction-modification (RM) enzymes for genetic engineering, and secondly, CRISPR-Cas9 for gene editing. This project aims to unravel the mechanisms and consequences of prokaryotic immune systems that target covalently-modified DNA, such as base methylation, hydroxymethylation and glucosylation. Very little is known about these Type IV restriction enzymes at a mechanistic level, or about their importance to the coevolution of prokaryotic-phage communities. I propose a unique interdisciplinary approach that combines biophysical and single-molecule analysis of enzyme function, nucleoprotein structure determination, prokaryotic evolutionary ecology, and epigenome sequencing, to link the molecular mechanisms of prokaryotic defence to individual, population and community-level phenotypes. This knowledge is vital to a full understanding of how bacterial immunity influences horizontal gene transfer, including the spread of virulence or antimicrobial resistance. In addition, a deeper analysis of enzyme function will support our reengineering of these systems to produce improved restriction enzyme tools for the mapping of eukaryotic epigenetics markers.
Summary
Interactions between bacteria and their viruses (bacteriophages) have led to the evolution of a wide range of bacterial mechanisms to resist viral infection. The exploitation of such systems has produced true revolutions in biotechnology; firstly, the restriction-modification (RM) enzymes for genetic engineering, and secondly, CRISPR-Cas9 for gene editing. This project aims to unravel the mechanisms and consequences of prokaryotic immune systems that target covalently-modified DNA, such as base methylation, hydroxymethylation and glucosylation. Very little is known about these Type IV restriction enzymes at a mechanistic level, or about their importance to the coevolution of prokaryotic-phage communities. I propose a unique interdisciplinary approach that combines biophysical and single-molecule analysis of enzyme function, nucleoprotein structure determination, prokaryotic evolutionary ecology, and epigenome sequencing, to link the molecular mechanisms of prokaryotic defence to individual, population and community-level phenotypes. This knowledge is vital to a full understanding of how bacterial immunity influences horizontal gene transfer, including the spread of virulence or antimicrobial resistance. In addition, a deeper analysis of enzyme function will support our reengineering of these systems to produce improved restriction enzyme tools for the mapping of eukaryotic epigenetics markers.
Max ERC Funding
2 196 414 €
Duration
Start date: 2018-08-01, End date: 2023-07-31
