Project acronym 5D Heart Patch
Project A Functional, Mature In vivo Human Ventricular Muscle Patch for Cardiomyopathy
Researcher (PI) Kenneth Randall Chien
Host Institution (HI) KAROLINSKA INSTITUTET
Call Details Advanced Grant (AdG), LS7, ERC-2016-ADG
Summary Developing new therapeutic strategies for heart regeneration is a major goal for cardiac biology and medicine. While cardiomyocytes can be generated from human pluripotent stem (hPSC) cells in vitro, it has proven difficult to use these cells to generate a large scale, mature human heart ventricular muscle graft on the injured heart in vivo. The central objective of this proposal is to optimize the generation of a large-scale pure, fully functional human ventricular muscle patch in vivo through the self-assembly of purified human ventricular progenitors and the localized expression of defined paracrine factors that drive their expansion, differentiation, vascularization, matrix formation, and maturation. Recently, we have found that purified hPSC-derived ventricular progenitors (HVPs) can self-assemble in vivo on the epicardial surface into a 3D vascularized, and functional ventricular patch with its own extracellular matrix via a cell autonomous pathway. A two-step protocol and FACS purification of HVP receptors can generate billions of pure HVPs- The current proposal will lead to the identification of defined paracrine pathways to enhance the survival, grafting/implantation, expansion, differentiation, matrix formation, vascularization and maturation of the graft in vivo. We will captalize on our unique HVP system and our novel modRNA technology to deliver therapeutic strategies by using the in vivo human ventricular muscle to model in vivo arrhythmogenic cardiomyopathy, and optimize the ability of the graft to compensate for the massive loss of functional muscle during ischemic cardiomyopathy and post-myocardial infarction. The studies will lead to new in vivo chimeric models of human cardiac disease and an experimental paradigm to optimize organ-on-organ cardiac tissue engineers of an in vivo, functional mature ventricular patch for cardiomyopathy
Summary
Developing new therapeutic strategies for heart regeneration is a major goal for cardiac biology and medicine. While cardiomyocytes can be generated from human pluripotent stem (hPSC) cells in vitro, it has proven difficult to use these cells to generate a large scale, mature human heart ventricular muscle graft on the injured heart in vivo. The central objective of this proposal is to optimize the generation of a large-scale pure, fully functional human ventricular muscle patch in vivo through the self-assembly of purified human ventricular progenitors and the localized expression of defined paracrine factors that drive their expansion, differentiation, vascularization, matrix formation, and maturation. Recently, we have found that purified hPSC-derived ventricular progenitors (HVPs) can self-assemble in vivo on the epicardial surface into a 3D vascularized, and functional ventricular patch with its own extracellular matrix via a cell autonomous pathway. A two-step protocol and FACS purification of HVP receptors can generate billions of pure HVPs- The current proposal will lead to the identification of defined paracrine pathways to enhance the survival, grafting/implantation, expansion, differentiation, matrix formation, vascularization and maturation of the graft in vivo. We will captalize on our unique HVP system and our novel modRNA technology to deliver therapeutic strategies by using the in vivo human ventricular muscle to model in vivo arrhythmogenic cardiomyopathy, and optimize the ability of the graft to compensate for the massive loss of functional muscle during ischemic cardiomyopathy and post-myocardial infarction. The studies will lead to new in vivo chimeric models of human cardiac disease and an experimental paradigm to optimize organ-on-organ cardiac tissue engineers of an in vivo, functional mature ventricular patch for cardiomyopathy
Max ERC Funding
2 149 228 €
Duration
Start date: 2017-12-01, End date: 2022-11-30
Project acronym BrainInBrain
Project Neural circuits underlying complex brain function across animals - from conserved core concepts to specializations defining a species’ identity
Researcher (PI) Stanley HEINZE
Host Institution (HI) LUNDS UNIVERSITET
Call Details Starting Grant (StG), LS5, ERC-2016-STG
Summary The core function of all brains is to compute the current state of the world, compare it to the desired state of the world and select motor programs that drive behavior minimizing any mismatch. The circuits underlying these functions are the key to understand brains in general, but so far they are completely unknown. Three problems have hindered progress: 1) The animal’s desired state of the world is rarely known. 2) Most studies in simple models have focused on sensory driven, reflex-like processes, and not considered self-initiated behavior. 3) The circuits underlying complex behaviors in vertebrates are widely distributed, containing millions of neurons. With this proposal I aim at overcoming these problems using insects, whose tiny brains solve the same basic problems as our brains but with 100,000 times fewer cells. Moreover, the central complex, a single conserved brain region consisting of only a few thousand neurons, is crucial for sensory integration, motor control and state-dependent modulation, essentially being a ‘brain in the brain’. To simplify the problem further I will focus on navigation behavior. Here, the desired and actual states of the world are equal to the desired and current headings of the animal, with mismatches resulting in compensatory steering. I have previously shown how the central complex encodes the animal’s current heading. Now I will use behavioral training to generate animals with highly defined desired headings, and correlate neural activity with the animal’s ‘intentions’ and actions - at the level of identified neurons. To establish the involved conserved core circuitry valid across insects I will compare species with distinct lifestyles. Secondly, I will reveal how these circuits have evolved to account for each species’ unique ecology. The proposed work will provide a coherent framework to study key concepts of fundamental brain functions in unprecedented detail - using a single, conserved, but flexible neural circuit.
Summary
The core function of all brains is to compute the current state of the world, compare it to the desired state of the world and select motor programs that drive behavior minimizing any mismatch. The circuits underlying these functions are the key to understand brains in general, but so far they are completely unknown. Three problems have hindered progress: 1) The animal’s desired state of the world is rarely known. 2) Most studies in simple models have focused on sensory driven, reflex-like processes, and not considered self-initiated behavior. 3) The circuits underlying complex behaviors in vertebrates are widely distributed, containing millions of neurons. With this proposal I aim at overcoming these problems using insects, whose tiny brains solve the same basic problems as our brains but with 100,000 times fewer cells. Moreover, the central complex, a single conserved brain region consisting of only a few thousand neurons, is crucial for sensory integration, motor control and state-dependent modulation, essentially being a ‘brain in the brain’. To simplify the problem further I will focus on navigation behavior. Here, the desired and actual states of the world are equal to the desired and current headings of the animal, with mismatches resulting in compensatory steering. I have previously shown how the central complex encodes the animal’s current heading. Now I will use behavioral training to generate animals with highly defined desired headings, and correlate neural activity with the animal’s ‘intentions’ and actions - at the level of identified neurons. To establish the involved conserved core circuitry valid across insects I will compare species with distinct lifestyles. Secondly, I will reveal how these circuits have evolved to account for each species’ unique ecology. The proposed work will provide a coherent framework to study key concepts of fundamental brain functions in unprecedented detail - using a single, conserved, but flexible neural circuit.
Max ERC Funding
1 500 000 €
Duration
Start date: 2017-01-01, End date: 2021-12-31
Project acronym CC-MEM
Project Coordination and Composability: The Keys to Efficient Memory System Design
Researcher (PI) David BLACK-SCHAFFER
Host Institution (HI) UPPSALA UNIVERSITET
Call Details Starting Grant (StG), PE6, ERC-2016-STG
Summary Computer systems today are power limited. As a result, efficiency gains can be translated into performance. Over the past decade we have been so effective at making computation more efficient that we are now at the point where we spend as much energy moving data (from memory to cache to processor) as we do computing the results. And this trend is only becoming worse as we demand more bandwidth for more powerful processors. To improve performance we need to revisit the way we design memory systems from an energy-first perspective, both at the hardware level and by coordinating data movement between hardware and software.
CC-MEM will address memory system efficiency by redesigning low-level hardware and high-level hardware/software integration for energy efficiency. The key novelty is in developing a framework for creating efficient memory systems. This framework will enable researchers and designers to compose solutions to different memory system problems (through a shared exchange of metadata) and coordinate them towards high-level system efficiency goals (through a shared policy framework). Central to this framework is a bilateral exchange of metadata and policy between hardware and software components. This novel communication will open new challenges and opportunities for fine-grained optimizations, system-level efficiency metrics, and more effective divisions of responsibility between hardware and software components.
CC-MEM will change how researchers and designers approach memory system design from today’s ad hoc development of local solutions to one wherein disparate components can be integrated (composed) and driven (coordinated) by system-level metrics. As a result, we will be able to more intelligently manage data, leading to dramatically lower memory system energy and increased performance, and open new possibilities for hardware and software optimizations.
Summary
Computer systems today are power limited. As a result, efficiency gains can be translated into performance. Over the past decade we have been so effective at making computation more efficient that we are now at the point where we spend as much energy moving data (from memory to cache to processor) as we do computing the results. And this trend is only becoming worse as we demand more bandwidth for more powerful processors. To improve performance we need to revisit the way we design memory systems from an energy-first perspective, both at the hardware level and by coordinating data movement between hardware and software.
CC-MEM will address memory system efficiency by redesigning low-level hardware and high-level hardware/software integration for energy efficiency. The key novelty is in developing a framework for creating efficient memory systems. This framework will enable researchers and designers to compose solutions to different memory system problems (through a shared exchange of metadata) and coordinate them towards high-level system efficiency goals (through a shared policy framework). Central to this framework is a bilateral exchange of metadata and policy between hardware and software components. This novel communication will open new challenges and opportunities for fine-grained optimizations, system-level efficiency metrics, and more effective divisions of responsibility between hardware and software components.
CC-MEM will change how researchers and designers approach memory system design from today’s ad hoc development of local solutions to one wherein disparate components can be integrated (composed) and driven (coordinated) by system-level metrics. As a result, we will be able to more intelligently manage data, leading to dramatically lower memory system energy and increased performance, and open new possibilities for hardware and software optimizations.
Max ERC Funding
1 610 000 €
Duration
Start date: 2017-03-01, End date: 2022-02-28
Project acronym CellTrack
Project Cellular Position Tracking Using DNA Origami Barcodes
Researcher (PI) Björn HÖGBERG
Host Institution (HI) KAROLINSKA INSTITUTET
Call Details Consolidator Grant (CoG), LS7, ERC-2016-COG
Summary The research I propose here will provide an enabling technology; spatially resolved transcriptomics, to address important problems in cell- and developmental-biology, in particular: How are stem cells in the skin and gut proliferating without turning into cancers? How are differentiated cells related, in their transcriptome and spatial positions, to their progenitors?
To investigate these problems on a molecular level and open up paths to find completely new spatiotemporal interdependencies in complex biological systems, I propose to use our newly developed DNA-origami strategy (Benson et al, Nature, 523 p. 441 (2015) ), combined with a combinatorial cloning technique, to build a new method for deep mRNA sequencing of tissue with single-cell resolution. These new types of origami are stable in physiological salt conditions and opens up their use in in-vivo applications.
In DNA-origami we can control the exact spatial position of all nucleotides. By folding the scaffold to display sequences for hybridization of fluorophores conjugated to DNA, we can create optical nano-barcodes. By using structures made out of DNA, the patterns of the optical barcodes will be readable both by imaging and by sequencing, thus enabling the creation of a mapping between cell locations in an organ and the mRNA expression of those cells.
We will use the method to perform spatially resolved transcriptomics in small organs: the mouse hair follicle, and small intestine crypt, and also perform the procedure for multiple samples collected at different time points. This will enable a high-dimensional data analysis that most likely will expose previously unknown dependencies that would provide completely new knowledge about how these biological systems work. By studying these systems, we will uncover much more information on how stem cells contribute to regeneration, the issue of de-differentiation that is a common theme in these organs and the effect this might have on the origin of cancer.
Summary
The research I propose here will provide an enabling technology; spatially resolved transcriptomics, to address important problems in cell- and developmental-biology, in particular: How are stem cells in the skin and gut proliferating without turning into cancers? How are differentiated cells related, in their transcriptome and spatial positions, to their progenitors?
To investigate these problems on a molecular level and open up paths to find completely new spatiotemporal interdependencies in complex biological systems, I propose to use our newly developed DNA-origami strategy (Benson et al, Nature, 523 p. 441 (2015) ), combined with a combinatorial cloning technique, to build a new method for deep mRNA sequencing of tissue with single-cell resolution. These new types of origami are stable in physiological salt conditions and opens up their use in in-vivo applications.
In DNA-origami we can control the exact spatial position of all nucleotides. By folding the scaffold to display sequences for hybridization of fluorophores conjugated to DNA, we can create optical nano-barcodes. By using structures made out of DNA, the patterns of the optical barcodes will be readable both by imaging and by sequencing, thus enabling the creation of a mapping between cell locations in an organ and the mRNA expression of those cells.
We will use the method to perform spatially resolved transcriptomics in small organs: the mouse hair follicle, and small intestine crypt, and also perform the procedure for multiple samples collected at different time points. This will enable a high-dimensional data analysis that most likely will expose previously unknown dependencies that would provide completely new knowledge about how these biological systems work. By studying these systems, we will uncover much more information on how stem cells contribute to regeneration, the issue of de-differentiation that is a common theme in these organs and the effect this might have on the origin of cancer.
Max ERC Funding
1 923 263 €
Duration
Start date: 2017-08-01, End date: 2022-07-31
Project acronym CIO
Project Common Interactive Objects
Researcher (PI) Susanne Bødker
Host Institution (HI) AARHUS UNIVERSITET
Call Details Advanced Grant (AdG), PE6, ERC-2016-ADG
Summary In CIO, common interactive objects are developed and explored to extend human control over the technological environment by human beings, both individually and together. CIO leads to a coherent framework of user interfaces to be applied in interaction design. Common interactive objects will provide a useful frame for furthering human computer interaction (HCI) theory, development of interaction design methods and the underlying technical platforms. Common interactive objects will empower users to better understand and develop the technologies they use.
When carried through, the project offers new ways for people to construct and configure human physical and virtual environments, together, over time and within communities.
The main objectives of CIO are to
1. develop the conception of common interactive objects in order to offer a new understanding of human-computer interaction, focusing on human control.
2. develop support for building user interfaces in a coherent and unified framework.
3. make common interactive objects that will empower users to better understand and develop the technologies they use.
4. carry out ground-breaking research regarding the technological basis of common interactive objects with focus on malleability, control and shareability over time.
CIO is methodologically rooted in HCI. CIO’s research methods combine empirical, analytical, theoretical, and design approaches, all with focus on the relationship between common interactive objects and their human users.
CIO presents the idea that common interactive objects may radically innovate our understanding of use and building user interfaces. The gains of CIO will be a coherent new, high-impact way of understanding and building HCI across physical and virtual structures, bringing control back to the users. The risks are in delivering this alternative in a manner that is able to confront the current strong commercial interests in the Internet-of-Things and the 'new' Artificial Intelligence
Summary
In CIO, common interactive objects are developed and explored to extend human control over the technological environment by human beings, both individually and together. CIO leads to a coherent framework of user interfaces to be applied in interaction design. Common interactive objects will provide a useful frame for furthering human computer interaction (HCI) theory, development of interaction design methods and the underlying technical platforms. Common interactive objects will empower users to better understand and develop the technologies they use.
When carried through, the project offers new ways for people to construct and configure human physical and virtual environments, together, over time and within communities.
The main objectives of CIO are to
1. develop the conception of common interactive objects in order to offer a new understanding of human-computer interaction, focusing on human control.
2. develop support for building user interfaces in a coherent and unified framework.
3. make common interactive objects that will empower users to better understand and develop the technologies they use.
4. carry out ground-breaking research regarding the technological basis of common interactive objects with focus on malleability, control and shareability over time.
CIO is methodologically rooted in HCI. CIO’s research methods combine empirical, analytical, theoretical, and design approaches, all with focus on the relationship between common interactive objects and their human users.
CIO presents the idea that common interactive objects may radically innovate our understanding of use and building user interfaces. The gains of CIO will be a coherent new, high-impact way of understanding and building HCI across physical and virtual structures, bringing control back to the users. The risks are in delivering this alternative in a manner that is able to confront the current strong commercial interests in the Internet-of-Things and the 'new' Artificial Intelligence
Max ERC Funding
2 398 993 €
Duration
Start date: 2017-12-01, End date: 2022-11-30
Project acronym DisDyn
Project Distributed and Dynamic Graph Algorithms and Complexity
Researcher (PI) Danupon NA NONGKAI
Host Institution (HI) KUNGLIGA TEKNISKA HOEGSKOLAN
Call Details Starting Grant (StG), PE6, ERC-2016-STG
Summary This project aims to (i) resolve challenging graph problems in distributed and dynamic settings, with a focus on connectivity problems (such as computing edge connectivity and distances), and (ii) on the way develop a systematic approach to attack problems in these settings, by thoroughly exploring relevant algorithmic and complexity-theoretic landscapes. Tasks include
- building a hierarchy of intermediate computational models so that designing algorithms and proving lower bounds can be done in several intermediate steps,
- explaining the limits of algorithms by proving conditional lower bounds based on old and new reasonable conjectures, and
- connecting techniques in the two settings to generate new insights that are unlikely to emerge from the isolated viewpoint of a single field.
The project will take advantage from and contribute to the developments in many young fields in theoretical computer science, such as fine-grained complexity and sublinear algorithms. Resolving one of the connectivity problems will already be a groundbreaking result. However, given the approach, it is likely that one breakthrough will lead to many others.
Summary
This project aims to (i) resolve challenging graph problems in distributed and dynamic settings, with a focus on connectivity problems (such as computing edge connectivity and distances), and (ii) on the way develop a systematic approach to attack problems in these settings, by thoroughly exploring relevant algorithmic and complexity-theoretic landscapes. Tasks include
- building a hierarchy of intermediate computational models so that designing algorithms and proving lower bounds can be done in several intermediate steps,
- explaining the limits of algorithms by proving conditional lower bounds based on old and new reasonable conjectures, and
- connecting techniques in the two settings to generate new insights that are unlikely to emerge from the isolated viewpoint of a single field.
The project will take advantage from and contribute to the developments in many young fields in theoretical computer science, such as fine-grained complexity and sublinear algorithms. Resolving one of the connectivity problems will already be a groundbreaking result. However, given the approach, it is likely that one breakthrough will lead to many others.
Max ERC Funding
1 500 000 €
Duration
Start date: 2017-02-01, End date: 2022-01-31
Project acronym EcoImmuneCosts
Project Immunity in Ecology and Evolution: 'Hidden' costs of disease, immune function and their consequences for Darwinian fitness
Researcher (PI) Dennis Lennart HASSELQUIST
Host Institution (HI) LUNDS UNIVERSITET
Call Details Advanced Grant (AdG), LS8, ERC-2016-ADG
Summary Eco-immunology targets one of the great challenges in biology and medicine - how the immune system has evolved to optimize protection and minimize immunopathology (incl. autoimmune) costs. A primary target of my proposal is to study low-virulent pathogens causing mild infections, which for long have been considered harmless. Recent research suggests that this notion is false and that seemingly harmless pathogens entail delayed (‘hidden’) fitness costs. However, the mechanisms mediating these costs are still unknown. I will experimentally test if accelerated telomere degradation is a causative mechanism through which small immune costs can accumulate and be translated into senescence and reduced Darwinian fitness. Another key target is immune costs, which may be ‘hidden’ because of sexually antagonistic effects, and I will study how this may affect immune gene variation, immune costs and Darwinian fitness. These aspects are central for advancing our understanding of the evolution of disease resistance and immune function, incl. immune over-reactions (autoimmunity).
My project exploits a comprehensive 32-year study of great reed warblers to analyze selection patterns in the wild (Fig. 1a), and uses established captive songbird set-ups to conduct carefully designed experiments. The exceptional quality of the long-term data set, together with cutting-edge techniques to measure and manipulate parasite infection, telomere length, oxidative stress and immune gene diversity, provides exciting opportunities to conduct research that previously was unfeasible, pushing the rapidly growing field of eco-immunology (Fig. 1b) to new frontiers. The work integrates theory and methods of evolutionary ecology, immunology and molecular biology, and has broad significance including for e.g. epidemiology and ageing research. I envision my research to change how we look upon causes, consequences (and precautions) of mild infectious, autoimmune and degenerative diseases.
Summary
Eco-immunology targets one of the great challenges in biology and medicine - how the immune system has evolved to optimize protection and minimize immunopathology (incl. autoimmune) costs. A primary target of my proposal is to study low-virulent pathogens causing mild infections, which for long have been considered harmless. Recent research suggests that this notion is false and that seemingly harmless pathogens entail delayed (‘hidden’) fitness costs. However, the mechanisms mediating these costs are still unknown. I will experimentally test if accelerated telomere degradation is a causative mechanism through which small immune costs can accumulate and be translated into senescence and reduced Darwinian fitness. Another key target is immune costs, which may be ‘hidden’ because of sexually antagonistic effects, and I will study how this may affect immune gene variation, immune costs and Darwinian fitness. These aspects are central for advancing our understanding of the evolution of disease resistance and immune function, incl. immune over-reactions (autoimmunity).
My project exploits a comprehensive 32-year study of great reed warblers to analyze selection patterns in the wild (Fig. 1a), and uses established captive songbird set-ups to conduct carefully designed experiments. The exceptional quality of the long-term data set, together with cutting-edge techniques to measure and manipulate parasite infection, telomere length, oxidative stress and immune gene diversity, provides exciting opportunities to conduct research that previously was unfeasible, pushing the rapidly growing field of eco-immunology (Fig. 1b) to new frontiers. The work integrates theory and methods of evolutionary ecology, immunology and molecular biology, and has broad significance including for e.g. epidemiology and ageing research. I envision my research to change how we look upon causes, consequences (and precautions) of mild infectious, autoimmune and degenerative diseases.
Max ERC Funding
2 500 000 €
Duration
Start date: 2017-08-01, End date: 2022-07-31
Project acronym FatemapB
Project High Resolution Mapping of Fetal and Adult B Cell Fates During Ontogeny
Researcher (PI) Joan YUAN
Host Institution (HI) LUNDS UNIVERSITET
Call Details Starting Grant (StG), LS6, ERC-2016-STG
Summary FateMapB aims to understand how the unique differentiation potential of fetal hematopoietic stem and progenitor cells
(HSPCs) contribute to functionally distinct cell types of the adult immune system. While most immune cells are replenished
by HSPCs through life, others emerge during a limited window in fetal life and sustain through self-renewal in situ. The
lineage identity of fetal HSPCs, and the extent of their contribution to the adult immune repertoire remain surprisingly
unclear. I previously identified the fetal specific RNA binding protein Lin28b as a post-transcriptional molecular switch
capable of inducing fetal-like hematopoiesis in adult bone marrow HSPCs (Yuan et al. Science, 2012). This discovery has
afforded me with unique perspectives on the formation of the mammalian immune system. The concept that the mature
immune system is a mosaic of fetal and adult derived cell types is addressed herein with an emphasis on the B cell lineage.
We will use two complementary lineage-tracing technologies to stratify the immune system as a function of developmental
time, generating fundamental insight into the division of labor between fetal and adult HSPCs that ultimately provides
effective host protection.
Aim 1. Determine the qualitative and quantitative contribution of fetal HSPCs to the mature immune repertoire in situ
through Cre recombination mediated lineage-tracing.
Aim 2. Resolve the disputed lineage relationship between fetal derived B1a cells and adult derived B2 cells by single cell
lineage-tracing using cellular barcoding in vivo.
Aim 3. Characterize the mechanism and effector functions of Lin28b induced B1a cell development for assessing the
clinical utility of inducible fetal-like lymphopoiesis.
The implications of FateMapB extend beyond normal development to immune regeneration and age-related features of
leukemogenesis. Finally, our combinatorial lineage-tracing approach enables dissection of cell fates with previously
unattainable resolution.
Summary
FateMapB aims to understand how the unique differentiation potential of fetal hematopoietic stem and progenitor cells
(HSPCs) contribute to functionally distinct cell types of the adult immune system. While most immune cells are replenished
by HSPCs through life, others emerge during a limited window in fetal life and sustain through self-renewal in situ. The
lineage identity of fetal HSPCs, and the extent of their contribution to the adult immune repertoire remain surprisingly
unclear. I previously identified the fetal specific RNA binding protein Lin28b as a post-transcriptional molecular switch
capable of inducing fetal-like hematopoiesis in adult bone marrow HSPCs (Yuan et al. Science, 2012). This discovery has
afforded me with unique perspectives on the formation of the mammalian immune system. The concept that the mature
immune system is a mosaic of fetal and adult derived cell types is addressed herein with an emphasis on the B cell lineage.
We will use two complementary lineage-tracing technologies to stratify the immune system as a function of developmental
time, generating fundamental insight into the division of labor between fetal and adult HSPCs that ultimately provides
effective host protection.
Aim 1. Determine the qualitative and quantitative contribution of fetal HSPCs to the mature immune repertoire in situ
through Cre recombination mediated lineage-tracing.
Aim 2. Resolve the disputed lineage relationship between fetal derived B1a cells and adult derived B2 cells by single cell
lineage-tracing using cellular barcoding in vivo.
Aim 3. Characterize the mechanism and effector functions of Lin28b induced B1a cell development for assessing the
clinical utility of inducible fetal-like lymphopoiesis.
The implications of FateMapB extend beyond normal development to immune regeneration and age-related features of
leukemogenesis. Finally, our combinatorial lineage-tracing approach enables dissection of cell fates with previously
unattainable resolution.
Max ERC Funding
1 499 905 €
Duration
Start date: 2017-10-01, End date: 2022-09-30
Project acronym FRAGMENT2DRUG
Project Jigsaw puzzles at atomic resolution: Computational design of GPCR drugs from fragments
Researcher (PI) Jens CARLSSON
Host Institution (HI) UPPSALA UNIVERSITET
Call Details Starting Grant (StG), LS7, ERC-2016-STG
Summary Despite technological advances, industry struggles to develop new pharmaceuticals and therefore novel strategies for drug discovery are urgently needed. G protein-coupled receptors (GPCRs) play important roles in numerous physiological processes and are important drug targets for neurological diseases. My research focuses on modelling of GPCR-ligand interactions at the atomic level, with the goal to increase knowledge of receptor function and develop new methods for drug discovery. Breakthroughs in GPCR structural biology and access to sensitive screening assays provide opportunities to utilize fragment-based lead discovery (FBLD), a powerful approach for drug design. The objective of the project is to create a computational platform for FBLD, with a vision to transform the early drug discovery process for GPCRs. As structural information for these targets is limited, predictive models of receptor-fragment complexes will be crucial for the successful use of FBLD. In this project, computational structure-based methods for discovery of fragment ligands and further optimization of these to potent leads will be developed. These techniques will be applied to address two difficult problems in drug discovery. The first of these is to design ligands of peptide-binding GPCRs that have been challenging for existing methods. One of the promises of FBLD is to provide access to difficult targets, which will be explored by combining molecular docking and biophysical screening against peptide-GPCRs to identify novel lead candidates. A second challenge is that efficient treatment of neurological disorders often requires modulation of multiple targets, which also will be the focus of the project.
Summary
Despite technological advances, industry struggles to develop new pharmaceuticals and therefore novel strategies for drug discovery are urgently needed. G protein-coupled receptors (GPCRs) play important roles in numerous physiological processes and are important drug targets for neurological diseases. My research focuses on modelling of GPCR-ligand interactions at the atomic level, with the goal to increase knowledge of receptor function and develop new methods for drug discovery. Breakthroughs in GPCR structural biology and access to sensitive screening assays provide opportunities to utilize fragment-based lead discovery (FBLD), a powerful approach for drug design. The objective of the project is to create a computational platform for FBLD, with a vision to transform the early drug discovery process for GPCRs. As structural information for these targets is limited, predictive models of receptor-fragment complexes will be crucial for the successful use of FBLD. In this project, computational structure-based methods for discovery of fragment ligands and further optimization of these to potent leads will be developed. These techniques will be applied to address two difficult problems in drug discovery. The first of these is to design ligands of peptide-binding GPCRs that have been challenging for existing methods. One of the promises of FBLD is to provide access to difficult targets, which will be explored by combining molecular docking and biophysical screening against peptide-GPCRs to identify novel lead candidates. A second challenge is that efficient treatment of neurological disorders often requires modulation of multiple targets, which also will be the focus of the project.
Max ERC Funding
1 467 500 €
Duration
Start date: 2017-11-01, End date: 2022-10-31
Project acronym GENOMIS
Project Illuminating GENome Organization through integrated MIcroscopy and Sequencing
Researcher (PI) Marzena Magda BIENKO
Host Institution (HI) KAROLINSKA INSTITUTET
Call Details Starting Grant (StG), LS2, ERC-2016-STG
Summary In human cells, two meters of DNA sequence are compressed into a nucleus whose linear size is five orders of magnitude smaller. Deciphering how this amazing structural organization is achieved and how DNA functions can ensue in the environment of a cell’s nucleus represent central questions for contemporary biology.
Here, I embrace this challenge by establishing a comprehensive framework of microscopy and sequencing technologies coupled with advanced analytical approaches, aimed at addressing three fundamental highly-interconnected questions: 1) What are the design principles that govern DNA compaction? 2) How does genome structure vary between different cell types as well as among cells of the same type? 3) What is the link between genome structure and function? In preliminary experiments, we have devised a powerful method for Genomic loci Positioning by Sequencing (GPSeq) in fixed cells with optimally preserved nuclear morphology. In parallel, we are developing high-end microscopy tools for simultaneous localization of dozens of genomic locations at high resolution in thousands of single cells.
We will obtain first-ever genome-wide maps of radial positioning of DNA loci in the nucleus, and combine them with available DNA contact probability maps in order to build 3D models of the human genome structure in different cell types. Using microscopy, we will visualize chromosomal shapes at unprecedented resolution, and use these rich datasets to discover general DNA folding principles. Finally, by combining high-resolution chromosome visualization with gene expression profiling in single cells, we will explore the link between DNA structure and function. Our study shall illuminate the design principles that dictate how genetic information is packed and read in the human nucleus, while providing a comprehensive repertoire of tools for studying genome organization.
Summary
In human cells, two meters of DNA sequence are compressed into a nucleus whose linear size is five orders of magnitude smaller. Deciphering how this amazing structural organization is achieved and how DNA functions can ensue in the environment of a cell’s nucleus represent central questions for contemporary biology.
Here, I embrace this challenge by establishing a comprehensive framework of microscopy and sequencing technologies coupled with advanced analytical approaches, aimed at addressing three fundamental highly-interconnected questions: 1) What are the design principles that govern DNA compaction? 2) How does genome structure vary between different cell types as well as among cells of the same type? 3) What is the link between genome structure and function? In preliminary experiments, we have devised a powerful method for Genomic loci Positioning by Sequencing (GPSeq) in fixed cells with optimally preserved nuclear morphology. In parallel, we are developing high-end microscopy tools for simultaneous localization of dozens of genomic locations at high resolution in thousands of single cells.
We will obtain first-ever genome-wide maps of radial positioning of DNA loci in the nucleus, and combine them with available DNA contact probability maps in order to build 3D models of the human genome structure in different cell types. Using microscopy, we will visualize chromosomal shapes at unprecedented resolution, and use these rich datasets to discover general DNA folding principles. Finally, by combining high-resolution chromosome visualization with gene expression profiling in single cells, we will explore the link between DNA structure and function. Our study shall illuminate the design principles that dictate how genetic information is packed and read in the human nucleus, while providing a comprehensive repertoire of tools for studying genome organization.
Max ERC Funding
1 499 808 €
Duration
Start date: 2018-01-01, End date: 2022-12-31