Project acronym ACCENT
Project How antibodies and complement orchestrate protective immune responses against bacteria
Researcher (PI) suzan ROOIJAKKERS
Host Institution (HI) UNIVERSITAIR MEDISCH CENTRUM UTRECHT
Country Netherlands
Call Details Consolidator Grant (CoG), LS6, ERC-2020-COG
Summary Due to antibiotic resistance, there is now great interest in the development of antibody-based therapies against bacterial infections, for instance via antibodies that boost the host immune system. In order to kill bacteria, antibodies should trigger activation of the complement cascade, which forms bactericidal Membrane Attack Complex (MAC) pores and strongly enhances phagocytosis. Although the power of complement could be exploited for antibody therapies, such developments are hampered by our limited insights into the mechanisms underlying antibody-dependent complement activation on bacteria. My team has developed unique assays to study complement activation on bacteria. In this proposal, we will combine our function-driven approaches with novel B cell sequencing methods to identify anti-bacterial antibodies with strong complement-activating potential. We will develop novel approaches to identify the variable (VH:VL) sequences of human antibodies that recognize whole bacterial cells. After FACS sorting of memory B cells or yeast Fab display, we will use multi-well functional assays to select monoclonal antibodies driving potent complement activation and subsequent killing of E. coli (via neutrophils or MAC). Thanks to our unique tools and unprecedented insights, we are in an unique position to decipher basic mechanisms by which antibodies induce bacterial killing via neutrophils or MAC. We will combine live-cell imaging and structural approaches to determine how bactericidal antibodies assemble lethal MAC pores in the bacterial cell envelope. Finally, we will explore the design of potent antibody combinations and study the mechanisms by which antibodies steer different effector functions, both in the context of clinical and non-pathogenic E. coli strains. Altogether, this grant will lead to fundamental knowledge about the functioning of the immune system and provide a biological basis for the development of antibody-based therapies against bacteria.
Summary
Due to antibiotic resistance, there is now great interest in the development of antibody-based therapies against bacterial infections, for instance via antibodies that boost the host immune system. In order to kill bacteria, antibodies should trigger activation of the complement cascade, which forms bactericidal Membrane Attack Complex (MAC) pores and strongly enhances phagocytosis. Although the power of complement could be exploited for antibody therapies, such developments are hampered by our limited insights into the mechanisms underlying antibody-dependent complement activation on bacteria. My team has developed unique assays to study complement activation on bacteria. In this proposal, we will combine our function-driven approaches with novel B cell sequencing methods to identify anti-bacterial antibodies with strong complement-activating potential. We will develop novel approaches to identify the variable (VH:VL) sequences of human antibodies that recognize whole bacterial cells. After FACS sorting of memory B cells or yeast Fab display, we will use multi-well functional assays to select monoclonal antibodies driving potent complement activation and subsequent killing of E. coli (via neutrophils or MAC). Thanks to our unique tools and unprecedented insights, we are in an unique position to decipher basic mechanisms by which antibodies induce bacterial killing via neutrophils or MAC. We will combine live-cell imaging and structural approaches to determine how bactericidal antibodies assemble lethal MAC pores in the bacterial cell envelope. Finally, we will explore the design of potent antibody combinations and study the mechanisms by which antibodies steer different effector functions, both in the context of clinical and non-pathogenic E. coli strains. Altogether, this grant will lead to fundamental knowledge about the functioning of the immune system and provide a biological basis for the development of antibody-based therapies against bacteria.
Max ERC Funding
2 000 000 €
Duration
Start date: 2021-06-01, End date: 2026-05-31
Project acronym AutoEngineering
Project Engineering antibodies in B cells using endogenous AID activity
Researcher (PI) Kathrin de la Rosa
Host Institution (HI) MAX DELBRUECK CENTRUM FUER MOLEKULARE MEDIZIN IN DER HELMHOLTZ-GEMEINSCHAFT (MDC)
Country Germany
Call Details Starting Grant (StG), LS6, ERC-2020-STG
Summary The AutoEngineering project aims to develop an innovative strategy for B cell engineering by exploiting natural DNA breaks to generate antibodies that surpass common reactivity profiles. The project is based on our surprising finding that in B cells endogenous AID (activation-induced cytidine deaminase) activity can lead to the insertion of a pathogen receptor resulting in broadly reactive antibodies. To unravel this new mechanism of diversification, my laboratory established and developed new methodologies to identify insert-containing antibodies in genomic DNA, mRNA, proteins and cells. We found that insertions in antibody transcripts derive from distant genes, occur across individuals and are inducible in vitro, and we have preliminary evidence that in vitro activation of AID enables integration of a nucleofected DNA substrate. Avoiding exogenous nucleases, this project aims at developing efficient and safe engineering of B cells to produce antibodies by design. Aim 1. By screening for genomic insertions in antibody genes of healthy donors, DNA-repair deficient patients, and manipulated in vitro B cell cultures, we will gain insights into the mechanism of insertion and define biomarkers of DNA repair. Aim 2. The knowledge gained will be used to optimize substrate design and insert integration, while minimizing the potential for off-target integration. We will also explore the possibility to guide AID to target sites using RNAs, and design substrates that allow efficient splicing of an inserted exon. Aim 3. To gain breadth on pathogen recognition and to circumvent the limitation of the heterodimeric antibody binding site, we will use the above approach to engineer B cells to produce antibodies containing receptors for HIV (CD4) and HCV (CD81). Insertion of slim receptor-domains with precise targeting of crucial sites may generate B cells with exceptional potency to reduce the risk for escape mutants, thereby paving a way for artificial immunity.
Summary
The AutoEngineering project aims to develop an innovative strategy for B cell engineering by exploiting natural DNA breaks to generate antibodies that surpass common reactivity profiles. The project is based on our surprising finding that in B cells endogenous AID (activation-induced cytidine deaminase) activity can lead to the insertion of a pathogen receptor resulting in broadly reactive antibodies. To unravel this new mechanism of diversification, my laboratory established and developed new methodologies to identify insert-containing antibodies in genomic DNA, mRNA, proteins and cells. We found that insertions in antibody transcripts derive from distant genes, occur across individuals and are inducible in vitro, and we have preliminary evidence that in vitro activation of AID enables integration of a nucleofected DNA substrate. Avoiding exogenous nucleases, this project aims at developing efficient and safe engineering of B cells to produce antibodies by design. Aim 1. By screening for genomic insertions in antibody genes of healthy donors, DNA-repair deficient patients, and manipulated in vitro B cell cultures, we will gain insights into the mechanism of insertion and define biomarkers of DNA repair. Aim 2. The knowledge gained will be used to optimize substrate design and insert integration, while minimizing the potential for off-target integration. We will also explore the possibility to guide AID to target sites using RNAs, and design substrates that allow efficient splicing of an inserted exon. Aim 3. To gain breadth on pathogen recognition and to circumvent the limitation of the heterodimeric antibody binding site, we will use the above approach to engineer B cells to produce antibodies containing receptors for HIV (CD4) and HCV (CD81). Insertion of slim receptor-domains with precise targeting of crucial sites may generate B cells with exceptional potency to reduce the risk for escape mutants, thereby paving a way for artificial immunity.
Max ERC Funding
1 489 500 €
Duration
Start date: 2021-07-01, End date: 2026-06-30
Project acronym CNSentinels
Project Spatiotemporal control of neuroinfection by meningeal macrophages
Researcher (PI) Rejane Rua
Host Institution (HI) INSTITUT NATIONAL DE LA SANTE ET DE LA RECHERCHE MEDICALE
Country France
Call Details Starting Grant (StG), LS6, ERC-2020-STG
Summary Due to the vital importance of the Central Nervous System (CNS), its infection and inflammation have to be tightly controlled. The surface of the CNS is connected to the periphery by a rich and complex tissue, the meninges. They contain a vast network of macrophages subdivided in two populations endowed with elusive functions. Using innovative depletion strategies in experimental mouse models, I discovered that meningeal macrophage populations represent the first line of protection against neuroinvasive pathogens. In their absence, specific areas in the meninges become highly infected, leading to fatal brain disease. The goal of ‘CNSentinels’ is to understand 1/the mechanisms controlling the spatiotemporal distribution of macrophage populations at the brain surface and 2/the relative contribution of the two macrophage populations in protecting the CNS against neuroinvasive pathogens. To this aim, I developed innovative strategies to visualize and manipulate meningeal macrophages in vivo that I will combine with cutting-edge gene editing techniques, in mice infected with lymphocytic choriomeningitis virus (LCMV). This pioneer work will help understand the spatial organization of the brain defence system and the molecular mechanisms involved in CNS protection, and will provide new avenues to design therapeutic strategies.
Summary
Due to the vital importance of the Central Nervous System (CNS), its infection and inflammation have to be tightly controlled. The surface of the CNS is connected to the periphery by a rich and complex tissue, the meninges. They contain a vast network of macrophages subdivided in two populations endowed with elusive functions. Using innovative depletion strategies in experimental mouse models, I discovered that meningeal macrophage populations represent the first line of protection against neuroinvasive pathogens. In their absence, specific areas in the meninges become highly infected, leading to fatal brain disease. The goal of ‘CNSentinels’ is to understand 1/the mechanisms controlling the spatiotemporal distribution of macrophage populations at the brain surface and 2/the relative contribution of the two macrophage populations in protecting the CNS against neuroinvasive pathogens. To this aim, I developed innovative strategies to visualize and manipulate meningeal macrophages in vivo that I will combine with cutting-edge gene editing techniques, in mice infected with lymphocytic choriomeningitis virus (LCMV). This pioneer work will help understand the spatial organization of the brain defence system and the molecular mechanisms involved in CNS protection, and will provide new avenues to design therapeutic strategies.
Max ERC Funding
1 912 500 €
Duration
Start date: 2021-05-01, End date: 2026-04-30
Project acronym DEFEND
Project Novel mechanisms of adaptive and innate bacteriophage immunity
Researcher (PI) Stan BROUNS
Host Institution (HI) TECHNISCHE UNIVERSITEIT DELFT
Country Netherlands
Call Details Consolidator Grant (CoG), LS6, ERC-2020-COG
Summary Microbes are engaged in an evolutionary arms-race with their viruses and have evolved a spectrum of adaptive and innate defense systems to limit viral predation. Mechanistic insights into defense systems have yielded truly revolutionary genetic tools ranging from CRISPR-based genome editing nucleases to restriction enzymes used for molecular cloning. Despite the ongoing effort to understand defense systems, many antiviral defense systems remain virtually unstudied in and outside their native microbial context, creating huge potential for scientific breakthroughs and development of further game changing applications.
In the timely research proposed here I aim to uncover how adaptive (CRISPR) and innate immune systems protect bacteria from bacterial viruses (phages) at the molecular, cellular and population level. Based on our exiting unpublished observation that extremely phage resistant pathogens in our bacterial strain collection are true collectors of defense systems, I propose to investigate the contribution of each defense system and cooperativity between defense systems for broad and specific bacteriophage resistance. I furthermore aim to determine the molecular mechanism of a dominant set of related innate immune systems found in clinical pathogens, and to reveal how individual phages achieve immune evasion.
To accomplish my goals, I plan to use an interdisciplinary approach combining state-of-the-art molecular microbiology and biophysics at the single molecule and single cell level, with bioinformatics and high-throughput synthetic genomics screens. The project may lead to fundamentally new insights into the mechanism and evolution of virus immunity and will further explore the genetic treasure trove at the interface of virus and host interactions. Our findings will have implications for controlling virus resistance, and will be vital to develop effective therapeutic strategies to treat antibiotic resistant pathogens based on bacteriophages.
Summary
Microbes are engaged in an evolutionary arms-race with their viruses and have evolved a spectrum of adaptive and innate defense systems to limit viral predation. Mechanistic insights into defense systems have yielded truly revolutionary genetic tools ranging from CRISPR-based genome editing nucleases to restriction enzymes used for molecular cloning. Despite the ongoing effort to understand defense systems, many antiviral defense systems remain virtually unstudied in and outside their native microbial context, creating huge potential for scientific breakthroughs and development of further game changing applications.
In the timely research proposed here I aim to uncover how adaptive (CRISPR) and innate immune systems protect bacteria from bacterial viruses (phages) at the molecular, cellular and population level. Based on our exiting unpublished observation that extremely phage resistant pathogens in our bacterial strain collection are true collectors of defense systems, I propose to investigate the contribution of each defense system and cooperativity between defense systems for broad and specific bacteriophage resistance. I furthermore aim to determine the molecular mechanism of a dominant set of related innate immune systems found in clinical pathogens, and to reveal how individual phages achieve immune evasion.
To accomplish my goals, I plan to use an interdisciplinary approach combining state-of-the-art molecular microbiology and biophysics at the single molecule and single cell level, with bioinformatics and high-throughput synthetic genomics screens. The project may lead to fundamentally new insights into the mechanism and evolution of virus immunity and will further explore the genetic treasure trove at the interface of virus and host interactions. Our findings will have implications for controlling virus resistance, and will be vital to develop effective therapeutic strategies to treat antibiotic resistant pathogens based on bacteriophages.
Max ERC Funding
2 000 000 €
Duration
Start date: 2021-06-01, End date: 2026-05-31
Project acronym IMAP
Project Integrative mechanistic and multi-omics Modelling of Antigen Presentation to predict epitope dynamics
Researcher (PI) Juliane Liepe
Host Institution (HI) MAX-PLANCK-GESELLSCHAFT ZUR FORDERUNG DER WISSENSCHAFTEN EV
Country Germany
Call Details Starting Grant (StG), LS6, ERC-2020-STG
Summary The immune system can patrol cell status by recognising epitopes bound to Human Leukocyte Antigen class I (HLA-I) molecules and triggering cytotoxic T cell (CTL) activation. Epitopes arrive at the cell surface through several steps of the antigen processing and presentation pathway (APP). Despite major discoveries in the past decades, the precise dynamics of APP are still not fully understood. These dynamics, however, determine the types and quantities of epitopes and therefore regulate the CTL response.
The objective of my project is the development of an APP model from gene transcription to recognition by CTL clones that captures the underlying APP mechanisms and dynamics. Current approaches are mainly machine learning-based and focus only on parts of the APP. They neglect the underlying APP dynamics and do not elucidate novel mechanisms. Therefore, they fail to predict epitopes under altered cellular states such as infection. My project overcomes this pitfall by complementing large scale machine learning approaches with mechanistic modelling to comprehensively understand the APP and enable successful epitope prediction.
To achieve this goal, I will:
1) develop an APP integrated computational description that combines a mechanistic model of the APP (based on detailed quantitative in vitro data) with a large-scale machine learning-based multi-omics model;
2) apply the model in two therapeutic-relevant cellular systems – Measles virus infection and chemotherapy-induced senescence – resulting in the educated identification of canonical and non-canonical epitopes.
This project is at the cutting edge of the research with direct application in epitope discovery for therapies such as anti-cancer immunotherapy, vaccination against infection and modulatory immunotherapies against autoimmune diseases. The implemented computational framework will be made available to the community thereby providing a direct benefit to European scientific public and private sectors.
Summary
The immune system can patrol cell status by recognising epitopes bound to Human Leukocyte Antigen class I (HLA-I) molecules and triggering cytotoxic T cell (CTL) activation. Epitopes arrive at the cell surface through several steps of the antigen processing and presentation pathway (APP). Despite major discoveries in the past decades, the precise dynamics of APP are still not fully understood. These dynamics, however, determine the types and quantities of epitopes and therefore regulate the CTL response.
The objective of my project is the development of an APP model from gene transcription to recognition by CTL clones that captures the underlying APP mechanisms and dynamics. Current approaches are mainly machine learning-based and focus only on parts of the APP. They neglect the underlying APP dynamics and do not elucidate novel mechanisms. Therefore, they fail to predict epitopes under altered cellular states such as infection. My project overcomes this pitfall by complementing large scale machine learning approaches with mechanistic modelling to comprehensively understand the APP and enable successful epitope prediction.
To achieve this goal, I will:
1) develop an APP integrated computational description that combines a mechanistic model of the APP (based on detailed quantitative in vitro data) with a large-scale machine learning-based multi-omics model;
2) apply the model in two therapeutic-relevant cellular systems – Measles virus infection and chemotherapy-induced senescence – resulting in the educated identification of canonical and non-canonical epitopes.
This project is at the cutting edge of the research with direct application in epitope discovery for therapies such as anti-cancer immunotherapy, vaccination against infection and modulatory immunotherapies against autoimmune diseases. The implemented computational framework will be made available to the community thereby providing a direct benefit to European scientific public and private sectors.
Max ERC Funding
1 495 000 €
Duration
Start date: 2021-04-01, End date: 2026-03-31
Project acronym INSPIRE
Project IN-depth SPatiotemporal dissection of autoimmunity-induced Inflammation in RhEumatoid arthritis
Researcher (PI) Gerhard KRoeNKE
Host Institution (HI) UNIVERSITATSKLINIKUM ERLANGEN
Country Germany
Call Details Consolidator Grant (CoG), LS6, ERC-2020-COG
Summary Rheumatoid Arthritis (RA) is a prototypic T cell- and B cell-driven inflammatory autoimmune disease that affects around 1% of the population worldwide and creates a severe burden for patients as well as substantial socioeconomic costs for society. Hallmarks of RA are a destructive inflammation of peripheral joints as well as the presence of autoantibodies such as anti-citrullinated protein antibodies (ACPA). Although ACPA are considered to represent major drivers of RA pathology, they can be also found in otherwise healthy “individuals at risk” where they emerge decades before the eventual onset of RA. Factors and mechanisms that promote onset of tissue inflammation in such autoantibody-positive individuals still remain elusive. Due to this gap of knowledge, current therapies are primarily designed to suppress later stages of joint inflammation, rather than targeting the underlying processes of autoimmunity or the initial onset of inflammatory disease. RA patients thus still lack effective preventive or curative therapeutic concepts. Here we aim to exploit recent technical breakthroughs such as single-cell RNA- and ATAC-sequencing in conjunction with DNA bar-coded MHC dextramers and antigens, spatial transcriptomics and cutting-edge imaging to perform a comprehensive and in-depth spatiotemporal analysis of the molecular events underlying the initial onset of inflammatory disease in autoantibody-positive individuals. We will additionally profit from the access to a large and well-characterized cohort of ACPA-positive “individuals at risk” and ACPA-positive RA patients as well as from corresponding biomaterial. In combination with preclinical animal models of RA, we thereby seek to delineate the sequences of events that promote the early transition from autoimmunity to inflammation. The obtained data will yield key insights into basic mechanisms of inflammatory autoimmune diseases such as RA and provide the basis for novel treatment concepts.
Summary
Rheumatoid Arthritis (RA) is a prototypic T cell- and B cell-driven inflammatory autoimmune disease that affects around 1% of the population worldwide and creates a severe burden for patients as well as substantial socioeconomic costs for society. Hallmarks of RA are a destructive inflammation of peripheral joints as well as the presence of autoantibodies such as anti-citrullinated protein antibodies (ACPA). Although ACPA are considered to represent major drivers of RA pathology, they can be also found in otherwise healthy “individuals at risk” where they emerge decades before the eventual onset of RA. Factors and mechanisms that promote onset of tissue inflammation in such autoantibody-positive individuals still remain elusive. Due to this gap of knowledge, current therapies are primarily designed to suppress later stages of joint inflammation, rather than targeting the underlying processes of autoimmunity or the initial onset of inflammatory disease. RA patients thus still lack effective preventive or curative therapeutic concepts. Here we aim to exploit recent technical breakthroughs such as single-cell RNA- and ATAC-sequencing in conjunction with DNA bar-coded MHC dextramers and antigens, spatial transcriptomics and cutting-edge imaging to perform a comprehensive and in-depth spatiotemporal analysis of the molecular events underlying the initial onset of inflammatory disease in autoantibody-positive individuals. We will additionally profit from the access to a large and well-characterized cohort of ACPA-positive “individuals at risk” and ACPA-positive RA patients as well as from corresponding biomaterial. In combination with preclinical animal models of RA, we thereby seek to delineate the sequences of events that promote the early transition from autoimmunity to inflammation. The obtained data will yield key insights into basic mechanisms of inflammatory autoimmune diseases such as RA and provide the basis for novel treatment concepts.
Max ERC Funding
2 000 000 €
Duration
Start date: 2021-07-01, End date: 2026-06-30
Project acronym LOFlu
Project Controlling Influenza A Virus Liquid Organelles
Researcher (PI) Maria Joao AMORIM
Host Institution (HI) FUNDACAO CALOUSTE GULBENKIAN
Country Portugal
Call Details Consolidator Grant (CoG), LS6, ERC-2020-COG
Summary The world health organization monitors viral infections worldwide with the aim to coordinate strategies to control viral outbreaks. The on-demand development of vaccines or antibody treatment does not confer a first line of defense against unpredictable infections caused by new viruses in humans such as pandemic influenza, corona or Ebola viruses, and new approaches are needed. We propose to investigate the fundamental basis of novel host-pathogen interactions in influenza A virus (IAV) infection that may define new antiviral strategies. We discovered that the important pathogen IAV induces the intracellular assembly of viral inclusions that behave like liquid organelles. IAV inclusions serve as assembly sites for the IAV segmented genome, a key step in the viral lifecycle. We now find that the maintenance of the liquid character of IAV inclusions is essential for viral replication. As we identified some of the host and viral components of IAV inclusions, we now have the tools to interrogate how specific interactions and cellular processes result in phase-separated compartments. We aim to learn how the function of IAV inclusions is related to their material state and investigate the potential of imposing phase transitions in an organism to limit IAV infection. Phase separation provides a novel conceptual framework to tackle how viruses exploit cells to organize viral reactions in space and in time. It also provides alternative principles for exploring aspects of the IAV lifecycle not yet fully understood, including how influenza epidemic and pandemic genomes assemble. Taken together, we propose a new, integrated approach for studying phase separated phenomena, from the molecular to the organismal level, that will bring a deeper understanding and control to viral infections. Our work will also be of relevance to other fields of biomedicine, including in the science of soft matter that is involved in neurodegenerative diseases and some cancers.
Summary
The world health organization monitors viral infections worldwide with the aim to coordinate strategies to control viral outbreaks. The on-demand development of vaccines or antibody treatment does not confer a first line of defense against unpredictable infections caused by new viruses in humans such as pandemic influenza, corona or Ebola viruses, and new approaches are needed. We propose to investigate the fundamental basis of novel host-pathogen interactions in influenza A virus (IAV) infection that may define new antiviral strategies. We discovered that the important pathogen IAV induces the intracellular assembly of viral inclusions that behave like liquid organelles. IAV inclusions serve as assembly sites for the IAV segmented genome, a key step in the viral lifecycle. We now find that the maintenance of the liquid character of IAV inclusions is essential for viral replication. As we identified some of the host and viral components of IAV inclusions, we now have the tools to interrogate how specific interactions and cellular processes result in phase-separated compartments. We aim to learn how the function of IAV inclusions is related to their material state and investigate the potential of imposing phase transitions in an organism to limit IAV infection. Phase separation provides a novel conceptual framework to tackle how viruses exploit cells to organize viral reactions in space and in time. It also provides alternative principles for exploring aspects of the IAV lifecycle not yet fully understood, including how influenza epidemic and pandemic genomes assemble. Taken together, we propose a new, integrated approach for studying phase separated phenomena, from the molecular to the organismal level, that will bring a deeper understanding and control to viral infections. Our work will also be of relevance to other fields of biomedicine, including in the science of soft matter that is involved in neurodegenerative diseases and some cancers.
Max ERC Funding
2 870 250 €
Duration
Start date: 2021-04-01, End date: 2026-03-31
Project acronym Mal3D-BBB
Project Understanding Cerebral Malaria using 3D Blood-Brain Barrier models
Researcher (PI) Maria Bernabeu Aznar
Host Institution (HI) EUROPEAN MOLECULAR BIOLOGY LABORATORY
Country Germany
Call Details Starting Grant (StG), LS6, ERC-2020-STG
Summary Malaria is a major public health problem and it still causes more than 400,000 deaths per year. Cerebral malaria (CM) is one of the most serious complications, with 20% mortality rates even after administration of fast-acting antimalarials. CM pathology is characterized by sequestration of P. falciparum-infected red blood cells (iRBC) in the brain microvasculature, blood-brain barrier (BBB) disruption, and brain swelling.
Our current knowledge of CM is primarly based on autopsy studies, because of the absence of suitable animal models. However, there are numerous pathogenic aspects that cannot be studied from post-mortem samples, such as disease progression. In Mal3D-BBB, we bypass these limitations by recreating the human CM pathology with cutting-edge in vitro bioengineering approaches. Rather than using 2D endothelial monolayers, we will develop BBB models with 3D tubular geometry that incorporate multiple cell types: brain microvascular endothelial cells, astrocytes and pericytes. We will mimic vessel dimensions and flow dynamics of the brain vasculature with the goal to recreate physiological BBB permeability rates. Using such technology brings a unique angle to malaria research to evaluate in a controlled and systematic way 1) the molecular mechanisms of BBB disruption after P. falciparum sequestration, and 2) whether parasite and host factors synergize to increase pathology. The findings obtained by this cutting-edge technology will be further validated in samples from CM patients, whose neurovascular pathology has been thoroughly characterized using MRI.
Our interdisciplinary approach aims to provide a holistic understanding of CM malaria pathogenesis. In return, this knowledge will identify new pathways that could be counteracted to develop therapies to reduce patient mortality. In a broader context, we will build an innovative platform that captures the complex physiology of the BBB, and can be translated to the study of other neurovascular diseases.
Summary
Malaria is a major public health problem and it still causes more than 400,000 deaths per year. Cerebral malaria (CM) is one of the most serious complications, with 20% mortality rates even after administration of fast-acting antimalarials. CM pathology is characterized by sequestration of P. falciparum-infected red blood cells (iRBC) in the brain microvasculature, blood-brain barrier (BBB) disruption, and brain swelling.
Our current knowledge of CM is primarly based on autopsy studies, because of the absence of suitable animal models. However, there are numerous pathogenic aspects that cannot be studied from post-mortem samples, such as disease progression. In Mal3D-BBB, we bypass these limitations by recreating the human CM pathology with cutting-edge in vitro bioengineering approaches. Rather than using 2D endothelial monolayers, we will develop BBB models with 3D tubular geometry that incorporate multiple cell types: brain microvascular endothelial cells, astrocytes and pericytes. We will mimic vessel dimensions and flow dynamics of the brain vasculature with the goal to recreate physiological BBB permeability rates. Using such technology brings a unique angle to malaria research to evaluate in a controlled and systematic way 1) the molecular mechanisms of BBB disruption after P. falciparum sequestration, and 2) whether parasite and host factors synergize to increase pathology. The findings obtained by this cutting-edge technology will be further validated in samples from CM patients, whose neurovascular pathology has been thoroughly characterized using MRI.
Our interdisciplinary approach aims to provide a holistic understanding of CM malaria pathogenesis. In return, this knowledge will identify new pathways that could be counteracted to develop therapies to reduce patient mortality. In a broader context, we will build an innovative platform that captures the complex physiology of the BBB, and can be translated to the study of other neurovascular diseases.
Max ERC Funding
1 492 900 €
Duration
Start date: 2021-05-01, End date: 2026-04-30
Project acronym MALSWITCH
Project Uncovering the Mechanisms Behind Adaptive Gene Expression Switching in Malaria Parasites
Researcher (PI) Michael Filarsky
Host Institution (HI) UNIVERSITAET HAMBURG
Country Germany
Call Details Starting Grant (StG), LS6, ERC-2020-STG
Summary The malaria-causing parasite Plasmodium falciparum has evolved a strategy of clonally variant gene expression to control essential biological processes like antigenic variation and sexual commitment during its persistent blood-stage infection of the human host. Heritable epigenetic silencing of the underlying specialized gene families ensures the limited expression of only a subset of these genes at any time. Switching the expression of individual clonally variant genes enables the parasite to rapidly adapt to changes in its environment, evade the immune system and switch its cell cycle to the development of mosquito-transmissible gametocyte stages. Expression switching of these clonally variant genes therefore represents a key strategy for parasite survival and underlies the evolutionary success of this deadly pathogen. Despite decades of research, the molecular mechanisms coordinating this adaptive gene expression switching are not understood. In my recent research, I developed a unique experimental tool, which for the first time allows the conditional expression switching of endogenous genes in the parasite. I will combine this system with novel CRISPR/Cas derived methodology and proximity-based labelling approaches to deliver the first systematic identification and characterization of the molecular mechanisms controlling epigenetic gene expression switching. The experiments outlined in the proposal will reveal the core of the molecular machinery underlying this fundamental process and elucidate regulatory mechanisms that allow the parasite to translate environmental signals into adaptive switching of clonally variant genes. This will transform our understanding of the molecular mechanisms driving adaptation of this deadly parasite and in the long run might contribute to the design of intervention strategies that P. falciparum is unable to adapt to.
Summary
The malaria-causing parasite Plasmodium falciparum has evolved a strategy of clonally variant gene expression to control essential biological processes like antigenic variation and sexual commitment during its persistent blood-stage infection of the human host. Heritable epigenetic silencing of the underlying specialized gene families ensures the limited expression of only a subset of these genes at any time. Switching the expression of individual clonally variant genes enables the parasite to rapidly adapt to changes in its environment, evade the immune system and switch its cell cycle to the development of mosquito-transmissible gametocyte stages. Expression switching of these clonally variant genes therefore represents a key strategy for parasite survival and underlies the evolutionary success of this deadly pathogen. Despite decades of research, the molecular mechanisms coordinating this adaptive gene expression switching are not understood. In my recent research, I developed a unique experimental tool, which for the first time allows the conditional expression switching of endogenous genes in the parasite. I will combine this system with novel CRISPR/Cas derived methodology and proximity-based labelling approaches to deliver the first systematic identification and characterization of the molecular mechanisms controlling epigenetic gene expression switching. The experiments outlined in the proposal will reveal the core of the molecular machinery underlying this fundamental process and elucidate regulatory mechanisms that allow the parasite to translate environmental signals into adaptive switching of clonally variant genes. This will transform our understanding of the molecular mechanisms driving adaptation of this deadly parasite and in the long run might contribute to the design of intervention strategies that P. falciparum is unable to adapt to.
Max ERC Funding
1 434 330 €
Duration
Start date: 2021-09-01, End date: 2026-08-31
Project acronym PlasmoEpiRNA
Project Resolving m6A-mediated post-transcriptional control in the human malaria parasite
Researcher (PI) Sebastian Baumgarten
Host Institution (HI) INSTITUT PASTEUR
Country France
Call Details Starting Grant (StG), LS6, ERC-2020-STG
Summary Post-transcriptional regulation in malaria parasites is key to the progression through different developmental stages of the complex life cycle within the human and mosquito host. This includes the asexual proliferation within human red blood cells that is responsible for all clinical symptoms of the disease and the preparation for the environmental changes accompanying transmission from host to vector and vice versa. Although the process that controls the destiny of mRNA are of critical importance to parasite survival and transmission, the molecular mechanisms orchestrating post-transcriptional regulation on a transcriptome-wide level remain largely unknown. We recently identified extensive methylation of adenosines (m6A) at internal mRNA positions as a new layer of post-transcriptional regulation of gene expression in Plasmodium falciparum. With m6A, the parasite dynamically modulates its transcriptome through selective mRNA degradation and/or translational repression of modified transcripts during blood-stage development. This new epitranscriptomic layer provides a previously missing link between the transcriptional program and the observed post-transcriptional events throughout P. falciparum development. The proposed project aims to elucidate how m6A mediates different outcomes of mRNA at key developmental stages of the parasite life cycle. We will 1) characterize m6A-binding proteins and elucidate how different m6A ‘readers’ translate this mRNA modification into distinct biological pathways (i.e. degradation, repression) during blood-stage development and 2) investigate how m6A and its specific reader proteins designate mRNAs to facilitate transient quiescence in transmission stages (i.e. gametocytes and sporozoites) to ‘prime’ the transcriptome for new host/vector environments. Overall, exploring the epitranscriptome of this parasite will reveal novel principles and molecular determinants of post-transcriptional control that can be targeted to combat malaria.
Summary
Post-transcriptional regulation in malaria parasites is key to the progression through different developmental stages of the complex life cycle within the human and mosquito host. This includes the asexual proliferation within human red blood cells that is responsible for all clinical symptoms of the disease and the preparation for the environmental changes accompanying transmission from host to vector and vice versa. Although the process that controls the destiny of mRNA are of critical importance to parasite survival and transmission, the molecular mechanisms orchestrating post-transcriptional regulation on a transcriptome-wide level remain largely unknown. We recently identified extensive methylation of adenosines (m6A) at internal mRNA positions as a new layer of post-transcriptional regulation of gene expression in Plasmodium falciparum. With m6A, the parasite dynamically modulates its transcriptome through selective mRNA degradation and/or translational repression of modified transcripts during blood-stage development. This new epitranscriptomic layer provides a previously missing link between the transcriptional program and the observed post-transcriptional events throughout P. falciparum development. The proposed project aims to elucidate how m6A mediates different outcomes of mRNA at key developmental stages of the parasite life cycle. We will 1) characterize m6A-binding proteins and elucidate how different m6A ‘readers’ translate this mRNA modification into distinct biological pathways (i.e. degradation, repression) during blood-stage development and 2) investigate how m6A and its specific reader proteins designate mRNAs to facilitate transient quiescence in transmission stages (i.e. gametocytes and sporozoites) to ‘prime’ the transcriptome for new host/vector environments. Overall, exploring the epitranscriptome of this parasite will reveal novel principles and molecular determinants of post-transcriptional control that can be targeted to combat malaria.
Max ERC Funding
1 499 553 €
Duration
Start date: 2021-06-01, End date: 2026-05-31
