ERC FUNDED PROJECTS

The production of antibodies against pathogens is an effective mechanism of protection against a wide range of infections. However, some pathogens evade antibody responses by rapidly changing their composition. Designing vaccines that elicit antibody responses against invariant parts of the pathogen is a rational strategy to combat existing and emerging pathogens. Production of antibodies is initiated by binding of B cell receptors (BCRs) to foreign antigens presented on the surfaces of antigen presenting cells. This binding induces B cell signalling and internalisation of the antigens for presentation to helper T cells. Although it is known that T cell help controls B cell expansion and differentiation into antibody-secreting and memory B cells, how the strength of antigen binding to the BCR regulates antigen internalisation remains poorly understood. As a result, the response and the affinity maturation of individual B cell clones are difficult to predict, posing a problem for the design of next-generation vaccines. My aim is to develop an understanding of the cellular mechanisms that underlie critical B cell activation steps. My laboratory has recently described that B cells use mechanical forces to extract antigens from antigen presenting cells. We hypothesise that application of mechanical forces tests BCR binding strength and thereby regulates B cell clonal selection during antibody affinity maturation and responses to pathogen evasion. We propose to test this hypothesis by (1) determining the magnitude and timing of the forces generated by B cells, and (2) determining the role of the mechanical properties of BCR-antigen bonds in affinity maturation and (3) in the development of broadly neutralising antibodies. We expect that the results of these studies will contribute to our understanding of the mechanisms that regulate the antibody repertoire in response to infections and have practical implications for the development of vaccines.

1 999 386 €

Start date: 2015-09-01, End date: 2020-08-31

Cholera is one of the oldest infectious diseases known and remains a major burden in many developing countries. The World Health Organization estimates that up to 4 million cases of cholera occur annually. The transmission of cholera by contaminated water, particularly under epidemic conditions, was first reported in the 19th century. However, early volunteer studies suggested that an incredibly high infectious dose (ID) is required to produce disease symptoms, in contrast to most other intestinal pathogens. Therefore, the mechanism of infection of index cases at the onset of an outbreak is unclear. This proposal aims to fill this knowledge gap by studying how the environmental lifestyle of the causative agent of the disease, the bacterium Vibrio cholerae, may prime the pathogen for intestinal colonization. We hypothesize that one of the natural niches of the bacterium (chitinous surfaces) fosters biofilm formation and provides a competitive advantage over co-colonizing bacteria. As an adaptive trait, passage of chitin-attached sessile V. cholerae through the acidic environment of the human stomach might be vastly facilitated compared to planktonic bacteria. Moreover, interbacterial warfare exerted by V. cholerae on these biotic surfaces may help the pathogen overcome the colonization barrier imposed by the human microbiota upon ingestion. The mechanism by which V. cholerae leaves the sessile lifestyle and the regulatory circuits involved in this process will also be investigated in this project. In summary, our goal is to elucidate the environmental community structures of V. cholerae that may enhance transmissibility from the ecosystem to humans in endemic areas resulting in the infection of index cases.

1 999 988 €

Start date: 2018-02-01, End date: 2023-01-31

Every year chronic infections in patients due to biofilm formation of pathogenic bacteria are a multi-billion Euro burden to national healthcare systems. Despite improvements in technology and medical services, morbidity and mortality due to chronic infections have remained unchanged over the past decades. The emergence of a chronic infection disease burden calls for the development of modern diagnostics for biofilm resistance profiling and new therapeutic strategies to eradicate biofilm-associated infections. However, many unsuccessful attempts to address this need teach us that alternative perspectives are needed to meet the challenges. The project is committed to develop innovative diagnostics and to strive for therapeutic solutions in patients suffering from biofilm-associated infections. The objective is to apply data-driven science to unlock the potential of microbial genomics. This new approach uses tools of advanced microbiological genomics and machine learning in genome-wide association studies on an existing unprecedentedly large dataset. This dataset has been generated in my group within the last five years and comprises sequence variation and gene expression information of a plethora of clinical Pseudomonas aeruginosa isolates. The wealth of patterns and characteristics of biofilm resistance are invisible at a smaller scale and will be interpreted within context and domain-specific knowledge. The unique combination of basic molecular biology research, technology-driven approaches and data-driven science allows pioneer research dedicated to advance strategies to combat biofilm-associated infections. My approach does not only provide a prediction of biofilm resistance based on the bacteria´s genotype but also holds promise to transform treatment paradigms for the management of chronic infections and by interference with bacterial stress responses will promote the effectiveness of antimicrobials in clinical use to eradicate biofilm infections.

1 998 750 €

Start date: 2017-05-01, End date: 2022-04-30

Inflammatory diseases affect over 80 million people worldwide and accompany many diseases of industrialized countries, being the majority of them infection-free conditions. There are few efficient anti-inflammatory drugs to treat chronic inflammation and thus, there is an urgent need to validate novel targets. We now know that innate immunity is the main coordinator and driver of inflammation. Recently, we and others have shown that the activation of purinergic P2X7 receptors (P2X7R) in immune cells is a novel and increasingly validated pathway to initiate inflammation through the activation of the NLRP3 inflammasome and the release of IL-1β and IL-18 cytokines. However, how NLRP3 sense P2X7R activation is not fully understood. Furthermore, extracellular ATP, the physiological P2X7R agonist, is a crucial danger signal released by injured cells, and one of the most important mediators of infection-free inflammation. We have also identified novel signalling roles for P2X7R independent on the NLRP3 inflammasome, including the release of proteases or inflammatory lipids. Therefore, P2X7R has generated increasing interest as a therapeutic target in inflammatory diseases, being drug like P2X7R antagonist in clinical trials to treat inflammatory diseases. However, it is often questioned the functionality of P2X7R in vivo, where it is thought that extracellular ATP levels are below the threshold to activate P2X7R. The overall significance of this proposal relays to elucidate how extracellular ATP controls host-defence in vivo, ultimately depicting P2X7R signalling through and beyond inflammasome activation. We foresee that our results will generate a leading innovative knowledge about in vivo extracellular ATP signalling during the host response to infection and sterile danger.

1 794 948 €

Start date: 2014-09-01, End date: 2019-08-31

T lymphocytes display potent pro- or anti-inflammatory properties, which typically associate with distinct effector (Teff) versus regulatory (Treg) cell subsets. Based on published and our preliminary data showing a major impact of microRNAs on T cell differentiation and (auto)immune pathology, my proposal aims to dissect the miRNA networks that control the balance between Teff and Treg subsets in vivo, in various experimental models of infection and autoimmunity. We will focus on three critical mediators of T cell functions: interferon-gamma (IFN-g) and interleukin-17A (IL-17), highly pro-inflammatory Teff cytokines; and Foxp3, the transcription factor that confers Treg suppressive properties. To track the activity of these key genes, we will generate a new Ifng/ Il17/ Foxp3 triple reporter mouse, from which we will isolate Teff and Treg subsets to determine their genome-wide miRNA profiles and specific signatures in vivo. We will investigate both natural (thymic-derived and present in naïve mice) and induced (in the periphery upon challenge) Teff and Treg subsets, as they make distinct contributions to the immune response. We will identify miRNAs selectively expressed in Teff (Ifng+ or Il17+) versus Treg (Foxp3+) subsets of various lineages (CD4+, CD8+, gamma-delta or NKT) in each in vivo model; assess whether they are induced during thymic development or upon peripheral activation; and determine the robustness of subset-specific miRNA profiles across various in vivo challenges. We will then use loss- and gain-of-function strategies to define the individual miRNAs that impact Teff or Treg differentiation and disease pathogenesis; dissect the external cues and intracellular mechanisms that regulate miRNA expression; and identify the mRNA networks controlled by key miRNAs in Teff and Treg differentiation. I expect this project to provide major conceptual and experimental advances towards manipulating miRNAs either to boost immunity or to treat autoimmunity.

2 000 000 €

Start date: 2015-07-01, End date: 2020-06-30

A common strategy of bacterial pathogens is active or passive uptake into host cells. There, they can localize within a bacterial containing vacuole (BCV) or access the host cytoplasm through BCV rupture. Hence, intracellular pathogens are often classified as vacuole-bound or cytoplasmic. Recently, this definition has been challenged by the discovery that many vacuole-bound pathogens, including Mycobacterium tuberculosis and Salmonella enterica, access the host cytoplasm, and by the insight that cytoplasmic bacteria, like Shigella flexneri or Listeria monocytogenes, do not always escape the BCV. Despite this increasing complexity, a precise understanding lacks for why and how a pathogen “chooses” between a BCV or the cytoplasm and yet this is very important: because of differential pathogen sensing in membrane-bound and cytoplasmic compartments, intracellular localization leads to induction of different host responses. Therefore, a comprehensive understanding of the processes controlling BCV integrity is not only essential, but can provide new therapeutic targets. Our previous research has implemented innovative fluorescence microscopy to track the invasion steps of pathogenic bacteria. We have further integrated a large-volume, correlative, light/electron microscopy (CLEM) workflow via focused ion beam scanning electron microscopy. This uncovered the subversion of host Rab cascades by Shigella to rupture its BCV. Starting with the Shigella model of epithelial cell invasion, we will delineate the precise molecular mechanisms controlling BCV integrity in different host cell types. We will analyze (i) the scaffolds of host pathways for membrane remodeling, (ii) their subversion by various pathogens, and (iii) their differential regulation depending on pathophysiological conditions. Together, this will allow development of novel, rational antimicrobial strategies and will yield fundamental insight into understudied cell biological mechanisms of membrane trafficking.

2 000 000 €

Start date: 2017-01-01, End date: 2021-12-31

Identification of the full complement of genes and other functional elements in any virus is crucial to fully understand its molecular biology and guide the development of effective control strategies. Our recent discoveries of new 'hidden' genes in the potyviruses, alphaviruses, arteriviruses, flaviviruses and influenza A virus have demonstrated that, even in the most well-studied and economically-important viruses, small overlapping genes can remain undetected throughout decades of research. Comparative computational analyses can be used to efficiently identify hidden features and target experimental analyses, thus saving time and cost, and minimizing animal experiments. With the rapid increase in sequencing data, for the first time it is now possible to map out at high resolution functional elements genome-wide in hundreds of important virus species. Our research involves the development of powerful new tools for virus comparative genomics, and the application of these tools to uncover hidden genes and other functional elements in RNA virus and retrovirus genomes. Hidden genes are often translated via non-canonical mechanisms, such as programmed ribosomal frameshifting, and we are particularly interested in discovering and characterizing new types of non-canonical translation. Deciphering these 'exceptions-to-the-rule' enhances our understanding of the mechanics of protein synthesis. Further, these novel mechanisms may also be relevant to cellular gene expression. The goals of this project are: 1) To computationally identify all 'hidden' genes and major functional non-coding elements in the genomes of RNA viruses and retroviruses of medical, veterinary and agricultural importance. 2) To experimentally characterize the most interesting new features. 3) To characterize novel translation mechanisms utilized by RNA viruses. 4) To develop web interfaces to our software and an interactive RNA virus comparative genomics database.

1 780 000 €

Start date: 2015-09-01, End date: 2020-08-31

CD8+ T cells have a key role in eliminating intracellular pathogens and tumors that affect the liver. The protective capacity of these cells relies on their ability to migrate to and traffic within the liver, recognize pathogen- or tumor-derived antigens, get activated and deploy effector functions. While some of the rules that characterize CD8+ T cell behavior in the infected and cancerous liver have been characterized at the population level, we have only limited knowledge of the precise dynamics of intrahepatic CD8+ T cell conduct at the single-cell level. In preliminary data for this project we have developed several advanced imaging techniques that allow us to dissect the interactive behavior of CD8+ T cells within the mouse liver at an unprecedented level of spatial and temporal resolution. We predict that this approach, combined with unique models of hepatitis B virus pathogenesis and a new model of hepatocellular carcinoma created ad hoc for this proposal, will generate novel mechanistic insights into the spatiotemporal determinants that govern the capacity of CD8+ T cells to home and function in the virus- or tumor-bearing liver. Specifically, we plan to pursue two main goals: 1) To assess how the anatomical, hemodynamic and environmental cues that characterize hepatocellular carcinomas shape CD8+ T cell behavior and function; 2) To characterize intrahepatic T cell priming events that induce functionally defective T cell responses. Results emerging from these studies will advance our knowledge on how adaptive immunity mediates pathogen clearance and tumor elimination. This new knowledge may lead to improved vaccination and treatment strategies for immunotherapy of infectious diseases and cancer.

2 390 000 €

Start date: 2017-07-01, End date: 2022-06-30

Antibodies secreted by B cells of the adaptive immune system establish an essential barrier against bacteria and viruses and their presence is the hallmark of protective vaccinations. B cells are licensed for their tasks during germinal center (GC) reactions and differentiation into antibody-secreting plasma cells. Unfortunately, B cell-derived autoantibodies and proinflammatory cytokines can cause or contribute to autoimmune diseases. While major transcription factor networks regulating protective (or pathogenic) GCB cell responses have been identified and characterized, little is known about the post-transcriptional regulation by RNA-binding proteins (RBP), whose number rivals that of transcription factors. We postulate that RBPs exercise critical post-transcriptional control over germinal center B (GCB) and plasmacytic cell physiology and we aim to identify and molecularly characterize these regulatory mechanisms. To this end, we will complement sophisticated genetic mouse models with novel cell culture systems. We will monitor RBP activity with fluorescent sensors and use proteomics to reveal RBPs regulating the protein abundance of critical mediators of GCB and plasmacytic cell fates. In addition, we will conduct genetic screens to uncover relevant functions of a short list of 40 RBPs, whose protein expression we found to differ significantly between GCB and mantle zone B cells. Ultimately, we will use cellular immunology and RNA biochemistry to elucidate how these RBPs exert their post-transcriptional control. Through the integrated power of our multi-disciplinary approach we will thus pinpoint and investigate the functions of key RBPs regulating the biology of GCB and plasmacytic cells. GCB-PRID promises to uncover profoundly new insights into post-transcriptional regulation of adaptive immunity. Thereby, this groundbreaking research aims to reveal novel molecular targets for the treatment of autoimmune diseases, whose incidence is steadily on the rise.

1 998 066 €

Start date: 2016-09-01, End date: 2021-08-31

The interplay between intestinal microbes and immune cells ensures vital functions of the organism. However, inadequate host-microbe relationships lead to inflammatory diseases that are major public health concerns. Innate lymphoid cells (ILC) are an emergent family of effectors abundantly present at mucosal sites. Group 3 ILC (ILC3) produce pro-inflammatory cytokines and regulate mucosal homeostasis, anti-microbial defence and adaptive immune responses. ILC development and function have been widely perceived to be programmed. However, recent evidence indicates that ILC are also controlled by dietary signals. Nevertheless, how ILC3 perceive, integrate and respond to environmental cues remains utterly unexplored. We hypothesise that ILC3 sense their environment and exert their function as part of a novel epithelial-glial-ILC unit orchestrated by neurotrophic factors. Thus, we propose to employ genetic, cellular and molecular approaches to decipher how this unconventional multi-cellular unit is controlled and how glial-derived factors set ILC3 function and intestinal homeostasis. In order to achieve this, we will assess ILC3-autonomous functions of neurotrophic factor receptors. ILC3-specific loss and gain of function mutant mice for neuroregulatory receptors will be used to define the role of these molecules in ILC3 function, mucosal homeostasis, gut defence and microbial ecology. Sequentially we propose to decipher the anatomical and functional basis for the enteric epithelial-glial-ILC unit. To this end we will employ high-resolution imaging, genome-wide expression analysis and tissue-specific mutants for define target genes. Our ground-breaking research will establish a novel sensing program by which ILC3 integrate environmental cues and will define a key multi-cellular unit at the core of intestinal homeostasis and defence. Finally, our work will reveal new pathways that may be targeted in inflammatory diseases that are major Public Health concerns.

2 270 000 €

Start date: 2015-07-01, End date: 2020-06-30

This project stems from an ERC STG grant that I received in 2007 (DENDROworld) in which we analyzed several aspects of the homeostasis of the gut and how defects in controlling this process could result in different pathologies, including inflammatory bowel disease (IBD) and cancer. In the present project, we will continue working on the immune homeostasis of the gut and we will focus on fundamental questions in mucosal immunity. Three important and novel questions will be addressed in this project. The first aims at understanding how the gut microbiota is restrained from reaching systemic sites and hence it is tolerated only locally. We think that we have identified a new barrier at mucosal sites that avoids systemic spreading of bacteria via the blood stream. This is a very selective barrier that resembles the blood brain barrier and occurs at the level of enteric endothelial cells. The second question is closely related and tries to identify the role of the microbiota in the establishment/maintenance of this barrier and to understand its role during infection with enteric pathogens or in other circumstances (like pregnancy, liver disease). Finally, we want to characterize the activity of an anti-inflammatory mediator that we have identified. This is a short isoform of the well-known cytokine called TSLP. We think that this isoform is the one involved in the homeostasis of the intestine as it is the only one produced by epithelial cells in health and is downregulated during chronic inflammation. This project is divided into three major aims. 1. Analysis of a putative gut vascular barrier that resembles the blood brain barrier and of the mechanisms leading to its disruption 2. Analysis of the role of the microbiota in the formation and maintenance of the Gut vascular barrier (GVB). 3. Elucidation of the activity of TSLP short isoform. This is a multidisciplinary project requiring expertise in mucosal immunology, microbiology, bioinformatics and endothelium.

2 000 000 €

Start date: 2014-07-01, End date: 2019-06-30

The central challenge for the immune system is to efficiently recognize and neutralize foreign antigen while protecting self. If the latter fails, autoimmunity and/or autoinflammation may occur, as observed in many human diseases. Though several human genes involved in the process have been identified we still lack: i) a comprehensive appreciation of all contributing molecular pathways, ii) an understanding of the interplay and epistatic relationships among the various elements and iii) a satisfactory strategy to counteract dysregulation based on an understanding of the regulatory logic. I hypothesize that there is only a finite number of pathways involved and that it should be possible to mount a synergistic strategy to create a first chart of the entire “territory”. Key to this endeavor is the identification of sufficient elements by mapping immune dysregulation genes to “anchor” the chart onto signposts of which the human pathophysiological relevance is certain. From these signposts, contextualization and integration is achieved by interaction proteomics and network informatics mining the existing data universe, validated through biochemical and imaging tools to power an established set of immune assays. While it may be preposterous to claim feasibility with one ERC grant, I propose that once such a chart exists, even at initial low resolution, it can help reconcile disconnected observations and coalesce future work while being immensely improved in accuracy and mechanistic understanding by the entire community. iDysChart will work towards these goals by 1) identifying novel monogenic causes of autoimmune/autoinflammatory diseases, enabling elucidation of fundamental mechanisms, 2) creating a network-level understanding of molecular pathways of immune dysregulation and 3) employing chemical and genetic screens to complement human disease gene discovery in predicting the core human immune dysregulome and investigating potential avenues for therapeutic modulation.

1 999 263 €

Start date: 2019-06-01, End date: 2024-05-31

Metastatic disease is still largely unexplored, poorly understood and incurable. Accumulating evidence indicates that cells and mediators of the immune system can facilitate metastasis. Neutrophil accumulation in cancer patients has been associated with metastasis formation. In mouse tumor models, neutrophils have been reported to be pro- or anti- metastatic, but the underlying mechanisms involved in either function remain largely elusive. This proposal outlines a research program aimed at resolving the pro-metastatic role of neutrophils in breast cancer, as our preliminary data indicate that neutrophils proactively mediate breast cancer metastasis. Using a state-of-the art spontaneous breast cancer metastasis mouse model, we will mechanistically study how neutrophils facilitate metastasis formation and how mammary tumors provoke the metastasis-facilitating function of neutrophils. Building upon my previous studies and our current data, we will focus on the unexplored crosstalk between the adaptive immune system and neutrophils in facilitating spontaneous metastatic disease. These crucial questions will be addressed by undertaking a multidisciplinary approach, involving sophisticated mouse models for metastatic breast cancer, RNA sequencing on tumor-associated neutrophil populations, state-of-the-art mouse engineering, intravital imaging and in vivo neutrophil manipulations. Moreover, we will validate our findings from the mouse metastasis model in human breast cancer samples. We will determine the metastasis predicting power of the identified murine pro-metastatic neutrophil-specific pathways by immunohistochemistry and multi-parameter immunofluorescence on breast cancer samples and blood of untreated patients of which clinical follow-up is available. Thus, we will identify novel molecular pathways that can be targeted to selectively inhibit the pro-metastatic activity of the immune system.

1 999 360 €

Start date: 2014-03-01, End date: 2019-02-28

An infection is defined by the deleterious consequences of the interactions between a pathogen and a host. Thus, studying the biology of infection reveals critical properties of hosts and pathogens, and is a way forward to address basic biological questions and improve health. We study listeriosis, a systemic infection caused by Listeria monocytogenes (Lm). Lm is a human foodborne pathogen that crosses the intestinal barrier, disseminates systemically, replicates in liver and spleen and reaches the central nervous system (CNS) and fetoplacental unit. Given the remarkable journey Lm makes in its host, studying listeriosis offers unprecedented opportunities to understand host cell biology, physiology and immune responses, guided by Lm. The mucosal, CNS and fetoplacental tropisms of Lm are shared by other microbes which pathogenesis is far less understood. Lm therefore stands as a unique model microorganism of general biological and medical significance. The major challenge of this project is to go beyond reductionist approaches and embrace the complexity of actual infections. We will use stem cell-derived organoids, live imaging, genetically engineered mouse models, the clinical and biological data from a unique cohort of 900 patients and the corresponding causative Lm strains, to investigate the molecular mechanisms of Lm tissue invasion, dissemination and host responses. Specifically, we will (i) decipher the cell biology of microbial translocation across the intestinal epithelium; (ii) study the impact of microbial portal of entry on microbial fate, dissemination and host responses; (iii) harness Lm biodiversity to identify novel virulence factors and (iv) discover new host factors predisposing to invasive infections. Building on the unique combination of advanced experimental systems and exclusive clinical data, this integrative and innovative project will reveal novel, physiologically relevant mechanisms of infection, with scientific and biomedical implications.

2 750 000 €

Start date: 2016-11-01, End date: 2021-10-31

Molecular pathogenesis of most immune-mediated disorders, such as of autoimmune diseases, is poorly understood. These common maladies carry a heavy burden both on patients and on society. Current therapy is non-targeted and results in significant short- and long-term adverse effects. Large granular lymphocyte (LGL) leukemia is characterized by expansion of cytotoxic T- or NK-cells and represents an intriguing clinical continuum between a neoplastic and an autoimmune disorder. Patients suffer from autoimmune cytopenias and rheumatoid arthritis (RA), which are thought to be mediated by LGL cells targeting host tissues. My group recently discovered that 40-50% of LGL leukemia patients carry in their lymphoid cells acquired, activating mutations in the STAT3 gene – a key regulator of immune and oncogenic processes (Koskela et al, N Engl J Med, 2012). This breakthrough discovery gives insight to the pathogenesis of autoimmune disorders at large. I present here a hypothesis that a strong antigen-induced proliferation is a mutational driver, which causes somatic mutations in lymphoid cells. When mutations hit key activating pathways, autoreactive cells acquire functional advantage and expand. The target antigen of the expanded clone determines the clinical characteristics of the autoimmune disease induced. To prove this hypothesis, we will separate small lymphocyte clones from patients with autoimmune diseases and use sensitive next-generation sequencing methods to characterize the spectrum of somatic mutations in lymphoid cells. Further, we will study the function of mutated lymphocytes and examine the mechanisms of autocytotoxicity and end-organ/tissue damage. Finally, we aim to understand factors, which induce somatic mutations in lymphoid cells, such as the role of viral infections. The results will transform our understanding of molecular pathogenesis of autoimmune diseases and lead to accurate diagnostics and discovery of novel drug targets.

2 047 337 €

Start date: 2015-09-01, End date: 2020-08-31

"The deadliest form of human malaria is caused by the protozoan parasite, Plasmodium falciparum, which annually infects millions worldwide. Its virulence is attributed to its ability to evade the human immune system, by modifying the host red blood cell surface to adhere to the vascular endothelium and to undergo antigenic variation. Antigenic variation is achieved through switches in expression of hypervariable surface ligands named PfEMP1. These proteins are encoded by a multi-copy gene family called var. Each individual parasite expresses a single var gene at a time, whereas the remaining ~60 var genes found in its genome are maintained in a transcriptionally silent state, a phenomenon known as ""allelic exclusion"". These antigenic switches allow the parasite to avoid the human immune response and maintain a long-term infection. How mutually exclusive expression is regulated is still elusive. The rationale of the proposed study is that understanding the molecular mechanisms by which the parasite evade human immune attack would lead to the development of therapeutic approaches that disrupt this ability and would give the human immune system an opportunity to clear the infection and overcome the disease. I will focus this research project on understanding one of the unsolved mysteries in gene expression which is responsible for regulating antigenic variation in P. falciparum: the nature of ""communication"" between genes that allows expression of only a single gene at a time and the selection of the ""chosen one"" for activation while the rest of the gene family remains silent. The expected outcome of this knowledge is new concepts for disrupting the parasite’s ability to evade immune attack which will be exploited for the discovery of novel targets for drug and vaccine development. In addition, it will unravel mechanisms of allelic exclusion that extend beyond malaria virulence into fundamental aspect of gene expression in other organisms."

2 000 000 €

Start date: 2014-06-01, End date: 2020-05-31

MicroRNAs (miRNAs) can be transferred between cells, representing an exciting new dimension to intercellular communication, referred to as non-cell-autonomous gene regulation. We recently identified that distinct miRNAs are packaged and exported from TREG cells and delivered directly to TH1 cells, suppressing T cell-mediated disease. Different T cell populations express different miRNAs and release a distinctive set of extracellular miRNAs. In this proposal we will identify whether the transfer of miRNAs between cells contributes to T cell development, T cell differentiation and TH2-mediated allergy and anti-helminth immunity. miRNA-mediated gene silencing requires one of four catalytically active Argonaut (Ago) proteins to regulate gene expression. To investigate miRNA transport between cells, we have generated novel mice with miRNA-deficient T cells that can (Dicer–/–) or cannot (Dicer–/–Ago-1,-3,-4–/– Ago-2fl/fl) respond to exogenous miRNAs. Using these novel mice we will identify which Ago protein(s) specific miRNAs associate with and which Ago proteins are required for miRNA-mediated gene regulation in T cells. TH2 cells express unique miRNAs, which can be found within TH2 cells and in extracellular vesicles released from TH2 cells. We have generated several new TH2-associated miRNA-deficient mice to investigate the cell intrinsic (cell-autonomous) and extrinsic (non-cell-autonomous) role of these miRNAs in TH2-mediated allergy and anti-helminth immunity. Studies in plants and worms have identified various mechanisms of RNA transfer between cells, involving cell-contact dependent and independent mechanisms. We will translate these observations into mammalian systems and identify the mechanisms of miRNA transfer. Results from this work will identify novel miRNA-mediated pathways and incentivise state-of-the-art approaches for novel therapeutic intervention to treat inflammatory diseases.

1 762 510 €

Start date: 2015-08-01, End date: 2020-07-31

Immunometabolism is an emerging research field that promises to generate novel targets for manipulation of functional responses in immune cells. Pioneering studies are beginning to unveil how innate sensing leads to metabolic reprogramming of immune cells. We became interested in the possible metabolic consequences of innate sensing by myeloid cells because of our previous work showing how mouse and human dendritic cell (DC) subsets detect danger signals from microbes and damaged tissues. Our current data show that sensing of live bacteria triggers a profound reorganisation of the mitochondrial electron transport chain (ETC) in macrophages, with a switch in the relative contribution of ETC complexes I and II to mitochondrial respiration that impacts immune response. As we pursue novel strategies to manipulate DC function, and supported by our preliminary data in DCs, we hypothesise that innate sensing induces mitochondrial adaptations in DCs and that targeting mitochondrial metabolism will affect DC function. Our goals are: 1) to characterise how innate sensing of danger signals from microbes or from tissue damage modulate mitochondrial adaptations and metabolic reprogramming in mouse and human DC subsets; 2) to dissect the molecular mechanisms that connect innate sensing and mitochondrial adaptations in DCs, using biased and unbiased cutting-edge proteomics approaches; 3) to address the impact of manipulating mitochondrial biology on mouse and human DC metabolism and function; and 4) to assess the functional in vivo effects of targeting mitochondrial biology in DCs in homeostasis and disease. The characterisation of the molecular mechanisms that link innate sensing and mitochondrial metabolism with DC function will open new avenues for basic research in mitochondrial biology and for the emerging field of immunometabolism. Functional targeting of DC mitochondrial metabolism has great potential for the discovery of new strategies to modulate immunity and tolerance.

1 995 000 €

Start date: 2017-12-01, End date: 2022-11-30

Experience with adeno-associated virus (AAV) vector-mediated gene transfer in human trials has unveiled the therapeutic potential of this approach, with some of the most exciting results coming from clinical studies of gene transfer for hemophilia B, congenital blindness, and the recent market approval of the first AAV-based gene therapy in Europe. Follow-up data of subjects treated with AAV vectors is showing sustained correction of the disease phenotype for several years after gene transfer, and recent data confirmed that AAV vectors can drive expression of a transgene in humans for >10 years. With clinical development, however, some of the limitations of the approach, not entirely identified in preclinical studies, became obvious; in particular it is well established that the host immune system represents an important obstacle to be overcome in terms of both safety and efficacy of gene transfer in vivo with AAV vectors. The overall goal of this proposal is to gain critical, missing knowledge on the interactions between AAV vectors and the immune system in order to develop strategies to achieve safe, effective, and long-lasting gene transfer in humans. In this proposal we will: 1) Define the molecular signatures of the immune system in humans undergoing gene transfer with AAV vectors using cutting-edge, high-content immunophenotyping technologies; 2) Study the role of anti-AAV antibodies as determinants of AAV capsid immunogenicity using both in vitro and in vivo systems; 3) Identify novel pharmacological and cellular approaches to overcome T cell immunity to AAV; 4) Develop novel strategies to overcome pre-existing antibody responses to AAV. This proposal exploits the knowledge and the skills available in our lab to develop new tools and to provide novel, basic insights into the human immune responses to AAV that will have a direct impact on the quality of life of patients affected by inherited disorders.

2 730 800 €

Start date: 2014-07-01, End date: 2019-06-30

Survival of living organisms depends on their capacity to develop defence mechanisms against environmental challenges that cause tissue damage and infections. These protective functions involve the nervous system and the immune system, two systems traditionally considered as independent. However anatomical and cellular bases for bidirectional interactions between them have been established and a new paradigm on a regulatory role of the nervous system on immune functions is emerging. Pain is one of the major signs of inflammation. Upon acute injury, inflammation or infections noxious signals are perceived by nociceptors present in tissues, such as the skin. These sensory neurons convey the damaging information to the brain and release a number of mediators locally that could modulate immunity. The goal of this project is to decipher the functional role of sensory neurons and pain sensitivity on immune responses. We will tackle this highly challenging question by studying the immune responses to vaccination in genetic mouse models in which skin innervation by nociceptors is deficient. Our preliminary results are very promising as we already demonstrated that deficits in sensory skin innervation affect both the innate and adaptive immune responses to intradermal vaccine. We will further study the cellular and molecular mechanisms involved in this local and systemic modulation of the immune response by the nervous system. As a complementary approach, we will address the role of an exacerbated pain response on immunity through the selective stimulation of nociceptive neurons in wild type animals. This interdisciplinary study is designed to provide new insights into how the nervous system instructs the immune system. Results from NEURIMMUNE are expected to open new avenues of research on the integrated host response to pathogens with important implications for the design of innovative prophylactic vaccines and therapies.

2 000 000 €

Start date: 2015-10-01, End date: 2020-09-30

Within clonal bacterial populations not all cells exhibit the same phenotype, even though they grow in the same environment. The molecular sources contributing to phenotypic variation are diverse and can originate from noise in gene expression to heterogeneity in growth rates or cell cycle state. Phenotypic variation helps pathogenic bacteria to elude the host immune response or resist antibiotic pressure. Vice versa, there is cell-to-cell variability in the host’s response towards pathogens that can be exploited by bacteria. How the combined cellular heterogeneity of both host and microbe contribute to infection outcome is poorly understood. The role of phenotypic variation on antibiotic resistance development is also unclear. Recently, we developed novel single cell imaging systems as well as genetic engineering and screening platforms for application to the important opportunistic human pathogen Streptococcus pneumoniae. In addition, we generated a dual-transcriptomics overview of pneumococcal infection of human lung epithelial cells and setup collaborations to perform several infection models. This now places us in an excellent position to investigate the mechanisms and the importance of single cell behaviour for pneumococcal virulence and antibiotic resistance. The driving hypothesis of this application is that the combined heterogeneity of host cells and pneumococci influences infection and antibiotic therapy outcome. To test this, we will use innovative approaches for infection biology by combining synthetic biology and quantitative single cell biology including single cell RNA-seq, CRISPRi, engineered bistable switches and microfluidics. We will reveal the molecular mechanisms underlying cell-to-cell variability and its importance in virulence and antibiotic resistance. Insights obtained in this project will lead to a better understanding of phenotypic variation and might result in new treatment strategies for pneumococcal infections.

1 999 735 €

Start date: 2018-11-01, End date: 2023-10-31

CD8+ T cells are critical to fight infections and to clear tumor cells through the production of inflammatory cytokines and cytotoxic molecules. These effector molecules must be tightly controlled: too little leads to the inability to control the pathogen, and too much can result in a life-threatening cytokine storm and tissue damage. While transcriptional control of effector genes is well-studied, regulation at the levels of RNA stability and translation efficiency by RNA-binding proteins (RBPs) has remained underappreciated. We recently found that several cytokines are tightly regulated through these processes, and we identified ZFP36L2 as one of the responsible RBPs. However, much is still to be learned about the underlying molecular mechanisms. Moreover, there are >1000 putative RBPs, and a systematic analysis of their regulatory activity in T cells is lacking, particularly with regard to the control of effector proteins. Here, we will use a combination of mouse genetics, and molecular and cellular biology to gain a deep understanding of the control of cytokine production by RBPs, using ZFP36L2 as a paradigm. Next, we will take a novel, highly sensitive proteomics approach to systematically identify the RBP repertoire in resting and activated primary human T cells. Complementary functional screens will identify those RBPs that control specific effectors. Selected RBPs identified in these screens will be studied in-depth to understand their roles in T cell responses to acute infection and in tumor models. Lastly, we will define how RBPs can imprint and/or maintain the killer phenotype of human CD8+ T cells. This research will significantly advance our understanding of post-transcriptional regulation of T cell effector activity, and it should help us to develop novel tools to drive effective T cell responses against pathogens and malignant cells.

2 000 000 €

Start date: 2019-03-01, End date: 2024-02-29

The immune system with its complex interactions of cells and molecules needs a very tight and specific interplay of control elements to ensure the establishment and re-establishment of immune homeostasis after challenges. Regulatory T cells (Tregs) are key-players in this regulatory network. It is now well accepted that deficiency or dysfunction of Tregs causes various severe immune disorders due to immune hyperactivation. Conversely, an increased number of Tregs in tumor-bearing individuals suppresses efficient anti-tumor immunity and, thereby, is often associated with poor prognosis. Cancer immunology is now one of the most exciting and promising frontiers in cancer research, and recent clinical trials have proven that immunotherapies driving to activate T cells can induce durable responses. In this sense, harnessing the potential of Tregs is one of the most promising new approaches to control immune function and to treat cancer. This proposal has two objectives: 1, the identification and characterization of tissue-resident Tregs to principally understand the unique features of Treg specialization in tissues and their function in organ-homeostasis, a phenomenon that is hardly understood, but holds great promise for local, tissue-specific immune intervention. 2, to globally target Tregs, including the lymphoid organ Treg pool, by interfering with their survival and or suppression function. We expect from these studies new basic insights into a fascinating and still arcane aspect of organ-homeostasis as maintained by Tregs, as well as novel small molecule inhibitors and candidate molecules that target Tregs at the systemic level, and eventually at a tissue-specific level.

1 955 000 €

Start date: 2015-07-01, End date: 2020-06-30

"RNA editing is a type of programmed RNA sequence alteration that can result in a range of proteomic changes, from subtle fluctuations in output, to specific alterations in protein content. Editing is catalyzed by two classes of deaminases: those which convert adenosine to inosine (ADARs) and those which convert cytosine to uracil (APOBEC1). We have previously shown that APOBEC1-catalyzed editing in the transcriptome of macrophages leads to the generation of populations that are heterogeneous, and functionally diverse, enabling rapid population adaptation to different environmental settings. Our first aim for this proposal is to extend our studies to additional immune cell subsets, focusing on cells that are recently recognized as ""plastic"" to define the contribution of editing to this plasticity of fate and function. RNA editing of the type we study has also been demonstrated to be crucial for cancer progression. For instance, APOBEC1-deficiency significantly reduces tumour burden on cells of the intestine and colon that are prone to adenocarcinomas in the context of the APC-min mutation. This is also the case for testicular carcinomas in mouse models of such tumours. Thus, there is genetic evidence for a requirement for APOBEC1 and RNA editing to drive tumour progression, in two tumour contexts. Based on these data and on our recently deciphered role for APOBEC1 as a ""stealthy"" diversifier of cellular transcriptomes (and proteomic outcomes), we hypothesize that APOBEC1 drives tumour progression by editing select transcripts in tumour cells (or tumour stem cells), thus enabling the rapid adaptation of the tumour to the onslaught of the immune response. Our second aim is to characterize the subset of edited transcripts in these model tumours (either at the population or at the single cell level) and understand their role to tumour survival and progression, both in mouse models of disease, and in human tumour samples (in collaboration with QP Hammarstrom, KI)."

2 270 000 €

Start date: 2016-01-01, End date: 2020-12-31