ERC FUNDED PROJECTS

One of the most remarkable features of biological systems is their ability to self-organize in space and time. Even a relatively simple cell like the bacterium Escherichia coli has a precisely regulated cellular anatomy, which emerges from dynamic interactions between proteins and the cell membrane. Self-organization allows the cell to perform extremely challenging tasks. For example, for cell division, more than ten different proteins assemble into a complex, yet highly dynamic machine, which controls the invagination of the cell while constantly remodeling itself. Although the individual components involved have been largely identified, how they act together to accomplish this challenge is not understood. It has become clear that sophisticated biochemical networks give rise to intracellular organization, but we have yet to uncover the underlying mechanistic principles. In this research proposal, I aim to develop a detailed mechanistic understanding of the self-organizing, emergent properties of the cell. To this end, my research group will develop novel in vitro reconstitution experiments combined with high-resolution fluorescence microscopy and theoretical modeling. Following this “bottom-up” approach, we will quantitatively analyze collective protein dynamics and emergent mechanochemical properties of the bacterial cell division machinery. I aim to answer the following fundamental questions: 1) What is the biochemical network giving rise to the dynamic assembly of the divisome? 2) How do the components of the divisome interact to generate force? 3) How do peptidoglycan synthases build the cell wall? By comparing protein dynamics in vitro with those measured in vivo, we will provide a link between molecular properties and the processes found in the living cell. This project will not only improve our understanding of the bacterial cell, but also open new research avenues for eukaryotic cell biology, synthetic biology and biophysics.

1 496 687 €

Start date: 2016-04-01, End date: 2021-03-31

Ligand-gated and voltage-gated channels are key molecules in transforming chemical signals into electrical ones and electrical signals into chemical ones, respectively. At excitatory synaptic connections in the brain, activation of AMPA- and NMDA-type glutamate receptors elicits inward currents at the postsynaptic sites, and activation of voltage-gated calcium channels triggers vesicle release of glutamate in the presynaptic sites. Plastic changes in their number, location and property can lead to potentiation or depression of synaptic efficacy, alteration in time course, and coupling to effectors at both postsynaptic and presynaptic sites. These channels are all composed of distinct subunits and their compositions affect channel properties, trafficking to the synaptic sites, and interaction with associated molecules, creating a large diversity of synaptic functions. Although channels with different subunit compositions have been investigated using biochemical and electrophysiological detection methods, very little is known about single channel subunit composition in situ because of the lack of high resolution methods for analysis of protein complex in intact tissues. In this project, I will develop novel technologies to visualize subunit composition at the single channel level in individual synapses by electron microscopy, combining new EM tags, freeze-fracture replica labelling, and electron tomography. Synaptic plasticity will be induced by optogenetic stimulation of identified neurons or behavioural paradigms to examine the dynamic changes of subunit composition. Finally, physiological implications of such regulation of subunit composition will be investigated by genetic manipulation of mice combined with electrophysiological and behavioural analyses. This work will demonstrate unprecedented views of the subunit composition in situ and provide new insights into how regulation of subunit composition contributes to synaptic plasticity and animal behaviour.

2 481 437 €

Start date: 2016-07-01, End date: 2021-06-30

Microbial turnover of soil organic matter (SOM) is key for the terrestrial carbon (C) cycle. Its underlying mechanisms, however, are not fully understood. The role of soil microbes for organic matter turnover has so far been studied mainly from the point of view of microbial physiology, stoichiometry or community composition. I propose to shed new light on it from the perspective of complex systems science. Microbial decomposition of organic matter requires the concerted action of functionally different microbes interacting with each other in a spatially structured environment. From complex systems theory, it is known that interactions among individuals at the microscale can lead to an ‘emergent’ system behavior, or ‘self-organisation’, at the macroscale, which adds a new quality to the system that cannot be derived from the traits of the interacting agents. Importantly, if microbial decomposer systems are self-organised, they may behave in a different way as currently assumed, especially under changing environmental conditions. The aim of this project is thus to investigate i) if microbial decomposition of organic matter is driven by emergent behaviour, and ii) what consequences this has for soil C and nitrogen cycling. Combining state-of-the-art methods from soil biogeochemistry, microbial ecology, and complex systems science I will • Investigate mechanisms of spatial self-organization of microbial decomposer communities by linking microscale observations from experimental microcosms to mathematical, individual-based modelling, • Elucidate microbial interaction networks across the soil’s microarchitecture by linking microbial community composition, process rates and chemical composition of spatially explicit soil micro-units at an unprecedented small and pertinent scale. • Explore fundamental patterns of self-organisation by applying the framework of complex systems science to high-resolution spatial and temporal data of soil microstructure and process rates.

1 896 129 €

Start date: 2019-05-01, End date: 2024-04-30

CD8+ T cells play a key role in the control of infections by intracellular pathogens. Recently, several top-notch studies provided ample evidence that NK cells are important in the regulation of CD8+ T cell response. NKG2D is an activating NK cell receptor which plays a role in the adaptive immune response by co-stimulating CD8+ T cells. Due to unique pattern of immune response, live attenuated CMVs are attractive candidates as vaccine vectors for a number of clinically relevant infections. The main idea behind this project stems from our preliminary data which suggest that a recombinant CMV vector expressing NKG2D ligand has a tremendous potential for subverting viral immunoevasion and boosting the efficiency of CD8 T cell response. During the project we plan to systematically investigate the impact of all major innate immunity players on the CD8+ T cell response. A special focus will be given in obtaining new knowledge on the maintenance of memory CD8+ T cells during latent infection. This study will also provide novel insights on the role of NKG2D in both NK and T cell immunity. In order to test our hypothesis in vivo, we will employ state-of-the-art technology used in herpesvirus genetics coupled with high-end immune monitoring. Ultimately, we will translate our results to a human CMV vector, in order to gauge the impact of NKG2D signaling on immune response in a humanized mouse model. We believe that the significance of the proposed study is enormous since stimulating CD8+ T cells has been widely recognized as a method of choice for vaccine development. There are relatively large number of pathogens for which the immunity acquired post-infection does not fully shelter against re-infection and disease. Therefore, we are in a desperate need for vaccines which offer superior protection compared to the one following natural infection. This study will provide groundbreaking information which will set the stage for the development of new vaccines and vaccine vectors.

1 754 897 €

Start date: 2013-05-01, End date: 2018-04-30

There is currently no medical cure for the millions of individuals affected by inflammatory bowel disease (IBD). These patients suffer from bleeding along the gastrointestinal tract due to epithelial ulceration, which causes severe abdominal pain, diarrhoea and malnutrition. This is due to the severely compromised integrity of the intestinal epithelium. I propose that patients with IBD will benefit from an intestinal epithelial transplant. The objectives of this research programme are two fold. Firstly, I propose to perform preclinical testing of human intestinal epithelium to pave the way for their inclusion in clinical trials for IBD patients. This will be based on a combination of state-of-the-art cell culture methods with novel transplantation methodology. By combining analysis of intestinal epithelial cells from various developmental stages, I will be able to identify the most suitable source for transplantation and define how adult stem cells are specified in the tissue. Secondly, I will utilise an in vitro culture system to identify the transcriptional networks responsible for the maturation of the foetal intestinal epithelium. Tissue maturation currently constitutes a major roadblock in regenerative medicine as cells derived from foetal and pluripotent stem cells have foetal properties. Understanding this process will therefore improve our ability to generate sustainable sources of cells for transplantation, which is pivotal for future therapies relying on regenerative medicine and in vitro modelling of disease The proposed research programme will have significant clinical and biological impact. Clinically, it provides the framework for initiating clinical trials for patients with IBD and protocols to obtain mature adult epithelium for in vitro disease modelling. From a biological perspective, we will gain insights into how specific signalling networks maintain specific cell states and dictate tissue maturation.

2 000 000 €

Start date: 2016-08-01, End date: 2021-07-31

The emergence of complex eukaryotic life forms on Earth from prokaryotic cells is one of the most fundamental questions in biology and also one of the least understood transitions in evolution. Phylogenomic studies recently indicated that the eukaryotic line of descent arose from within the TACK+L superphylum of Archaea. This proposal addresses the systematic analysis of two newly discovered, but largely uncharacterized lineages of Archaea from this superphylum that mark crucial evolutionary transitions. Thaumarchaeota harbor unique ‘eukaryotic’ features and represent the sole group of Archaea that has successfully radiated into virtually any moderate habitat on Earth. The Lokiarchaeota lineage found recently in deep marine sediments forms a direct sister group of Eukaryotes and exhibits an unprecedented array of genes that might have been instrumental for the ancestor of eukaryotes to develop its cellular and genomic complexity. Obviously, the molecular and biochemical investigation of both groups is timely and important, yet, it requires easy access and cultivation. We have now discovered Lokiarchaeota in local, accessible environments and were able to successfully cultivate thermophilic Thaumarchaeota. In this proposal, we will characterize the metabolic and structural traits of these two archaeal lineages and reconstruct their evolutionary ancestry in the context of the TACK+L superphylum. Beside the use of cutting edge techniques for cultivation, metagenomics and stable-isotope-based imaging, a novel method will be developed for in situ metatranscriptomic analyses of archaea. This project will give fundamental insights into the ecological success of Archaea in commonplace environments and into the biology of the closest living prokaryotic relatives of Eukaryotes. Reconstructing the ancestral gene repertoire and biological features of lineages of the TACK+L superphylum will help resolve the enigma of the emergence of eukaryotes.

2 500 000 €

Start date: 2016-08-01, End date: 2021-07-31

Recent advances using immune checkpoint inhibitors demonstrate the great potential of immunemodulation in cancer and metastasis treatment. However, the effective treatment of only a subset of patients shows that this is only the start to utilize the power of the immune system to fight cancer. An interesting approach is to harness innate immune cells, such as plasmacytoid dendritic cells (pDCs) and tumor-associated macrophages (TAM) to attack tumors and to enhance the effect of standard anti-cancer therapies. Recently, using mouse models we identified two independent mechanisms by which modulation of these two cell types restrained tumor growth. First, the direct killing of tumor cells by pDCs that occurs independent of the adaptive immune system. Second, we identified a tumor-promoting role of EGFR-expressing (EGFR+) TAMs during tumorigenesis. This enables us to look at the role of EGFR in tumorigenesis in a completely new way and we plan to exploit this novel finding to reevaluate the mechanism by which anti-EGFR drugs are effective in tumors. The mechanisms endowing pDCs with tumor-killing capacities and determining the specificity of tumor cell recognition by activated pDCs are poorly understood. Furthermore, the interaction of pDCs with macrophages has never been investigated in tumors. Here I propose to define the molecular mechanisms by which pDCs and TAMs can be instructed to adopt an anti-tumorigenic phenotype. Inducible and cell-specific genetic mouse models mimicking human cancers will allow to molecularly dissect the immunemodulatory capacity of pDCs and TAMs. State-of-the-art large scale in vitro and in vivo RNAi screens will provide a platform to identify novel molecular pathways and open the possibility for testing new strategies in cancer immunetherapy. The clinical significance of our findings will be validated in human cancer samples in close cooperation with clinicians, which ensures a fast predictive and therapeutic translation of our results.

2 499 646 €

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

Obesity and T2D affect large populations and cause a decline in life expectancy if untreated. The pandemic proportion of obesity and inaptitude of anti-obesity approaches reflect our limited understanding of its complex environmental and genetic etiology. Genome-wide association studies revealed that disease-associated risk variants are often situated in those 98% of the genome not encoding for proteins. This noncoding genomic space yet does not reflect ‘Junk DNA’ but gives rise to >10,000 noncoding RNAs like microRNAs and long, noncoding RNAs (lncRNAs) that implicated in control of glucose metabolism and energy homeostasis also by the applicant (Kornfeld et al. Nature 2013). LncRNAs were paraphrased as 'Dark matter of the genome' due to their tissue-specific and dynamic expression that contrast their poorly understood role in gene regulation. In the 1st part of this proposal, we ask if lncRNAs regulate glucose metabolism and are involved in the obesity-associated dysregulation of insulin signaling in the liver, the major glucoregulatory organ in mammals. Using RNA-Seq and novel lncRNA prediction algorithms, we observed that obesity alters expression of 28 annotated and 15 hitherto unknown lncRNAs in two mouse models of obesity. To identify lncRNAs causally controlling glucose metabolism, we established a siRNA screening system that allows functional interrogation of >650 lncRNAs. These in vitro findings serve as entry for the generation of lncRNA knockout mice that are metabolically phenotyped. In the 2nd part, we hypothesize that germline ncRNAs could control the transgenerational consequences of paternal obesity as shown for lower organisms. This builds upon unpublished findings from our lab showing that obesity profoundly changes expression of germline ncRNAs. In-vitro fertilization and intergenerational breedings will trace the legacy of paternal obesity across generations and reveal ncRNAs involved in this ‘Lamarckian’ control of glucose metabolism.

1 344 498 €

Start date: 2016-05-01, End date: 2021-04-30

The adult mammalian stomach can be divided into three distinct parts: From the proximal fore-stomach over the corpus to the distal pylorus. Due to constant exposure to mechanical stress and to hostile contents of the lumen, highly specialized cell types have to be constantly reproduced in order to maintain the function of the gastrointestinal tract. Recently, the applicant identified Troy+ chief cells as a novel stem cell population in the corpus epithelium. Troy+ chief cells displayed a very low proliferation rate indicating their quiescent nature compared to other known gastro-intestinal tract stem cells. Interestingly, these stem cells can actively divide upon tissue damage, suggesting distinctive statuses under conditions of homeostasis and injury. As Troy+ stomach stem cells exhibit interconvertible characteristics i.e. quiescent and proliferative, they represent a unique model of adult stem cells with which we can study 1) the dynamics of stem cell propagation in homeostasis and regeneration and the underlying mechanism of this switch by analysing molecular and epigenetic profiles. Subsequently, by analysing mRNA expression profiles and epigenetic changes in Troy+ stem cells between homeostasis and injury repair, we will generate a list of genes with potentially interesting functions in cell fate decisions. We will therefore investigate 2) the stomach stem cell programme in homeostasis and regeneration using in vitro and in vivo functional genetics. Lastly, we will characterise 3) human stomach stem cells in normal and pathological conditions. Here we pursue three main aims: - Investigating Troy+ stem cell dynamics during homeostasis and injury repair - Unmasking the stomach stem cell programme using in vitro and in vivo functional genetics - Characterising human stomach stem cells

1 570 399 €

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

For practice of personalized medicine in cancer, non-invasive tools for diagnosing at the molecular level are needed. Molecular imaging methods are capable of this while at the same time circumventing sampling error as the whole tumor burden is evaluated. We recently developed and performed the first-ever clinical PET scan of uPAR, a proteolytic system known to be strongly associated with metastatic potential in most cancer forms. We believe this new concept of uPAR-PET is a major breakthrough and has the potential to become one of the most used PET tracers as it fulfils unmet needs in prostate and breast cancer. Based on this, together with additional proof-of-concept data we obtained on targeting uPAR for optical imaging and radionuclide therapy, we now plan to develop and take into patients these new technologies for improved outcome. Specific aims are to develop and translate into human use: 1. A PET uPAR imaging ligand platform for visualization of the aggressive phenotype and risk-stratification to be used in tailoring therapy, e.g. in prostate cancer to decide whether prostatectomy is necessary. 2. uPAR-PET combined with simultaneous 13C-hyperpolarized pyruvate MRSI (Warburg effect). This will increase prognostic power, refine tumor phenotyping and thereby allow for better tailoring of therapy and early prediction of treatment response. 3. A uPAR optical imaging technology for guiding removal of cancer tissue during surgery. This will help delineate cancer tissue for removal while leaving healthy tissue behind. We expect better outcome with removal of less tissue. 4. Selective radionuclide therapies targeting uPAR positive, invasive cancer cells using β or α emitters. Dose planning will be performed using uPAR-PET imaging. This image-therapy pairing is also known as theranostics. Our endeavour is ambitious, yet realistic considering our competencies and track-record. We expect cancer patients to benefit from our new methods within the 5 year time-frame.

2 072 000 €

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

Viral infections are responsible for significant morbidity and mortality and frequency and impact of epidemics are expected to increase. Thorough understanding of basic virology is critical for informed development of prevention and control. Most systematic studies of virus-host interactions have focused on proteins, however, with recent methodological advances the intersecting fields of viral infection and RNA biology hold great promise for basic and therapeutic exploration. The goal of this application therefore is to discover and dissect RNA-based virus-host interactions and related regulatory mechanisms of gene expression. Micro-RNAs (miRNAs) fine-tune gene expression by repressing mRNA targets. However, cellular miRNAs increase translation and replication of certain viruses. Thus, hepatitis C virus (HCV) critically depends on the liver specific miR-122, which emerged as a therapeutic target. Further, HCV sequesters enough miR-122 to indirectly regulate cellular gene expression. I hypothesize that this RNA-based mechanism contributes to virus induced liver cancer, and aim to address this using our recently developed rodent model for HCV infection (Aim 1). Better understanding of viral RNA (vRNA) interactions could significantly contribute to basic infection biology and novel therapeutics. I therefore aim to systematically identify vRNA interactions with other cellular RNAs and proteins (Aim 2). I expect to identify interactions of value for functional regulation and therapeutic targeting. I finally hypothesize that translation of certain cellular mRNAs – similarly to viruses – increase upon miRNA binding, and aim to systematically screen for such virus-like alternative regulation, with potential to change understanding of post-transcriptional regulation (Aim 3). In conclusion, this high-risk high-gain project has potential to shape novel dogmas for virus and RNA biology and to identify novel RNA-based therapeutic targets; a promising upcoming field of discovery.

1 500 000 €

Start date: 2019-07-01, End date: 2024-06-30