ERC FUNDED PROJECTS

"Bicuspid aortic valve, a heart valve with only two leaflets instead of three, is the most common congenital heart defect with an estimated prevalence of about 1-2%. The heart defect often remains asymptomatic but in at least 10% of the bicuspid aortic valve patients, an ascending aortic aneurysm develops as well. If not detected in a timely fashion, this can lead to an aortic aneurysm dissection with a high mortality. In view of the prevalent nature of this heart defect, this implies an important health care problem. Historically, it was always hypothesized that abnormal blood flow across the bicuspid aortic valve led to aneurysm formation. However in recent years, the importance of a genetic contribution has been suggested based on the high heritability and it is currently believed that the same genetic factors predispose to the developmental valve defect and the aortic aneurysm formation. The inheritance pattern is most consistent with an autosomal dominant disorder with variable penetrance and expressivity. Until now, the latter have significantly hampered the causal gene identification but the era of next generation sequencing is now offering unprecedented opportunities for a major breakthrough in this area. Through detailed signalling pathway analysis, miRNA profiling and next generation sequencing, this project will contribute significantly to resolving the genetic causes of bicuspid related aortopathy, provide critical knowledge on the pathogenesis of aortic aneurysmal disease and deliver a mouse model for future therapeutical trials."

1 497 895 €

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

In recent years, genome-wide association studies (GWAS) have discovered hundreds of single nucleotide polymorphisms (SNPs) which are significantly associated with coronary artery disease (CAD). However, the SNPs identified by GWAS explain typically only small portion of the trait heritability and vast majority of variants do not have known biological roles. This is explained by variants lying within noncoding regions such as in cell type specific enhancers and additionally ‘the lead SNP’ identified in GWAS may not be the ‘the causal SNP’ but only linked with a trait associated SNP. Therefore, a major priority for understanding disease mechanisms is to understand at the molecular level the function of each CAD loci. In this study we aim to bring the functional characterization of SNPs associated with CAD risk to date by focusing our search for causal SNPs to enhancers of disease relevant cell types, namely endothelial cells, macrophages and smooth muscle cells of the vessel wall, hepatocytes and adipocytes. By combination of massively parallel enhancer activity measurements, collection of novel eQTL data throughout cell types under disease relevant stimuli, identification of the target genes in physical interaction with the candidate enhancers and establishment of correlative relationships between enhancer activity and gene expression we hope to identify causal enhancer variants and link them with target genes to obtain a more complete picture of the gene regulatory events driving disease progression and the genetic basis of CAD. Linking these findings with our deep phenotypic data for cardiovascular risk factors, gene expression and metabolomics has the potential to improve risk prediction, biomarker identification and treatment selection in clinical practice. Ultimately, this research strives for fundamental discoveries and breakthrough that advance our knowledge of CAD and provides pioneering steps towards taking the growing array of GWAS for translatable results.

1 498 647 €

Start date: 2019-01-01, End date: 2023-12-31

Dynamic interplay between histone modifications and DNA methylation defines the chromatin structure of the humane genome and serves as a conceptual framework to understand transcriptional regulation in normal development and human disease. The ultimate goal of this research proposal is to study the chromatin architecture during normal and malignant T cell differentiation in order to define how DNA methylation drives oncogenic gene expression as a novel concept in cancer research. T-cell acute lymphoblastic leukemia (T-ALL) accounts for 15% of pediatric and 25% of adult ALL cases and was originally identified as a highly aggressive tumor entity. T-ALL therapy has been intensified leading to gradual improvements in survival. However, 20% of pediatric and 50% of adult T-ALL cases still relapse and ultimately die because of refractory disease. Research efforts have unravelled the complex genetic basis of T-ALL but failed to identify new promising targets for precision therapy. Recent studies have identified a subset of T-ALLs whose transcriptional programs resemble those of early T-cell progenitors (ETPs), myeloid precursors and hematopoietic stem cells. Importantly, these so-called ETP-ALLs are characterized by early treatment failure and an extremely poor prognosis. The unique ETP-ALL gene expression signature suggests that the epigenomic landscape in ETP-ALL is markedly different as compared to other genetic subtypes of human T-ALL. My project aims to identify genome-wide patterns of DNA methylation and histone modifications in genetic subtypes of human T-ALL as a basis for elucidating how DNA methylation drives the expression of critical oncogenes in the context of poor prognostic ETP-ALL. Given that these ETP-ALL patients completely fail current chemotherapy treatment, tackling this completely novel aspect of ETP-ALL genetics will yield new targets for therapeutic intervention in this aggressive haematological malignancy.

958 750 €

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

Glucose is key source of nutritional energy and raw material for biosynthetic processes. Maintaining glucose homeostasis requires a regulatory network that functions both in the systemic level through hormonal signaling and locally at the intracellular level. Insulin signalling is the main hormonal mechanism involved in maintaining the levels of circulating glucose through regulation of cellular glucose intake and metabolism. While the signalling pathways mediating the effects of insulin have been thoroughly studied, the transcriptional networks downstream of insulin signalling are not comprehensively understood. In addition to insulin signalling, intracellular glucose sensing mechanisms, including transcription factor complex MondoA/B-Mlx, have recently emerged as important regulators of glucose metabolism. In the proposed project we aim to take a systematic approach to characterize the transcriptional regulators involved in glucose sensing and metabolism in physiological context, using Drosophila as the main model system. We will use several complementary screening strategies, both in vivo and in cell culture, to identify transcription factors regulated by insulin and intracellular glucose. Identified transcription factors will be exposed to a panel of in vivo tests measuring parameters related to glucose and energy metabolism, aiming to identify those transcriptional regulators most essential in maintaining glucose homeostasis. With these factors, we will proceed to in-depth analysis, generating mutant alleles, analysing their metabolic profile and physiologically important target genes as well as functional conservation in mammals. Our aim is to identify and characterize several novel transcriptional regulators involved in glucose metabolism and to achieve a comprehensive overview on how these transcriptional regulators act together to achieve metabolic homeostasis in response to fluctuating dietary glucose intake.

1 496 930 €

Start date: 2012-01-01, End date: 2017-02-28

The considerable variability within tissue microenvironments as well as the multiclonality of cancers leads to intratumoral heterogeneity. This increases the probablility of cellular states that promote resistance to therapy and eventually lead to reconstitution of the tumor by treatment-resistant cancer cells, which in some cases have properties of normal tissue stem cells. Wnt signals are important in the maintenance of stem cells in various epithelial tissues, including in lung development and regeneration. We hypothesized that Wnt signals contribute to tumor heterogeneity in genetically engineered KrasG12D; Tp53Δ/Δ (”KP”) mouse lung adenocarcinomas (LUAD). We observed that a subpopulation of LUAD cells exhibited high Wnt reporter activity and had increased tumor forming ability, which could be suppressed by silencing of Wnt signaling pathway components or by small molecule Wnt inhibitors in vitro and in vivo. KP LUAD cells show hierarchical features with two distinct populations, one with increased Wnt reporter activity and another forming a niche that provides the Wnt signal. Lineage-tracing experiments in the autochthonous KP tumors demonstrated that Wnt responder cells have increased tumor propagation ability in vivo. Strikingly, selective ablation of the Wnt responder cells resulted in tumor stasis. CRISPR-based targeting or small molecules targeting Wnt signaling reduced tumor growth and prolonged survival in the autochthonous KP mouse lung cancer model. These results indicate that maintenance of heterogeneity within tumors may be advantageous for the tumor cell population collectively. We propose to elucidate the molecular and cellullar mechanisms that control stem-like and niche cell phenotypes using a combination of novel lentiviral vectors and genetically modified mice in the context of the KP LUAD model. These efforts may lead to novel therapeutic concepts in human lung cancer.

1 972 905 €

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

This proposal aims to clarify mitochondrial contribution to obesity and thinness, using carefully characterized mitochondrial disease and obese patient materials, and genetically modified disease models. Manifestations of mitochondrial respiratory chain (RC) defects range from infantile multisystem disorders to adult-onset myopathies or neurodegeneration, and even aging-related wasting. Why defects in oxidative ATP production can lead to such variety of manifestations and tissue specificity is unknown. We have previously identified a number of gene defects that lead to RC disorders. In addition to neurological symptoms, these patients often show various metabolic manifestations: specific gene defects associate with short stature and thinness, whereas others with metabolic syndrome or obesity. This implies that specific mitochondrial defects can have opposing effects for fat storage or utilization. The involved pathways may contribute to mitochondrial disease progression, but are unknown. We propose to a) undertake a major clinical study on genetically defined, obese or thin, mitochondrial patients, and examine their metabolic phenotype in finest detail. These data will be compared to those from normal obesity, to search for common mechanisms between mitochondrial and general obesity. b) generate a set of disease models for mitochondrial disorders associated with obesity, and knock-out models for specific signallers for crossing with the disease models. c) identify in detail the involved regulatory pathways, and utilize these for searching chemical compounds that could modulate the response, and have therapeutic potential. The project has potential for major breakthroughs in the fields of mitochondrial disease pathogenesis and treatment, neurodegeneration and obesity.

2 500 000 €

Start date: 2011-06-01, End date: 2016-05-31

Mitochondria play a central role in the energy metabolism of our bodies and their defects give rise to a large variety of clinical phenotypes that can affect practically any tissue. The mechanisms for the tissue-specific outcomes of mitochondrial diseases are poorly understood. Mitochondrial energy production relies on two separate protein synthesis machineries, cytoplasmic and mitochondrial, but the mechanisms regulating the concerted actions between the two are largely to be discovered. Defects in either protein synthesis system that lead to accumulation of mistranslated mitochondrial proteins, intrinsic or imported from the cytoplasm, result in stress signals from mitochondria and in adaptive responses within the organelle and the entire cell. My hypothesis is that some of these signals and adaptive mechanisms are tissue-specific. My group will test the hypothesis by 1) generating and characterizing mouse models of cytoplasmic and mitochondrial mistranslation to be able to address our questions in different tissues. 2) We will develop methods for detection of ribosome stalling in mouse tissues to identify the consequences of mistranslation for individual proteins. 3) We will use systems biology approaches to identify stress signal responses to mitochondrial and/or cytoplasmic mistranslation using different tissues of our models, to identify those that are unique or global. 4) Our previous study has identified an interesting candidate responder to mistranslation stress and we will test the role of this factor in knockout animal models and by crossing with the mistranslation mice. I expect to gain important new knowledge of in vivo responses to mistranslation and execution of quality control. This proposal investigates key questions in understanding differential tissue involvement in metabolic defects, and will provide new directions for utilization of tissue-specific adaptations in finding interventions for mitochondrial diseases.

1 354 508 €

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

Metabolic adaptations in central carbon metabolism play a key role in cancer. Yet, the success of therapeutic interventions in major pathways has been limited, although some of the changes have been known to exist for almost 100 years. Biochemical textbooks present intermediary metabolism as something canonical, and the molecular identity of most enzymes required for the production of known intermediary metabolites is indeed known. Yet, the function of many putative enzymes is still unknown, indicating that novel metabolic pathways containing so far unknown metabolites exist. We have recently discovered a novel metabolic pathway containing two metabolites that have never been described before. Preliminary data indicate that this pathway might play an important role in a group of cancers sharing specific mutations. Furthermore, genetic inactivation of a component of this pathway in mice is compatible with normal development, indicating that pharmacological inhibition should be well tolerated. In the present project, we will use a multi-dimensional approach combining biochemical, genetic and pharmacological techniques, to identify missing components of this metabolic pathway and assess its role in cellular metabolism and cancer development. In the process of this, we will develop tools that will allow us to test whether this pathway can be targeted in vivo. Thus, our work will lead to the description of a novel metabolic pathway, should reveal novel regulatory circuits and might open novel therapeutic avenues in cancer and beyond.

1 989 103 €

Start date: 2018-05-01, End date: 2023-04-30

Macrophages exist in distinct differentiation states. Proangiogenic/immunosuppressive (M2-like) macrophages and antitumoral/proinflammatory (M1-like) macrophages represent two extremities of a continuum. Because lineage-defined subsets have not been identified yet, macrophage heterogeneity is likely to reflect the plasticity of these cells in response to microenvironmental signals. The concept that hypoxia can induce inflammation has gained general acceptance. However, little is known on how extravasated monocytes and their macrophage progeny react to a condition of low oxygen. Different macrophage phenotypes have been positively and negatively associated with the clinical outcome of vascular disorders as cancer and ischemia. These pathological conditions are characterized not only by dysfunctional vessels, which impair oxygenation, but also by strong immunoregulatory responses. Recently we have shown that reduced activity of the oxygen sensor PHD2 in macrophages skews their polarization towards a proarteriogenic (M2-like) phenotype, which confers protection against ischemia. Based on these findings, we propose to dissect upstream and downstream signals to the oxygen sensing machinery and hypoxia-response in macrophages. By using a genome-wide transcriptional profiling approach and a high-throughput interactome analysis, combined with mouse genetic tools, we will identify the gene signature of macrophages in hypoxia and unravel the molecular executors of this response. The identification of the effectors responsible for macrophage skewing in relation to oxygen availability will contribute to a better understanding of immunoregulatory cues during disease progression and unveil the multifaceted function of macrophages during vessel formation. With the focus of our research on macrophage manipulation towards a desired phenotype, we will offer new treatment options for cancer and ischemia that might result in optimized therapies and overcome resistance to current drugs.

1 499 306 €

Start date: 2012-11-01, End date: 2017-10-31