ERC FUNDED PROJECTS

The fundamental evolutionary nature of cancer is well recognized but an understanding of the dynamic evolutionary changes occurring throughout a tumour’s lifetime and their clinical implications is in its infancy. Current approaches to reveal cancer evolution by sequencing of multiple biopsies remain of limited use in the clinic due to sample access problems in multi-metastatic disease. Circulating tumour DNA (ctDNA) is thought to comprehensively sample subclones across metastatic sites. However, available technologies either have high sensitivity but are restricted to the analysis of small gene panels or they allow sequencing of large target regions such as exomes but with too limited sensitivity to detect rare subclones. We developed a novel error corrected sequencing technology that will be applied to perform deep exome sequencing on longitudinal ctDNA samples from highly heterogeneous metastatic gastro-oesophageal carcinomas. This will track the evolution of the entire cancer population over the lifetime of these tumours, from metastatic disease over drug therapy to end-stage disease and enable ground breaking insights into cancer population evolution rules and mechanisms. Specifically, we will: 1. Define the genomic landscape and drivers of metastatic and end stage disease. 2. Understand the rules of cancer evolutionary dynamics of entire cancer cell populations. 3. Predict cancer evolution and define the limits of predictability. 4. Rapidly identify drug resistance mechanisms to chemo- and immunotherapy based on signals of Darwinian selection such as parallel and convergent evolution. Our sequencing technology and analysis framework will also transform the way cancer evolution metrics can be accessed and interpreted in the clinic which will have major impacts, ranging from better biomarkers to predict cancer evolution to the identification of drug targets that drive disease progression and therapy resistance.

2 000 000 €

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

All organisms in nature are targets for parasite attack. Over a century ago, it was first observed that symbiotic species living in hosts can provide a strong barrier against infection, beyond the host’s own defence responses. We now know that ‘protective’ microbial symbiont species are key components of plant, animal, and human microbiota, shaping host health in the face of parasite infection. I have shown that microbes can evolve within days to protect, providing the possibility that microbe-mediated defences can take-over from hosts in fighting with parasites over evolutionary time. This new discovery of an evolvable microbe-mediated defence challenges our fundamental understanding of the host-parasite relationship. Here, I will use a novel nematode-microbe interaction, an experimental evolution approach, and assays of phenotypic and genomic changes (the latter using state-of-the-art sequencing and CRISPR-Cas9 technologies) to generate new insights into the drivers and consequences of coevolving protective symbioses. Specifically, the objectives are to test: (i) the ability of microbe-mediated protection to evolve more rapidly than host-encoded resistance, (ii) the impacts of evolvable protective microbes on host-parasite coevolution, and the effect of community complexity, in the form of (iii) parasite and (iv) within-host microbial heterogeneity, in shaping host-protective microbe coevolution from scratch. Together, these objectives will generate a new, synthetic understanding of how protective symbioses evolve and influence host resistance and parasite infectivity, with far-reaching implications for tackling coevolution in communities.

1 499 275 €

Start date: 2019-02-01, End date: 2024-01-31

Group-living has been predicted to have opposing effects on disease risk and immune strategies. First, since repeated contacts between individuals facilitate pathogen transmission, sociality may favour high investment in personal immunity. Alternatively, because social animals can limit disease spread through collective sanitary actions (e.g., mutual grooming) or organisational features (e.g., division of the group’s social network into distinct subsets), sociality may instead favour low investment in personal immunity. The overall goal of this project is to experimentally test these conflicting predictions in ants using advanced data collection and analytical tools. I will first quantify the effect of social organisation on disease transmission using a combination of automated behavioural tracking, social network analysis, and empirical tracking of transmission markers (fluorescent beads). Experimental network manipulations and controlled disease seeding by a robotic ant will allow key predictions from network epidemiology to be tested, with broad implications for disease management strategies. I will then study the effect of colony size on social network structure and disease transmission, and how this in turn affects investment in personal immunity. This will shed light on far-reaching hypotheses about the effect of group size on social organisation ('size-complexity’ hypothesis) and immune investment (‘density-dependent prophylaxis’). Finally, I will explore whether prolonged pathogen pressure induces colonies to reinforce the transmission-inhibiting aspects of their social organisation (e.g., colony fragmentation) or to invest more in personal immunity. This project will represent the first empirical investigation of the role of social organisation in disease risk management, and allow its importance to be compared with other immune strategies. This will constitute a significant advance in our understanding of the complex feedback between sociality and health.

1 499 995 €

Start date: 2019-04-01, End date: 2024-03-31

The goal of ENDOMICS is to drive forward a new paradigm of Raman endoscopic technology that enables proteomic and lipidomic analysis for diagnosis of bladder cancers in vivo. Raman endoscopy is a label-free optical technique that can provide a point-wise vibrational molecular fingerprint of tissue “optical biopsy” for cancer diagnosis in vivo. State-of-the-art Raman endoscopy, however, does not offer specific compositional analysis or insights into molecular biology of tissue. This is because the vibrational Raman bands are overlapping and cannot be deciphered into the myriad of biomolecules in complex tissue. We will introduce a ground-breaking new methodology to enable Raman proteomic and lipidomic analysis in vivo. To this end, heterospectral co-registered Raman and mass spectrometry imaging will be used to develop a multivariate regression model “Rosetta Stone” for translating vibrational structural information (Raman spectroscopy) into compositional information. To meet the unmet clinical needs in urology we will tailor the first fibre-optic Raman endoscopic technology that can measure depth-dependent molecular profiles to simultaneously enable detection, grading and staging of bladder cancers. We will finally conduct a clinical trial by applying the technique to measure a comprehensive molecular database of bladder pathologies in vivo. The latter will allow for the identification of proteomic and lipidomic biomarkers to develop novel algorithms for real-time diagnosis of bladder cancers. The synergy between scientific and technological advances in ENDOMICS will break ground for shedding new light on the molecular biology of bladder cancer in vivo including new insights into clinical diversity and identification of biomarkers for diagnostics, prognostics and novel therapeutic targets.

1 490 950 €

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

Spiral cleavage is a highly stereotypical early embryonic program, and the ancestral, defining feature to Spiralia, a major phylogenetic clade including almost half of the animal phyla. Remarkably, spiral-cleaving embryos specify homologous cell fates (e.g. the progenitor cell of posterodorsal structures) conditionally –via cell interactions– or autonomously –via segregation of maternal inputs. This variation occurs naturally, even between closely related species, and has been related to the precocious formation of adult characters (adultation) in larvae of autonomous spiral-cleaving species. How spiralian lineages repeatedly shifted between these two cell fate specification modes is largely unexplored, because the mechanisms controlling spiral cleavage are still poorly characterized. This project tests the hypothesis that maternal chromatin and transcriptional regulators differentially incorporated in oocytes with autonomous spiral cleavage explain the evolution of this mode of cell fate specification. Through a comparative and phylogenetic-guided approach, we will combine bioinformatics, live imaging, and molecular and experimental techniques to: (i) Comprehensively identify differentially supplied maternal factors among spiral cleaving oocytes with distinct cell fate specification modes using comparative RNA-seq and proteomics; (ii) Uncover the developmental mechanisms driving conditional spiral cleavage, which is the ancestral embryonic mode; and (iii) Investigate how maternal chromatin and transcriptional regulators define early cell fates, and whether these factors account for the repeated evolution of autonomous specification modes. Our results will fill a large gap of knowledge in our understanding of spiral cleavage and its evolution. In a broader context, this project will deliver fundamental insights into two core questions in evolutionary developmental biology: how early embryonic programs evolve, and how they contribute to phenotypic change.

1 500 000 €

Start date: 2019-02-01, End date: 2024-01-31

The molecular communication between mitochondria and nucleus is an integrated bi-directional crosstalk - anterograde (nucleus to mitochondria) and retrograde (mitochondria to nucleus) signalling pathways. The mitochondrial retrograde response (MRR) is driven by defective mitochondrial function, which increases cytosolic reactive oxygen species (ROS) and Ca2+. Metabolic reprogramming is a key feature in highly proliferative cells to meet the energy needs for rapid growth by generating substrates for cellular biogenesis. In these mitochondria retro-communicate with the nucleus to induce wide-ranging cytoprotective effects exploited to develop resistance against treatment and sustain uncontrolled growth. Recently, the mitochondrial management of cholesterol-derived intermediates for the synthesis of steroids has been demonstrated as a determinant in the oncogenic reprogramming of cellular environment. We hypothesise that cholesterol-enriched domains facilitate the communication between remodelled mitochondria and nucleus to expedite MRR. This mechanism may be exploited during abnormal cell growth in which cholesterol metabolism and associated molecules are increased. This application capitalizes on expertise in cell signalling and metabolism to interrogate core pathways and unveil molecular sensors and effectors that define form and function of the MRR by: I. Elucidating the mechanism of metabolic regulation of MRR, describing the role exerted by cholesterol trafficking; II. Unveiling microdomains for mito-nuclear communication established by remodelled, autophagy escaped, mitochondria; III. Validating protocols to modulate and target MRR for diagnostic and therapeutic benefit; The experimental plan will (i) define a molecular signalling axis that currently stands uncharacterized, (ii) provide mechanistic knowledge for preventive, and (iii) therapeutic applications to counteract deficiencies associated with stressed, dysregulated mitochondria.

1 450 060 €

Start date: 2019-04-01, End date: 2024-03-31

Blood vessels form a versatile transport network and provide inductive signals called angiocrine factors to regulate tissue-specific functions. Blood vessels in bone are heterogeneous with distinct capillary subtypes that exhibit remarkable alterations with age. Bone is the most prevalent site of metastasis, and ageing is linked to the reactivation of dormant tumor cells (dorTCs) and metastatic relapse. Bone remodeling processes are also associated with metastatic relapse. Here, I will define the role of distinct vascular niches in regulating the fate of DTCs in bone. Finally, I will unravel the age-related angiocrine factors and identify key angiocrine signals that drive the reactivation of dorTCs. I will employ a powerful combination of advanced 3D, intravital, and whole body imaging, cell specific-inducible mouse genetics, transcriptional profiling and bioinformatics in an unprecedented manner to achieve my goals. New cutting-edge techniques such as advanced 3D and 4D bone imaging are important aspects of my proposal. I will also define the role of highly promising novel candidate age-related angiocrine signals with sophisticated inducible endothelial-specific humanised mouse models. My work will break new ground by unraveling a repertoire of age-related angiocrine factors and will contribute to a wider scientific community in bone, blood, and age-related diseases. This interdisciplinary work at the frontiers of bone, cancer and vascular biology will provide the first conceptual link between vascular ageing and bone metastasis and will contribute towards the development of therapeutic strategies for targeting DTCs in bone.

1 496 613 €

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

Mitochondrial DNA (mtDNA) is a multi-copy genome that works with the nuclear genome to control energy production and various cellular processes. To date, disorders associated with mutations in mtDNA are among the most common genetically inherited metabolic diseases1. However, our knowledge regarding many aspects of mtDNA biology remains limited, and we know even less about how it influences development and organismal traits. This is largely due to our inability to manipulate mtDNA. Recently, a colleague and I developed novel genetic tools in Drosophila that allowed us to isolate animal mitochondrial mutants for the first time, and to create heteroplasmic organisms containing two mitochondrial genotypes2,3. These advances make Drosophila a powerful system for mtDNA studies. Importantly, I showed that Drosophila mtDNA could undergo homologous recombination. Furthermore, I established a system to induce recombination at specific sites and select for progeny containing only the recombinant genome4. Thus, my work has demonstrated the existence of recombination in animal mitochondria, and opens up the possibility of developing a recombination system for functional mapping and manipulating animal mtDNA. Here I propose to 1) identify components of the mitochondrial recombination machinery by a candidate RNAi screen; 2) develop a recombination toolkit to map trait-associated mtDNA sequences/SNPs; and 3) build a site-directed mutagenesis system by establishing robust ways to deliver DNA into fly mitochondria. Given the essential functions of mitochondria and their involvement in incurable diseases, the genetic tools developed in this proposal will transform the field by making it possible to link mtDNA variations to phenotypic differences and introduce specific mutations into mtDNA for functional studies at organismal level. These advances will open many possibilities to accelerate our understanding on how mtDNA impacts health, disease and evolution.

1 473 732 €

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

Precise control of shape is key to cell physiology, and cell shape deregulation is at the heart of many pathologies. As cell morphology is controlled by forces, studies integrating physics with biology are required to truly understand morphogenesis. NanoMechShape will take such an interdisciplinary approach to investigate the regulation of animal cell shape. In animal cells, actin networks are the primary determinants of shape. Most cell shape changes fall into two categories: 1) those driven by contractions of the actin cortex, a thin network underlying the membrane in rounded cells; and 2) those resulting from transitions between the cortex and other actin networks, such as lamellipodia and filopodia. To understand cell deformations, it is thus essential to understand the regulation of cortex contractile tension and the mechanisms controlling transitions in actin architecture. NanoMechShape will comprise three aims. First, we will explore how cortex tension is regulated. We will focus on the role of cortex architecture, which remains elusive due to the difficulty in probing the organisation of the thin cortical network. We will unveil cortex architecture using super-resolution and electron microscopy, and systematically investigate how nanoscale architectural features affect tension. Second, we will explore how the identified regulatory mechanisms contribute to the establishment of a cortical tension gradient. We will focus on the gradient driving cytokinetic furrow ingression, an exemplar tension-driven shape change. Third, we will investigate transitions in actin architecture underlying cell spreading. We will compare spreading at the end of mitosis and during differentiation of mouse embryonic stem cells, paving the way to investigations of the crosstalk between cell shape and fate. By bridging a fundamental gap between molecular processes and cell-scale behaviors, our multidisciplinary study will unveil some of the fundamental principles of cell morphogenesis.

1 943 071 €

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