Targeted drugs, which inactivate specific molecular targets upon which cancer tumours rely to drive cell growth, have delivered therapies that are more specific and thus with less side-effects than traditional cytotoxic chemotherapy. Unfortunately, these therapies are only effective in some patients and it is still very challenging to identify these responsive patients before giving the drug. However, the fast-growing availability of data from molecular profiling technologies and drug screenings constitutes an unprecedented opportunity to improve our ability to predict which patients will respond to a drug from the molecular profiles of their tumours. Another challenge is that there are many cancer types for which no effective targeted drug has been found yet. Drug Repositioning (DR) is a strategy to accelerate the discovery of new drugs. Combined with Phenotypic Screening, DR can find innovative cancer drug candidates while discovering novel targets. However, a model able to predict which drugs will be effective on a given tumour is required due to the prohibitive cost and time of wet-lab-only DR strategies. Furthermore, tools to predict the molecular targets of the resulting phenotypic hits are needed to understand their efficacy and side-effects as well as to predict novel drug combinations to delay the emergence of acquired resistance. This multidisciplinary project will deliver new methods for biomarker discovery and large-scale phenotypic-based DR. The exploited data will be either recently provided by the community or the host laboratory. While these methods will be applicable to any cancer type, this pilot project will focus on the identification of drug candidates and associated biomarkers for blood and pancreatic cancers with poor prognosis. As the developed methods for preclinical biomarker discovery face the same methodological challenges as those for clinical biomarkers, this project will make progress towards the ambitious goal of personalised medicine.

TRAJECTORY is a highly interdisciplinary and intersectoral training network focused on training 14 doctoral candidates (DN) in the field of tumor heterogeneity for improving treatment of cancer relapses. In TRAJECTORY, we support the idea, that in order to advance in the implementation of adapted therapeutic approaches to treat relapsing patients, we need to train the next generation of early-stage researchers (ESRs) to i) be aware of the limitations and shortcomings of the current methodology used to explore ITH, ii) have a multidisciplinary approach to their future research project ii) engage in the validation, standardization, and implementation of clinically-relevant models. Therefore, the main scientific objectives of TRAJECTORY are to combine the most advanced technologies to explore ITH in cancer relapses while focusing on training. TRAJECTORY brings together world leaders in the field of tumor heterogeneity with experts in tumor ecosystems (Itay Tirosh and Sarah-Maria Fendt ), tumor evolution (Trevor Graham ), or drug design (Raphael Rodriguez ). Moreover, we aggregate experts with a significant interdisciplinarity ranging from tumor biology (Itay Tirosh, Sarah-Maria Fendt, Christophe Ginestier ), to preclinical modeling (Julie Pannequin , Emmanuelle Charafe-Jauffret , HUB organoids), system biology (Francesca Ciccarelli ), mathematical modelling (Trevor Graham) robotics (Roderick Beijersbergen ), bioengineering (EpiQMAx, Miltenyi), chemistry (Raphael Rodriguez) or philosophy (Lucie Laplane , Javier Suarez). All beneficiaries, including three industrials companies focused on technology development (EpiQMAx, HUB Organoids, Miltenyi) will deliver research objectives through the supervision of one doctoral candidate and will lead several of the research and transferable skills training modules. Ultimately this industry-academic interaction will increase the innovation capacity of all participating organizations by facilitating intersectoral exchanges that contribute to European competitiveness. It will strengthen the European research and Innovation potential by fostering entrepreneurial skills of academic young researchers

Heme is an essential and ubiquitous cofactor for a plethora of enzymes. Moreover, unbound heme works as a signaling molecule which regulates a number of pathways by modulating the activity of “so-called” heme-sensor proteins. In particular, it has been shown that unbound heme regulates cell signaling by modulating protein degradation via the Ubiquitin-Proteasome System (UPS). Recently, I uncovered a molecular network that links lung cancer-associated mutations of the master regulator of oxidative stress response, the ubiquitin ligase KEAP1, to alteration of the heme-dependent protein degradation, which ultimately promotes oncogenesis. The proposed project aims to use a broad spectrum of experimental systems and levels of resolution – molecular, network and organismal – to define the molecular machineries mediating heme-dependent degradation and to discover how deregulation of this pathway contributes to cancer pathogenesis. This represents a fundamental question in cancer biology that has yet not been fully understood. My ultimate goal is to identify new therapeutic approaches for cancer patients harboring alterations of the heme-UPS pathway.

The MCCproteome project aims at understanding how multiciliated cells (MCCs) are built, a question of high relevance to human health. MCCs harbor myriads of motile cilia beating coordinately to generate directional flows of biological fluids, or to move particles and cells, at the surface of specialized epithelial tissues. In human, MCCs are involved in circulation of the cerebro-spinal fluid in the central nervous system, in transportation of gametes, and in evacuation of soiled mucus from upper airways. Mutations in genes necessary for multiple cilia formation have been shown to be responsible for familial syndromes characterized by chronic airway infections, and an elevated risk of infertility. The severity of these symptoms points to the importance of studying fundamental principles of MCC biology. In recent years, the global MCC transcriptome has been decrypted in Xenopus, mouse and human. It is now time to elucidate the functional MCC proteome, which is the main objective of this project. Ciliogenesis is initiated when a centriole migrates underneath the cell membrane, is anchored to an actin-based scaffold and matures into a basal body, which acts as a microtubule-organizing structure necessary for axoneme extension. In the case of multiciliogenesis, a key additional step consists of a massive increase in the number of centrioles after permanent exit from the cell cycle. Our project is designed to shed light on this step, which is unique to MCCs and still poorly understood. In vertebrate MCCs, bulk centriole biogenesis occurs around poorly characterized platforms, called deuterosomes, although modest multiplication from parental centrioles also occurs. Deuterosomes have been described five decades ago by electron microscopy as non-centriolar globular structures. A first core deuterosome component, called Deup1 was identified in 2013. Recent work in Kodjabachian’s team has identified Pericentrin and ?-Tubulin as additional deuterosome components. These studies have opened the way to further molecular and functional characterization of deuterosomes, which is the overarching objective of our project. We will use three experimental paradigms to study deuterosome biology. i. The Xenopus embryonic epidermis, which is covered with functional MCCs 24h after fertilization, and represents a powerful and simple model to study multiciliogenesis in vivo. ii. A newly established Xenopus inducible cell line, which provides homogeneous and synchronized populations of MCCs. iii. Mouse post-natal ependymal MCCs, well-suited for in vivo fluorescent imaging and amenable to functional manipulation by electroporation. We will use a combination of super-resolution fluorescent microscopy, 2D and 3D electron microscopy, proteomics and functional manipulations to study deuterosome molecular composition, architecture, and activity. To date, very few studies have addressed deuterosome biology at the molecular level. Through this project, our consortium is poised to make important contributions in this field. Regarding its relevance to human health, this project may help to identify potential candidate genes for diseases caused by reduced multiciliogenesis.

The ambition of the project AbSoluTe is to decipher how fat-soluble vitamins D and E (FSV) enter and traffic across the enterocyte. FSV are small lipids essential to sustain life. Intense research is dedicated to increasing their absorption to tackle deficiencies. However, this research is considerably limited by our partial knowledge of FSV intestinal absorption pathways. Lipid transporters involved in FSV intestinal absorption have been identified using targeted approaches, but these approaches are limited. No functional tools are available to visualize FSV transport across the enterocytes and FSV partner proteins still remain to be identified. The project aims at deciphering FSV absorption process through the intestinal cell by following 3 objectives: - DESIGN: we will design and synthetize functional FSV probes, - VIZUALIZE: we will use FSV probes to visualize FSV transport across the enterocyte at the subcellular level, - IDENTIFY: we will use FSV probes and proteomics to identify FSV partner proteins in an unbiased manner. To this aim, we will implement a combination of in vitro and in vivo techniques from microscopy to thermal proteome profiling. This project will allow us to understand whether FSV absorption is driven by lipid fluxes and/or whether unidentified proteins are involved in their transport. This project will provide data relevant for i) other lipids/ lipophilic drugs absorbed by the enterocytes and ii) other cell types metabolizing FSV. The developed functional FSV probes will be of major interest in all aspects of nutritional sciences dealing with FSV metabolism and health effects. The findings from this study will support research aiming at improving FSV bioavailability and will constitute a strong knowledge base for the establishment of tailored recommendations, which can have far-reaching consequences in human nutrition, and thereby also public health.