In tissues, cells have their physical space constrained by neighbouring cells and extracellular matrix. In the PROMICO ERC project, our team proposed to specifically address the effect of physical confinement on normal and cancer cells that are dividing and migrating, using new pathophysiologically relevant in vitro approaches based on innovative micro-fabrication techniques. One of the devices we developed was meant to quantitatively control two key parameters of the cell environment: its geometry and its surface chemical properties. The main technical breakthrough was achieved using micro-fabricated elastomeric structures bound to a hard substrate (Le Berre Integrative Biology, 2012). The method led to important fundamental discoveries in cell biology (Lancaster Dev Cell 2013, Le Berre PRL 2013, Liu Cell 2015, Raab Science 2016). In part based on our findings, the notion that confinement is a crucial parameter for cell physiology has spread through the cell biology. Based on this, our idea is that cell confinement could be used as a powerfull cell conditioning technology, to change the cell state and offer new opportunities for fundamental research in cell biology, but also in cell therapies and drug screening. However, our current method to confine cells is not adapted to large scale cell conditioning applications, because the throughput and reliability of the device is still too low and because the recovery of cells after confinement remain poorly controlled. It is thus now timely to develop a robust and versatile cell confiner adapted to use in any cell biology lab, in academy and in industry, with no prior experience in micro-fabrication. Achieving this goal involves a complete change of technology compared to the ‘homemade’ PDMS device we have been using so far. We will also perform proofs of concept of its use for its application in cell based therapies, such as cancer immunotherapy, by testing the possibility to mechanically activate dendritic cells.

Tissue development requires the orchestration of stem cell differentiation and morphogenesis, a process that is conspicuously observed in mammary gland (MG) branching. The MG develops from an embryonic bud of mammary stem cells (MaSCs). Although these stem cells are initially bipotent, giving rise to the outer (basal) and inner (luminal) layers of the adult gland, they become lineage restricted very early in embryogenesis, at around the time of the onset of branching morphogenesis. The timing of lineage restriction coincides with the differential expression of cell polarity and cell adhesion transcripts. Branching morphogenesis then relies on differential cell division, as well as cell rearrangements and migration, but the mechanisms regulating this process in the embryo remain poorly understood. Based on these observations, we postulate that basal-biased and luminal-biased MaSCs have distinct molecular features during branching morphogenesis. We therefore propose to functionally link the signaling pathways involved in restriction of stem cell potency to the cellular dynamics that ensure branching. To this end, we will characterize the dynamic behaviour of individually labeled MaSCs during the growth of embryonic MG explants and assess their fate, creating a complete fate-behavior map of MG development. Through genetic manipulation, we will probe how cell adhesion, migration, and division impact on lineage specification and tissue growth. Simultaneously, we will skew stem cell differentiation trajectories and assess their influence on cell behavior and organ shape. The outcomes of this project will provide novel insights into the coordinated developmental programs governing stem cell fate and morphogenetic events, both essential to tissue formation. Moreover, they might uncover potential connections to cancer, where differentiatiom and cell polarity play pivotal roles.

Signaling pathways are cascades of biochemical reactions that transduce environmental signals to the cell interior. The cells rely on the information transduced through signalling pathways to govern biological functions and maximise the fitness of the organism. Conversely, defects in the signalling pathways are implicated in various diseases, e.g. carcinogenesis. The intricate network of signalling pathways indicates the existence of sophisticated information processing mechanisms, motivating the key questions of this project: How much information is transmitted from the environment through the signalling pathway? How many features of the signals are conveyed? Are signals integrated over time? To answer these questions, the project combines state of the art quantitative optogenetic experiments and theoretical modelling using information theory to quantify the information flow in the canonical MAPK signaling pathway. Experimentally, a well-defined stimulus will be applied at the beginning of the pathway while measuring the response at the end of the signaling cascade. The results will be integrated into a theoretical framework based on statistical physics and information theory to quantify how much static and dynamic information is being transmitted, offering key insights into cell function — the building blocks of living organisms — with potential application in drug design. The strong interdisciplinary nature of this project and the detailed dissemination strategy promotes collaboration between research communities of physicists and biologists, as well as reinforces information as a key concept in life sciences. The included training plan ensures the candidate will acquire skills in advanced experimental and theoretical techniques, and the two-way transfer of knowledge provides mutual benefit between the candidate and the host institution.