Open vacancy

The nucleolus is a biomolecular condensate formed through liquid–liquid phase separation, where the initial steps of ribosome biogenesis occur. It acts as a biosensor that rapidly responds to stress of diverse origins, reflected by changes in its composition, function, and morphology. As such, the nucleolus is a powerful disease biomarker in cancer and other pathologies.

The nucleolus can be viewed as a liquid droplet whose material state can be tuned, for example, by converting it into a gel through optogenetics. This project aims to investigate whether the material state of the nucleolus is altered in cancer, and to determine the consequences of these alterations on nucleolar function. We will assess material state by Digital holographic microscopy, and use RNA processing and RNA modification as readouts, combining both short-read sequencing and state-of-the-art nanopore sequencing approaches.

1. Digital Holographic Microscopy (DHM) is a stain-free imaging technique that captures optical path length variations, allowing assessment of the nucleolar material state. We have preliminary evidence that treating cancer cells with chemotherapeutic agents (e.g., CX-5461, oxaliplatin) modifies this state. We will analyze a panel of cancer cell lines of diverse origins and grades, exposed or not to chemotherapeutics, as well as engineered cell lines in which the nucleolar state can be tuned optogenetically. Using DHM, we will systematically investigate material state changes in the nucleolus across these models.
2. Ribosomal RNA Modifications generate distinct molecular “fingerprints” that reflect cell type, tissue of origin, developmental stage, and disease grade. We have evidence that nucleolar material state influences RNA processing, and we will test whether it also impacts rRNA modification. To this end, we will employ high-resolution methods combining short-read and long-read (nanopore) sequencing to establish comprehensive modification profiles.
3. ADAR-Mediated A-to-I Editing is frequently altered in cancer and rewires gene expression, including pre-mRNA splicing. ADAR proteins are conspicuously enriched in the nucleolus, which is often structurally altered in cancer, yet no substrates have been described in this compartment. We hypothesize that ADAR is sequestered in the nucleolus to limit excessive activity. To test this, we will enforce nucleolar localization of ADAR and analyze the resulting effects on RNA processing and global gene expression.
   This PhD project will provide novel insight into how changes in the material state of the nucleolus intersect with RNA metabolism and modification in cancer, aligning with the objectives of the EURECA network.