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RNA topology of test samples and single extracellular vesicles: how cells package RNA messages to communicate (RNA-top)

Project description

Topology of RNA associated with extracellular vesicles

Cells communicate by exchanging RNA that is associated with extracellular vesicles (EV-RNA), and analysis of EV-RNA may thus provide disease biomarkers. However, so far EV-RNA biomarkers are irreproducible. Since RNA is thought to be present within EVs, current procedures focus on isolating intra-vesicular EV-RNA. Recent evidence suggests, however, that EV-RNA may also be present on the EV surface. Funded by the Marie Skłodowska-Curie Actions programme, the goal of RNA-top is to investigate the precise location of EV-RNA (RNA topology) to improve EV-RNA biomarker development. Synthetic EV-mimicks with known RNA topology will be produced to set-up workflows to detect EV-RNA by super resolution microscopy and spectral flow cytometry. Workflows will then be extrapolated to study the RNA topology of cell-derived EVs.

Objective

In “RNA-top”, I will investigate the precise location(s) and quantity of RNA associated with extracellular vesicles (e.g. EV-RNA topology). To achieve this goal, I will set-up innovative liposome-based synthetic vesicle models (herafter referred to as test samples), resembling EVs, with a known RNA topology. I will use these test samples to create workflows for super resolution microscopy (SRM) and spectral flow cytometry (sFCM) to study RNA topology. These workflows will be extrapolated to EV samples, to define EV-RNA topology of single EVs for the first time. The research will be conducted in the Amsterdam UMC under the supervision of Dr. Rienk Nieuwland. Nieuwland and his team have the knowledge, experience and technical infrastructure to perform SRM and sFCM to study EVs. Therefore, RNA-top will allow me to deepen my knowledge on EVs and gain skills to perform SRM and sFCM. Conversely, I will bring my expertise in liquid biopsies and RNA, obtained during my PhD in Pangaea Oncology in Barcelona (H2020-MSCA-ITN). I will carry out a secondment in the lab of Dr. Zoltán Varga (Research Center for Natural Sciences in Budapest), an expert in the field of creating test samples, to get hands-on training. At the end of the project, I will join Exometry, supervised by Dr. Edwin van der Pol (CSO), for a 6-month non-academic placement to (1) develop an analysis software to process RNA topology data and (2) gain commercialization skills. The unique interdisciplinary and inter-sectoral combination of the participating organizations and myself, unites all the expertise and infrastructure required to reach the objectives of RNA-top.

Coordinator

STICHTING AMSTERDAM UMC
Net EU contribution
€ 234 530,40
Address
DE BOELELAAN 1117
1081 HV Amsterdam
Netherlands

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Region
West-Nederland Noord-Holland Groot-Amsterdam
Activity type
Research Organisations
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Total cost
No data

Partners (2)