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Deciphering signalling pathway dynamics during cell-fate commitment in stem cells

Project description

Extracellular signal perturbations and stem cell fate

Cell differentiation into mature cells with specialised form and function is driven by specific extracellular signals. This is a highly complex process that is regulated with spatial and temporal resolution. Funded by the European Research Council, the i-SignalTrace project aims to predict which signalling pathways are activated in stem cells when subject to different extracellular signals. Researchers will employ the CRISPR/Cas9 gene-editing technology to unveil the mechanisms of cell fate commitment and understand how different perturbations may affect stem cells. The work is expected to provide fundamental knowledge on developmental biology and improve regenerative medicine protocols of cell therapies.


Understanding the identity and intensity of the specific extracellular signals that a cell experiences at different times during its differentiation is essential to develop advanced cellular therapies. However, uncovering the sequence of these signaling events, their intensities, timing, and relevance in development and disease is proving to be very challenging.

Here, I propose to build i-SignalTrace: a CRISPR/Cas9-based molecular recorder with the capacity to store both lineage information and signalling pathway activity for multiple signals over time in single cells. By performing kinetic experiments and mathematical modeling, I will use i-SignalTrace to extract the probability of signalling pathways to be activated in stem cells when subject to different extracellular signals and reconstruct the lineage tree of pathway activities during differentiation with single-cell resolution. In combination with single-cell RNA sequencing, i-SignalTrace will make it possible to characterize transition and intermediate states along differentiation trajectories, and quantify the integration between extracellular signals and autonomous programs of gene expression. These results will allow predicting the differentiation trajectories that stem cells follow when subject to external perturbations, and deciphering the role of heterogeneity in signalling pathway activity during cell-fate commitment.

Using i-SignalTrace, I will identify missing or redundant signalling pathways induced during in vitro differentiation protocols. Therefore, I expect that exploitation of i-SignalTrace will allow establishing new criteria to design protocols to differentiate stem cells on demand. As a proof-of-concept, I propose a framework to improve the functionality of monolayer-derived cardiomyocytes. Taken together, i- SignalTrace will find applications in both fundamental developmental biology and translational regenerative medicine, which will benefit a much wider scientific community.

Host institution

Net EU contribution
€ 1 500 000,00
2333 ZA Leiden

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West-Nederland Zuid-Holland Agglomeratie Leiden en Bollenstreek
Activity type
Higher or Secondary Education Establishments
Total cost
€ 1 500 000,00

Beneficiaries (1)