Gene Regulatory Network Architecture in Neuronal Development

Project Information

GRAIN

Grant agreement ID: 101060244

DOI

10.3030/101060244

Project closed

EC signature date 14 July 2022

Start date 1 September 2023

End date 31 August 2025

Funded under

• Marie Skłodowska-Curie Actions (MSCA)

Total cost

No data

EU contribution

€ 214 934,40

Coordinated by

KOBENHAVNS UNIVERSITET
Denmark

Periodic Reporting for period 1 - GRAIN (Gene Regulatory Network Architecture in Neuronal Development)

Reporting period: 2023-09-01 to 2025-08-31

Summary of the context and overall objectives of the project

In the original GRAIN project, we set out to define the gene regulatory network (GRN), i.e. the downstream set of genes that interact with one another to control a process, activated in the development of mesencephalic dopaminergic neurons, the cell type affected in Parkinson’s disease. Such network is driven by HES1, a downstream effector of Notch receptors, which mediates cell-cell contact dependent signalling and is crucial for fine tuning the balance between the maintenance of an adequate progenitor pool and the initiation of differentiation in many tissues. Due to unforeseen circumstances, six months within the start of the fellowship the project was subjected to a forced refocusing. Together with the new supervisor, we devised a project that addressed similar overarching questions and aims, in the context of a different signalling pathway (FGF/Erk signalling instead of Notch) and at a different developmental stage: the transition from naïve stem cells to primitive endoderm.
During development, a single cell gives eventually rise to an embryo and its extraembryonic, supportive tissues. This process is highly inefficient, as only 30-40% of conceptions will lead to live births. Recent studies have highlighted an association between correct specification of primitive endoderm (PrE), a tissue that will become the yolk sac, and successful embryo implantation. On a molecular level, it’s been shown that these cells are, to some extent, plastic: they maintain the potential to regenerate themselves and other cell types. How is this possible? Recent research from the Brickman group has revealed that some pluripotency factors, such as Sox2, presumably more active in stem cells and gradually repressed in more differentiated tissues, like PrE, remain bound to their target genes even after the differentiation into PrE has begun. We hypothesize this could be a mechanism to allow for the memory of a previous plastic state.
While the project tackles a fundamental question in biology, its results will help discover biomarkers or druggable targets that will become candidates for future translational research in the context of in vitro fertilization, to maximise successful embryo implantation.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

Here, we further explore the plasticity potential of naïve-extraembryonic endoderm (nEnd, an in vitro model for PrE), by characterizing in vitro mouse embryo models called blastoids generated from nEnd and by using a panel of engineered cell lines for the controlled degradation of SOX2 to evaluate changes to the pluripotency network and in its plasticity potential in absence of these key transcription factors. In the context of Sox2, we find its presence is not required during initial PrE differentiation, but its loss impairs plasticity in the expanded nEnd culture.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

Results from the project include the characterization of PrE plastic potential in mouse blastoids generated from a primitive endoderm culture. Furthermore, we generated a panel of engineered cell lines, as well as sequencing datasets and differentiation protocols that ultimately will lead us to the definition of the gene regulatory networks driven by Sox2 and Oct4 in the context of early mouse development. Such results provide novel insight into the molecular mechanisms that stem cells can activate to maintain plasticity and could instruct future research, as well as lead to the identification of new biomarkers and druggable targets to improve successful implantation in IVF treatments.