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Dissecting the crosstalk between metabolism and transcriptional regulation in pluripotent stem cells.

Periodic Reporting for period 2 - MetEpiStem (Dissecting the crosstalk between metabolism and transcriptional regulation in pluripotent stem cells.)

Reporting period: 2019-04-01 to 2020-09-30

Pluripotent stem cells (PSCs) have the capacity to give rise to all cells of our body, such as neurons or cells of our skin or blood. They also expand easily in our laboratories and it is possible, via a process named “reprogramming”, to make personalised PSCs.
From a small skin biopsy or a blood sample of a patient, affected, for instance, by a neurodegenerative disease, it is now possible to obtain PSCs and to differentiate them into neurons that will display defects found also in the patient. In other words, PSCs give the unprecedented possibility to study human diseases and test drugs in a dish. This is one of the reasons why I firmly believe stem cells are revolutionising modern medicine.

However, our understanding of the behaviours of human PSCs is partial, we need to better understand how they differentiate, in order to make the process more efficient. For example, in some cases, the neurons obtained are not fully matured as those found in the adult brain.
The process of reprogramming could also be optimised, both in terms of efficiency and costs and in terms of obtaining PSCs of better quality.

Metabolism is defined as a large set of chemical reactions that maintain a cell alive, or an entire organism, by providing energy, by providing the “building blocks” of the cell and by eliminating the waste products.
Metabolism has been for a long time considered as a static component of cellular physiology, a sort of “cellular housekeeping”. However, we increasingly appreciate how metabolism has the capacity to dynamically affect the behaviour of the cell.

This project started from the observation that by boosting or blocking some metabolic pathways we were able to make the proliferation and differentiation of PSCs faster or slower. We also observed that a mild inhibition of energy production was enough to completely block the generation of PSCs by reprogramming.
In other words, we want to understand how metabolism affects the behaviour of PSCs and their production. We want to know whether providing the right “metabolic environment” will allow us improving differentiation of PSCs into cells of our body, or to generate PSCs more effectively.

Moreover, we already have collected evidence that the mechanisms we are studying in PSCs are also relevant for other stem cells. The stem cells that constantly renew our intestine, or those that participate in brain formation, appear to be under the same metabolic control we identified in PSCs, further demonstrating how metabolism has the potential to control key aspect of our physiology.
We have identified two mechanisms whereby a single metabolite controls the activity of the DNA of the stem cell, ultimately affecting how fast stem cells proliferate and also their differentiation propensity.
We have also verified that such metabolic control of stem cell proliferation occurs also in stem cells of the intestine and of the developing brain in fish.
We have also generated more efficient protocols for reprogramming by using computational approaches. We first tested in a “virtual cell” hundreds of different experimental conditions and then tested in the lab only the most promising ones.
We also used novel bioengineering approaches for the generation of stem cells from human cells, called microfluidics, making the process more efficient also when starting from just a few hundred cells. We are currently investigating how metabolism changes during the reprogramming process.
Compared to the state of the art at the beginning of the project 2017, we have identified two novel mechanisms whereby metabolites control stem cell behaviour. We have also demonstrated that one of them is relevant in stem cells of other tissues.
By the end of the project, we expect to obtain a better understanding of how such metabolites affect stem cell behaviour and what their role is during the generation of PSCs by reprogramming.