Interdisciplinary approaches continue to demonstrate its potential: research conducted by our Institute together with the Max Planck Institute for Molecular Physiology in Dortmund revealed that embryonic stem cells process cell differentiation signals through intermittent oscillations. This finding could pave the way for controlled manipulation of cell differentiation processes.

As a result of an Argentine-German collaboration between the theoretical physics group of our Institute and the experimental biology laboratory of Dr. Christian Schröter at the Max Planck Institute for Molecular Physiology in Dortmund, Germany, the journal Development published the paper “Intermittent ERK oscillations downstream of FGF in mouse embryonic stem cells”. The work was carried out by IBioBA (CONICET-Partner Max Planck) doctoral fellow Fiorella Fabris from Argentina and scientist Dhruv Raina from the European Institute. 

Although both groups were dedicated to studying the differentiation of embryonic stem cells, in this work the complementarity between biology and physics was key to achieve the results: while Fiorella Fabris and Luis Morelli, head of the physics group “Information processing in cells and tissues” were in charge of theory and data analysis; the team of biologists from Germany, Christian Schröter and Dhruv Raina focused on performing the necessary experiments to carry out the research.

Fiorella Fabris, Christian Schröter, Luis G. Morelli & Dhruv Raina (from left to right), during his visit to the Institute in 2019.

The object of study: stem cells

Stem cells derived from an embryo are known as pluripotent cells because they have the capacity to differentiate (become) into any cell type of the adult organism, i.e. they can eventually, at the end of the growth process, become skin cells, stomach cells, neurons, etcetera. 

In order to differentiate, stem cells sense the information they receive from the extracellular environment, process it and then translate it into a “differentiation decision” that sends a signal to the DNA, which then expresses itself as a function of differentiation. “What we study in this publication is how the stem cell translates and processes within itself an extracellular signal from FGF, a protein known to be one of the most important signals that the cell receives to differentiate during the early stages of embryonic development”, says Fiorella.

Embryonic stem cells. During embryonic development in mice, three days after fertilization, the embryo is composed of two cell types: the trophoblast cells (in green), which give rise to the placenta, and the cells of the Inner Cell Mass (in violet), which are pluripotent cells that give rise to all the cells found in the adult organism. Embryonic stem cells are cells extracted from the Inner Cell Mass represented in purple. [Figure adapted from: Schrode, N., Xenopoulos, P., Piliszek, A., Frankenberg, S., Plusa, B. and Hadjantonakis, A.-K. (2013), Anatomy of a blastocyst: Cell behaviors driving cell fate choice and morphogenesis in the early mouse embryo. Genesis, 51: 219-233].

Intermittent oscillations

With this goal in mind, the german team conducted experiments in which they integrated a sensor that measures the response of “ERK” second by second in a cell. ERK is the protein that emits the differentiation signal and whose function is to translate information from the environment received by the cell, which is then passed on to the DNA. So, “Dhruv exposed stem cells to different concentrations of FGF and observed the response of ERK. These measurements give us information on how the cell processes the information received, which we know is information for differentiation”, says Fabris. 

It is worth noting that this is the first time this type of experiment has been performed in which the temporal response of ERK is measured in stem cells: “The short time scale of the pulses has never before been resolved in this type of cells, which are very difficult to manipulate”

In the videos obtained thanks to these experiments, the scientists were able to see something that was not known until now: that the ERK protein has a pulsatile signal. Based on this, and through data analysis, Fiorella and Luis set out to elucidate where the signal -the information- of these pulses is encoded, and for this, they performed a new time series analysis protocol. 

And here they also found something novel: on the one hand, the time scale of the pulses is faster than similar signals previously known in other cells, since they have a duration of between six and seven minutes; and on the other hand, “and this is the novelty of this system, we saw that the information is encoded in the duration of the pulsing interval, since we can find pulses and silences. So we characterized this new dynamics that had not been found until now and we call it intermittent oscillations“, explains the fellow.

“Through this research we discovered two things: first, the way in which the stem cell interprets differentiation signals, and at the same time we found a new way of interpreting this signal thanks to the new data analysis protocol we devised: intermittent oscillations”, she adds. In other words, the team created a way to describe pulsed time series, and this allowed them to perform a much deeper characterization than they could have done with existing algorithms: “The approach with which we did this work was novel, because it was a new way to describe dynamics in time series”.

In addition, the research team saw that as the external FGF signal increases, while the pulse duration is robust and does not change, the number of pulses changes, i.e. the length of the pulsing intervals changes. “The time the cell is pulsing is correlated with the type of signal it receives”, Fiorella describes.

They were also able to observe that these types of signals (those of ERK) are more common at the beginning of the cell cycle, i.e. when the cell is dividing: as it differentiates or divides, the signal is turned off. However, they did studies in a more differentiated system -no longer in an embryonic stem cell but in a state closer to becoming a cell of the organism- and noticed that this way of transmitting the signal is preserved, although the oscillations are less prevalent.

Scheme of intermittent oscillations: time series with oscillatory intervals interspersed with silent intervals. As the cell differentiation stimulus (FGF) increases, the intervals of oscillations are longer and have more pulses.

A potential for the future

When embryonic stem cells sense ligands that induce their differentiation, in general, the response to those ligands is heterogeneous. That is, not all cells differentiate into the same type, and this leaves some of the process not understood. “I believe that understanding how the cell interprets the differentiation signal is the key to understanding why this response is heterogeneous, and if we manage to manipulate this response, i.e. differentiate it into a specific cell type, this could open the door to the use of stem cells in regenerative medicine. It is important to understand how differentiation works because in the long term it will be easier to regulate it”, concludes the fellow.