Biologists have figured out how stem cells turn into other types of cells at the molecular level

(ORDO NEWS) — An international group of scientists, with the participation of biologists from the Higher School of Economics, has developed a method that allows obtaining information simultaneously about changes in the expression and properties of proteins during the transition of cells from one state to another.

Thanks to the new method and the ProteoTracker web tool developed to visualize changes, scientists were able to find out the molecular mechanism for slowing down the rate of protein synthesis in stem cells, and also propose a way to maintain the pluripotent properties of cells in vitro (outside the body).

The ability of stem cells to differentiate – to transform into other cells of the body – formed the basis of regenerative medicine and tissue engineering. The transformation of stem cells into cells of a different type is carried out due to profound changes in their protein composition.

Therefore, of particular interest to molecular biologists are the chemical foundations of the process of differentiation – what changes undergo the proteins that make up stem cells, and under what conditions this occurs.

Understanding what happens to proteins during stem cell transformation requires examining the differences between the protein composition of undifferentiated stem cells and the cells they become.

For experiments, the authors of the work received cell cultures of different types. Scientists have reprogrammed human connective tissue cells (fibroblasts) into induced pluripotent stem cells, that is, cells that can turn into cells of almost any tissue.

These cells were then turned into the so-called embryoid bodies, which made it possible to simulate the stages of early differentiation in the process of embryogenesis (development of the organism’s embryo). Also, the authors of the article used to compare the lines of tumor and human embryonic stem cells.

To assess the changes occurring in cells, scientists proposed a method that combines the measurement of protein expression (that is, the amount of proteins that is synthesized in the cell) and the analysis of changes in the integrated protein solubility (PISA).

As part of the PISA method, a certain effect on the protein is performed – temperature profiling of the proteome (TPP, or CETSA-MS). It is based on the fact that when the protein structure changes, its thermal stability changes, that is, the resistance of the protein to temperature changes.

The researchers heated the cells of the types listed above over a narrow range of temperatures, then destroyed the cells and, using mass spectrometric analysis, obtained information about the proteins remaining in solution for each temperature.

As a result of this analysis, thermostability curves were obtained for more than 9000 proteins in each type of cells studied. Simultaneously with thermostability, protein expression in each cell type was also assessed.

For analysis, the authors of the work used the ProteoTracker multidimensional visualization tool they created , based on Sankey diagrams. They reflected changes in the properties of each protein (stability and expression level) during differentiation.

Scientists have shown that the thermal stability and expression of proteins change when stem cells become somatic.

This reflects fundamental differences in the cellular physiology and morphology of these cell types. It turned out that more than 75 percent of the studied proteins differed significantly in expression and thermal stability in pluripotent and differentiated cells.

In particular, during the transformation of stem cells into somatic cells, the expression and stability of proteins responsible for the density of chromatin, the substance that makes up chromosomes, changes.

In the process of transformation of a stem cell into a somatic cell, the type of glucose metabolism (energy production in the cell) changes in it.

In particular, in a stem cell, glucose undergoes glycolysis — successive enzymatic transformations that do not require the presence of oxygen, while in a somatic cell — oxidative phosphorylation in mitochondria, the necessary condition for which is a sufficient amount of oxygen.

Analyzing at what point in the cells the expression of the corresponding proteins changes, the researchers found that the change in metabolism occurs at the early stages of differentiation of pluripotent stem cells, even before the change in the structure of chromatin.

This suggests that it is the change in the type of metabolism that can trigger subsequent changes in the structure of chromatin during differentiation.

Earlier it was also noted that somatic stem cells are characterized by a low rate of protein synthesis in the cell and its increase during differentiation. This suggested that a decrease in the rate of protein synthesis is important for maintaining the stem properties of cells.

However, the mechanism of such rate regulation was unclear. In their study, the scientists showed that pluripotent stem cells have a lower content of mature ribosomes than differentiated cells. This is due to the low level of expression of the SBDS protein responsible for ribosome maturation.

“Thus, a low level of expression of the SBDS protein allows cells to maintain stem properties, while an increase in its expression promotes differentiation — transformation into other cells,” explains Diana Maltseva, head of the HSE Laboratory of Microphysiological Systems.

“Furthermore, suppressing the expression or activity of the SBDS protein may prove to be a versatile approach for maintaining stem cells in vitro.”

The data obtained in the work also help to better understand the nature of developmental defects caused by Shwachman-Diamond syndrome, a genetic disease associated with a mutation of the SBDS protein.

The proposed technique can be widely used in cell biology, in research related to regenerative medicine. In particular, it can be useful both for searching for optimal conditions for cultivating various cells and developing protocols for stem cell differentiation, as well as for in-depth study of the functions of individual proteins.

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