Biologists Figure Out How Stem Cells Turn Into Other Types of Cells at Molecular Level
An international team of researchers including biologists from HSE University has developed a method that helps obtain information on changes in protein expression and properties during cells’ transition from one state to another. One of the most interesting transitions is the transformation of cells from undifferentiated stem cells to differentiated cells of various organs and tissues. ProteoTracker, a newly developed method and web tool that visualizes the detected changes, helps researchers discover the molecular mechanism of parsimonious translation (low protein synthesis rate) in stem cells, as well as suggest a method to maintain pluripotency of cells during cultivation in vitro (out of body). The paper was published in Nature Communications.
Stem cells’ ability to differentiate—transform into other types of cells—is the foundation of regenerative medicine and tissue engineering. Stem cells turn into other kinds of cells thanks to deep changes in their protein composition. That’s why molecular biologists are particularly interested in the chemical foundations of the differentiation process: the changes that happen to proteins as part of stem cells and the conditions of this process.
To understand what happens to proteins during stem cell transition, it is necessary to study the differences between protein composition of undifferentiated stem cells and the resulting differentiated cells.
The researchers received cell cultures of different types to carry out the experiments and reprogrammed human connective tissue cells (fibroblasts) into induced pluripotent stem cells, the cells that are able to transform into cells of almost any tissue. These cells were then turned into so-called ‘embryoid bodies’ to use them as a model of early developmental specification during embryogenesis. The authors also used cell lines of human cancer and embryonic stem cells for comparison.
To investigate the changes happening in cells, the researchers proposed a method that combines protein expression (number of proteins that synthesize in a cell) measurement and ‘proteome-wide integral solubility alteration’ (PISA) assay.
The PISA method involves treating the protein with the method called ‘thermal proteome profiling’ (TPP or CETSA-MS). It is based on the property that when the protein structure changes, its thermal stability (protein’s resistance to temperature fluctuation) also changes.
The researchers heated the cells of the types listed above over a narrow range of temperatures, then lysed the cells and, using mass spectrometric analysis, obtained information about the proteins remaining in solution for each temperature. As a result of this analysis, thermal stability curves were obtained for more than 9000 proteins in each type of studied cells. Simultaneously with thermostability, protein expression in each cell type was also assessed.
To analyse the data they obtained, the authors used a multidimensional visualization tool they had created, ProteoTracker, which is based on Sankey diagrams that reflected the changes in each protein’s properties during differentiation.
The researchers demonstrated that thermal stability and expression of proteins change as stem cells turn into somatic ones, which reflects fundamental differences in cell physiology and morphology of these types of cells.
They found that over 75% of the analysed proteins had considerable differences in expression and thermal stability in pluripotent and differentiated cells. In particular, the expression and stability of proteins responsible for the density of chromatin (substance of which chromosomes consist) change during the process of stem cells’ transition into somatic cells.
As a stem cell becomes a somatic one, the type of glucose metabolism (energy production in a cell) changes in it: in a stem cell, glucose undergoes glycolysis (enzymatic transformations not requiring oxygen), while in a somatic cell, glucose is metabolized mostly via oxidative phosphorylation in mitochondria, which requires sufficient oxygen supplement. When the researchers analysed the moment at which expression of the relevant proteins starts in cells, they found out that the glucose metabolism changes at early stages of pluripotent stem cells’ differentiation, before the chromatin structure changes. This means that the change of metabolism type may trigger subsequent changes in chromatin structure during differentiation.
Previously, researchers observed that somatic stem cells are characterized with a low rate of protein synthesis in cells and growing speed during differentiation. That is why they assumed that the decreasing protein synthesis rate is important for maintaining the stem cell properties. But the mechanism of such regulation had been unclear. In their study, the researchers demonstrated that pluripotent stem cells have a lower proportion of functional ribosomes than differentiated cells. This is due to a low level of SBDS protein expression, which is responsible for maturation of ribosomes.
Diana Maltseva, Head of the HSE International Laboratory of Microphysiological Systems
‘The low level of SBDS protein expression allows the cells to maintain pluripotency, while an increase of its expression promotes differentiation—transformation into other types of cells. In addition, SBDS expression inhibition may be a universal approach to maintaining stem cells in vitro.’
The data obtained during the study can also help develop a better understanding of the nature of developmental defects related to Shwachman-Diamond syndrome—a genetic disease caused by SBDS protein mutation.
The proposed method may be widely used in cell biology, and in particular, in regenerative medicine research. It has the potential to be useful for the search of optimal conditions of various cells’ cultivation and development of stem cell differentiation protocols, as well as for in-depth studies of specific proteins’ functions.
Diana Maltseva
Laboratory Head, International Laboratory of Microphysiological Systems
See also:
Early Molecular Diagnosis of Cancer Proven More Cost-Effective Than Subsequent Treatment of Advanced Disease
Applying expensive diagnostic methods in clinical practice will ultimately cost society 5 to 10 times less than the expenditures associated with late-stage cancer treatment, including subsequent disability pensions and sick leave payments—these are the findings from a study conducted by researchers at the HSE Faculty of Economic Sciences Marina Kolosnitsyna and Anastasia Vladimirskaya in collaboration with colleagues at EVOGEN, a medical genetic laboratory, and the Department of Health of the Yamalo-Nenets Autonomous Okrug. The study results have been published in Social Aspects of Population Health.
Scientists Discover Cause of Metastasis Formation in Patients with Colorectal Cancer
An international team of researchers including scientists at the HSE Faculty of Biology and Biotechnology has identified factors which can increase the aggressiveness of tumours in patients with colorectal cancer. An isoform of CD44 protein has been found to play a pivotal role in the development of metastases. The study findings have been published in Molecular Oncology.
Scientists Have Developed a Model of Malignant Prostate Tumour and Used It to Test Drug Efficacy
Researchers from HSE University and the Russian Ministry of Health National Medical Research Radiological Centre have successfully generated a three-dimensional laboratory model of prostate cancer and used the model for testing an anti-tumour drug. In the future, this approach has the potential to significantly enhance the efficacy of cancer treatment for patients. The study’s findings have been published in Cancer Urology.
Nanai and Chukchi Found Intolerant to 'Mushroom Sugar'
A team of researchers from HSE University, the RAS Research Centre for Medical Genetics, and the Moscow State University Institute of Anthropology have examined the impact of the human genotype on the production of trehalase, an enzyme responsible for metabolising 'mushroom sugar'. The researchers examined 1,068 DNA samples collected from inhabitants of northern and Arctic regions of Russia and found that the overall risk of trehalase deficiency in certain indigenous northern populations can be as high as 60–70%. The paper has been published in Problems of Nutrition.
Conserved microRNAs and Flipons Shape Gene Expression
An international team, including researchers of the HSE Faculty of Computer Science, has discovered a new mechanism of gene regulation in which microRNA assumes a central role. These non-coding molecules influence the DNA regions within genes that govern embryonic development. The study contributes to our understanding of the mechanisms underlying the diverse genetic programs found in complex multicellular organisms. The paper has been published in the International Journal of Molecular Sciences.
Research Finds Genes Associated with Most Aggressive Kidney Cancer
HSE researchers have found genes characteristic of the most aggressive subtype of clear cell renal carcinoma. Having studied data on tumour samples from 456 patients, Grigory Puzanov, research fellow at the HSE Faculty of Computer Science International Laboratory of Bioinformatics, identified cancer subtypes associated with either a favourable or unfavourable course of the disease. The paper is published in Scientific Reports.
Microfluidic Chip Used to Test Drug Toxicity
A team including HSE researchers has developed a way to use microfluidic chips to assess the toxic effects of drugs on humans. This device will help identify and minimise the side effects of drugs during the preclinical trial stage and reduce the need for animal experiments. The study is published in Bulletin of Experimental Biology and Medicine.
Hormones Can Help Brain Recover after Injury
An international team of researchers including Alexander Tonevitsky, Professor at HSE’s Faculty of Biology and Biotechnology, found that pituitary hormones may produce different effects on the left and right sides of the body following a traumatic brain injury. These differences can accelerate the development of motor disorders. Researchers are trying to determine whether treatment that blocks the corresponding hormones can counteract these effects. The results of the study were published in the journal eLife.
Researchers Find Therapeutic Targets to Fight SARS-CoV-2
Researchers from HSE University have developed new approaches for regulating the expression of ACE2 and TMPRSS2 enzymes, which play a crucial role in cell infection with SARS-CoV-2. The scholars discovered that small non-coding microRNA (miRNA) molecules are capable of performing a targeted decrease in ACE2 and TMPRSS2. The results of the study have been published in PLOS ONE journal.
Joint Seminar of HSE Faculty of Biology and Biotechnology and George Mason University
First-year undergraduate students of the HSE Faculty of Biology and Biotechnology took part in an online seminar at George Mason University (USA). The seminar was part of the Coronavirus Research Update summer course, taught by Professor Ancha Baranova.