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Volume 90, Nº 5 (2025)

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Articles

Hypercellular proinflammatory microenvironment inhibits etoposide-induced DNA damage in acute monocytic leukemia cells

Kobyakova M., Krasnov K., Krestinina O., Baburina Y., Senotov A., Lomovskaya Y., Meshcheryakova E., Lomovsky A., Zvyagina A., Pyatina K., Fadeeva I., Fadeev R.

Resumo

The emergence of resistance in acute monocytic leukemia (AML-M5) cells to the action of antitumor agents is one of the main reasons for the extremely low survival and curability of patients with diagnosed AML-M5. It is well known that AML cells have an “inflammatory” phenotype and form a unique pro-inflammatory microenvironment. Previously, we identified an increase in the resistance of THP-1 human AML-M5 cells to the action of DNA topoisomerase I and II inhibitors (topotecan, etoposide, doxorubicin) in an in vitro model simulating the conditions of the pro-inflammatory microenvironment – a three-dimensional long-term high-density cell culture. In this research, we investigated the mechanisms of this phenomenon using fluorescence microscopy and spectrophotometry, the DNA comet method, western blot analysis, differential gene expression analysis, and flow cytometry. The results showed that an increase in resistance to the action of DNA topoisomerase inhibitors, in particular etoposide, in THP-1 AML-M5 cells in a hypercellular proinflammatory microenvironment is realized by reducing the accumulation of single- and double-stranded DNA breaks and, accordingly, the response to DNA damage. It may also be due to the pronounced activation of the signaling pathways of interferon types 1 and 2, NF-κB/STAT-dependent signaling pathways, occurring against the background of a significant suppression of the activity of transcription factors of the Myc and E2F families. The results of this work open up new ideas about the role of pro-inflammatory activation in increasing the resistance of AML cells to death induced by the action of DNA topoisomerase inhibitors.

Biohimiâ. 2025;90(5):595-610
pages 595-610 views

Differential expression of circular RNAs in the frontal cortex of rats under ischemia-reperfusion conditions

Mozgovoy I., Shpetko Y., Denisova A., Stavchansky V., Vinogradina M., Gubsky L., Dergunova L., Limborska S., Filippenkov I.

Resumo

Circular RNAs (circRNAs) are covalently closed non-coding RNAs that have increased metabolic stability and are capable of regulating gene expression. CircRNAs are considered as potential biomarkers and therapeutic targets for various diseases, including ischemic stroke. The transient right middle cerebral artery occlusion (tMCAO) model is actively used in stroke transcriptomics. In this study, we used whole-genome RNA sequencing to study the circRNA expression profile in the frontal cortex of rat brain 24 h after tMCAO. We identified 64 differentially expressed circRNAs (Fold change >1.5; Padj <0.05), which predominantly increased their levels compared to sham-operated animals. According to MRI data, the studied frontal cortex region included the penumbra zone, cell survival in which is important for stroke recovery. Also, using our previously obtained data on differential mRNA expression in this brain region, we bioinformatically predicted mRNA–miRNA–circRNA regulatory networks. Functional analysis of these networks showed that genes whose expression may depend on circRNA activity during ischemia are responsible for synaptic signaling and inflammatory response. Our study shows a significant role of circRNA-mediated transcriptome regulation in the penumbra-associated brain region during ischemia and allows us to consider circRNAs as potential targets for new strategies for the treatment of stroke and post-stroke complications.

Biohimiâ. 2025;90(5):611-626
pages 611-626 views

FOS promoter is overactive outside of genome context and weakly regulated by changes in the Na+i/K+i ratio

Gorbunov A., Fedorov D., Kvitko O., Lopina O., Klimanova E.

Resumo

Changes in the Na+ and K+ intracellular concentrations affect expression of the FOS gene. Here, we obtained a genetic construct coding for the TurboGFP-dest1 protein under control of the human FOS promoter (−549 to +155) and studied its expression in HEK293T cells exposed to monovalent metal cations. Amplification of the FOS promoter sequence from genomic DNA was efficient only in the presence of Li+ ions. Incubation of cells with ouabain or in a medium containing Li+ ions instead of Na+ ions caused intracellular accumulation of Na+ and Li+ ions, respectively. In addition, both stimuli increased the levels of endogenous FOS mRNA and the average fluorescence intensity of TurboGFP-dest1 in transfected cells. The mRNA levels of TurboGFP-dest1 were significantly higher than the FOS mRNA levels and were little affected by the stimuli.

Biohimiâ. 2025;90(5):627-635
pages 627-635 views

Method of multiplex immune profiling of mouse blood cells with highly sensitive detection of reporter β-galactosidase LacZ

Mihailovskaya V., Bogdanova D., Demidov O., Rybtsov S.

Resumo

Bacterial β-galactosidase (LacZ) has been widely used as a reporter in the creation of mouse lines to study gene expression. However, LacZ reporters have limitations related to the presence of endogenous β-galactosidase in cells, as well as the low sensitivity and penetrating ability of existing substrates to detect LacZ activity. Multicolor flow cytometry analysis of gene expression in living cells requires precise, sensitive, non-toxic fluorescent indicators. In this study, we evaluated the effectiveness of the immobilized SPiDER-βGal fluorescent probe for LacZ detection in main populations of blood cells of reporter mice by multicolored flow cytometry. The results showed that SPiDER-βGal was highly sensitive to LacZ, but it also detected endogenous β-galactosidase. Myeloid cells had the highest background activity. Application of the proton pump inhibitor Bafilomycin A1 elevates lysosomal pH and increases the resolution of LacZ detection in leukocyte populations by suppressing background endogenous β-galactosidase activity. Extending the incubation with the SPiDER-βGal to 60 minutes improved the sensitivity of the method tenfold. Thus, the use of specific inhibitors of lysosomal proton transport increases the resolution of LacZ activity analysis in reporter animals for multi-channel sorting of LacZ-expressing live leukocytes in the context of surface markers for further functional and genetic studies of blood populations.

Biohimiâ. 2025;90(5):636-644
pages 636-644 views

Assessing the diversity of the human ig repertoire after B cell cryopreservation and restimulation

Smirnova A., Ovchinnikova L., Mamedov I., Grigoreva T., Khazeev S., Akhmedova M., Lomakin Y.

Resumo

Cryopreservation of human B cells is widely employed in various clinical and research applications. However, it is still commonly believed that only freshly isolated B cells should be utilized for subsequent analyses to accurately evaluate the natural immunoglobulin (Ig) repertoire in both quantitative and qualitative dimensions. In this study, we use next-generation sequencing to investigate how the Ig repertoire reshapes after the cryopreservation of B cells. Our focus centers on examining the proportional representation of the Ig repertoire after freeze-thawing, both with and without subsequent restimulation. Our research findings encourage scientists to conduct experiments on the Ig repertoire using cryopreserved, patient-derived B cells, underscoring the potential clinical and experimental applications of monitoring the Ig repertoire with cryopreserved B cells.

Biohimiâ. 2025;90(5):645-655
pages 645-655 views

Accelerated proteomic sample preparation for accurate ultrafast mass spectrometry-based quantitative analysis of cell and tissue proteomes

Emekeeva D., Kusainova T., Garibova L., Shelepchikov A., Kononikhin A., Tretyakov V., Lavrukhina O., Nikolaev E., Gorshkov M., Tarasova I.

Resumo

Advances in liquid chromatography/mass spectrometry (LC-MS) have enabled proteome-wide quantitation in minutes, achieving rate of 1000 analyses per day. This necessitates revisiting the rapid sample preparation approaches to match this data acquisition speed. Despite the fact that these approaches have been developed decades ago, their application in quantitative ultrafast proteomics and comprehensive comparison of their performance under different conditions have not been explored. In this study, the ultrasound, microwave irradiation, and elevated temperature-assisted approaches for accelerated protein reduction, alkylation, and trypsin digestion were compared. Validation was carried out with label-free quantitative LC-MS/MS and fragmentation-free DirectMS1 methods of shotgun proteome analyses of Saccharomyces cerevisiae, human cell lines, and winter wheat shoots. These data acquisition methods were applied in ultrafast implementations employing 5 to 16 min LC gradients. Human–yeast proteome mixtures were used as standards to evaluate quantitation accuracy of the sample preparation workflows. Our findings indicate that the reduced time of sample preparation insignificantly decreased efficiency of reduction, alkylation, and digestion, yet, preserved reproducible peptide and protein identification. We also found that the 30-min microwave-assisted and overnight trypsin digestion yielded comparable quantitation accuracy in ultrafast analyses using DirectMS1 method.

Biohimiâ. 2025;90(5):656-672
pages 656-672 views

Glycerol kinase overexpression supresses lipid synthesis but enlarges mitochondrial membrane potential and thermogenesis activity in adipocytes

Michurina S., Beloglazova I., Agareva M., Mohammad R., Alekseeva N., Parfyonova E., Stafeev I.

Resumo

Obesity and type 2 diabetes mellitus are among the main factors contributing to the increase in mortality and disability in the modern world. Therefore, it is a priority to develop new methods, including genetic and cellular engineering, to create ectopic thermogenic fat depots capable of dissipating excess energy. In this study, we overexpressed glycerol kinase (GK), a key enzyme of the futile triacylglyceride cycle (TAG cycle) to generate thermogenic adipocytes. The protein-coding sequence of GK was amplified from mouse liver mRNA and delivered to adipocytes by lentiviral transduction. Adipocyte metabolism was analyzed by radioisotope monitoring of [3H]- and [14C]-labelled glucose analogues. Mitochondrial membrane potential, thermogenesis and lipid droplet morphology were assessed using fluorescent probes JC-1, ERthermAC and BODIPY493/503, respectively. Lentiviral delivery of the GK gene increases mRNA expression 130-fold and protein levels by 30% in adipocytes. GK overexpression enhances glucose uptake by adipocytes and suppresses fatty acids synthesis and re-esterification without altering lipid droplet morphology. The increase in glucose uptake upon GK overexpression is associated with an increase in mitochondrial potential and stimulation of thermogenesis. GK overexpression improves the metabolic profile of adipocytes, which may contribute to the elimination of metabolic disorders associated with obesity by increasing the utilization of excess glucose during thermogenesis. Nevertheless, the detailed mechanisms underlying the stimulation of these processes require further investigation.

Biohimiâ. 2025;90(5):673-687
pages 673-687 views