Biohimiâ

ISSN (print)0320-9725

Media registration certificate: ПИ № ФС77–71478 от 23.11.2017

Founder:  Russian Academy of Sciences

Editor-in-Chief: Dontsova Olga Anatolyevna, academician of the Russian Academy of Sciences, Professor, Doctor of Chemical Sciences

Number of issues per year: 12

Indexation:

Current Issue

Open Access Open Access  Restricted Access Access granted  Restricted Access Subscription Access

Vol 90, No 2 (2025)

Cover Page

Full Issue

Open Access Open Access
Restricted Access Access granted
Restricted Access Subscription Access

Articles

Memory T cells: research experience of original models with transgenic T-cell receptors
Kazansky D.B., Kalinina A.A., Khromykh L.M.
Abstract

This paper summarizes the experience of research conducted on original mouse models developed in the Laboratory of Regulatory Mechanisms in Immunity at the Carcinogenesis Institute of the N.N. Blokhin National Research Institute of Oncology of the Ministry of Health of the Russian Federation. The transgenesis of individual α- and β-chains of T-cell receptors (TCR) of memory cells led to the production of animal lines valuable for studies of T-lymphocyte homeostasis and patterns of formation of their activation marker profiles. The obtained models revealed new features of immune selection and tumor progression. With their help, a fundamental property of some TCRs, recently called chain centricity, was confirmed, which implies the functional dominance of one of the TCR chains during recognition of the MHC/peptide complex. This property allows to form significant pool of antigen-specific T cells, which can be used for the adoptive immunotherapy of oncological and infectious diseases. Transgenesis of dominant active TCR α-chains provides opportunities for the creation of organisms with innate specific immunological resistance to certain pathogens. The results of recent works indicate that TCR, by determining the relationship of the T-lymphocyte with its MHC microenvironment, has an instructive role in the formation of its functions and phenotype. One of these functions may be the production of cyclophilin A by cortisone-resistant memory cells localized in the thymus. There is accumulating evidence that expression of a TCR with a certain structure and specificity is a sufficient condition for the formation of the functional potential of memory cells in a T cell, regardless of the history of its interaction with antigenic MHC/peptide complexes.

Biohimiâ. 2025;90(2):175-188
pages 175-188 views
Selective labeling techniques of molecules and subcellular structures for cryo-electron tomography
Kazakov E.P., Kireev I.I., Golyshev S.A.
Abstract

Electron microscopy is one of the most effective methods for studying the fine structure of the cells with a resolution thousands of times higher than that of the visible light microscopy. The most advanced implementation of biological electron microscopy is EM tomography of samples stabilized by freezing without water crystallization (cryoET). By circumventing the drawbacks of chemical fixation and dehydration, this technique allows the investigation of cellular structures in three dimensions at molecular level, down to resolving the individual proteins and their sub-domains. However, the problem of effective identification and localization of the object of interest has not yet been solved, thus limiting the range of targets to easily recognizable or abundant subcellular components. Labeling techniques provide the only way for locating the subject of investigation in microscopic images. CryoET imposes conflicting demands on the labeling system. These requirements can be succinctly stated as the need to introduce particles, composed of substances, foreign to the cellular chemistry, into a living cell, conjugate it to the molecule of interest without disrupting its vital functions and the gross physiology of the cell. This review examines both the established and promising methods for selectively labeling of proteins and subcellular structures, enabling their localization in cryoET images.

Biohimiâ. 2025;90(2):189-206
pages 189-206 views
Mechanisms of glucocorticoid resistance in non-classic T helper populations Th17.1/ex-Th17
Kuklina E.M.
Abstract

The non-classical population of Th17 lymphocytes polarized toward Th1 (Th17.1/ex-Th17) is currently the focus of research attention. Possessing an unique pro-inflammatory potential and the ability to overcome histohematic barriers, these cells play a key role in the pathogenesis of many inflammatory diseases, primarily autoimmune ones: they prevail in autoimmune lesions and are considered as a promising therapeutic target for these pathologies. At the same time, recent studies have shown another distinctive feature of Th1-polarized Th17 – selective resistance to glucocorticoids. Since glucocorticoids are first-line drugs in the treatment of exacerbations in autoimmune diseases, understanding the causes of this phenomenon is fundamentally important for predicting patients’ response to therapy and for improving the effectiveness of such therapy. In this paper, we analyze the mechanisms of drug resistance formation in Th17 cells polarized toward Th1, compare them with similar processes in non-pathogenic, classical Th17, and discuss the role of such resistance in the response to glucocorticoid therapy.

Biohimiâ. 2025;90(2):207-220
pages 207-220 views
Tumor spheroids, tumor organoids, tumor explants, and tumoroids: what are the differences between them?
Durymanov M.O.
Abstract

Three-dimensional (3D) cell cultures that mimic tumor microenvironment have become an essential tool in cancer research and drug response analysis, significantly enhancing our understanding of tumor biology and advancing personalized medicine. Currently, the most widely mentioned 3D multicellular culture models include spheroids, organoids, tumor explants, and tumoroids. These 3D structures, exploited for various applications, are generated from cancer and non-cancer cells of different origin using multiple techniques. However, despite extensive research and numerous studies, consistent definitions of these 3D culture models are not clearly established. The manuscript provides a comprehensive overview of these models, detailing brief history of their research, unique biological characteristics, advantages, limitations, and specific applications.

Biohimiâ. 2025;90(2):221-236
pages 221-236 views
Direct neural reprogramming in situ: effectiveness of existing approaches and their possible optimizations
Dokukin N.V., Chudakova D.A., Shkap M.O., Kovalchuk A.M., Kibirsky P.D., Baklaushev V.P.
Abstract

Direct neuronal reprogramming (transdifferentiation) in situ of glial cells-astrocytes and microglia-has attracted a substantial interest as a potential approach for the treatment of a wide range of neurodegenerative diseases and injuries of the central nervous system (CNS). The nervous system of higher mammals has a very limited capacity for repair. Disruption of CNS functions due to traumatic injuries or neurodegenerative processes can significantly affect quality of life of patients, leading to mobility- and cognitive impairments, resulting in disability and in some cases death. Restoration of lost neurons in situ, based on direct reprogramming of glial cells without an intermediate stage of pluripotency, appears to be the most attractive approach from the point of view of translational biomedicine. The ability of astroglia to highly proliferate in response to the damage of neural tissue supports the view that these cells, already present at the lesion site and neuronal-like, are good candidates for transdifferentiation into neurons, especially because many independent authors have already shown the possibility of direct neuronal reprogramming of astrocytes in vitro and in vivo. Overexpression of proneuronal transcription factors (TFs), such as NeuroD1-4, NeuroG2, Ascl1, Dlx2, including pioneer factors capable of recognizing target sequences in “closed” chromatin and activating transcription of “silent” genes, has already proven to be a potential therapeutic strategy. Furthermore, blocking the action of PTB and REST TFs via microRNAs, using small molecules or various biomaterials are also utilized for neuronal reprogramming. However, the efficiency of direct in situ reprogramming is limited by a number of factors, including the cell-specificity of the transgene delivery systems, the cell-specificity of promoters in the genetically engineered constructs used for transgene delivery, the brain region in which transdifferentiation occurs, factors affecting the changes of cell metabolism, the influence of microenvironment, etc. Reprogramming in situ, where a large number of cell types are present, requires monitoring and precise phenotypic characterization of subpopulations of cells undergoing transdifferentiation, confirming the fact of reprogramming of astroglia into neurons and their subsequent integration into the CNS. Here, we review and summarize the most effective strategies of neuronal reprogramming, ways to visualize the transdifferentiation process, and also focus on the existing obstacles to effective neuronal conversion and possible approaches to overcome them.

Biohimiâ. 2025;90(2):237-257
pages 237-257 views
Evolution, possibilities and prospects in the application of methods for the assessment of pyridine nucleotides pool for studying the mechanisms of brain plasticity in normal and pathological conditions
Zubova A.V., Groshkov A.A., Berdnikov A.K., Novikova S.V., Rozanova N.A., Nikolaeva L.V., Salmin V.V., Kolotyeva N.A., Khaspekov L.G., Salmina A.B., Yurchenko S.O., Illarioshkin S.N.
Abstract

Nicotinamide adenine dinucleotide and its derivatives – NAD+, NADP+, NADH, NADPH – play an important role in cell metabolism, act as substrates or cofactors for a large number of enzymes involved in the regulation of replication, DNA repair, maintenance of calcium homeostasis in cells, biosynthetic processes and energy production mechanisms. Changes in the ratio of oxidized and reduced forms of pyridine nucleotides accompanies the development of oxidative and reductive stress, that significantly contribute to cell damage and induction of adaptive response. Currently, huge number of protocols aimed at quantitative or qualitative assessment of the pyridine nucleotide pool are in use, but all of them have their limitations associated with sample preparation processes, difficulties in the metabolite spectrum assessment, and complexity of data interpretation. Measuring pyridine nucleotide levels is relevant in the study of (patho)physiological regulatory mechanisms of cell functional activity and intercellular communication. This is of particular relevance when studying the mechanisms of plasticity of the central nervous system in health and disease, since significant changes in the pools of pyridine nucleotides in cells are evident in neurodevelopmental disorders, neurodegeneration, and aging. Simple and reliable non-invasive methods for measuring the levels of NAD+ and NADH are necessary to assess the brain cells metabolism with diagnostic and research purposes. The goal of this review is to analyze in a comparative aspect the main methods for measuring the levels of oxidized and reduced pyridine nucleotides in cells and to identify the key principles of their application for the correct interpretation of the data obtained, including those used for the study of the central nervous system.

Biohimiâ. 2025;90(2):258-274
pages 258-274 views
Differential expression of hsa-miR-134, hsa-miR-155, hsa-miR-122 as biomarkers of epileptogenesis in patients with acute cerebral injury
Vasilieva A.A., Timechko E.E., Paramonova A.I., Yakimov A.M., Lysova K.D., Severina M.I., Dmitrenko D.V.
Abstract

It is difficult to predict the process of occurrence of an epileptogenic focus in patients who have suffered acute cerebral damage. The aim of our study is to investigate and describe the possibility of using microRNAs as biomarkers of epileptogenesis. Objective of our work was to evaluate expression of hsa-miR-134-5p, hsa-miR-155-5p, and has-miR-122-5p in different groups of patients. Quantitative comparison of relative concentrations of the studied microRNAs in the blood plasma of three groups of patients was carried out: Group I – patients with temporal lobe epilepsy; Group II – patients with potential epileptogenic injuries; Group III – control group. The study showed increased expression of hsa-miR-134-5p in patients with temporal lobe epilepsy, which confirms the published data on its involvement in the mechanisms of epileptogenesis. Hsa-miR-155-5p was overexpressed in the Group II in comparison with other groups, the data indicate involvement in the mechanisms of inflammation, which could indirectly affect occurrence of epilepsy. Hsa-miR-122-5p was overexpressed in two study groups, but the levels were higher in the group of patients with acute cerebral injuries. The obtained results allow us to propose has-miR-122-5p as a potential biomarker of epileptogenesis.

Biohimiâ. 2025;90(2):275-287
pages 275-287 views
Inhibitors of transketolase from Mycobacterium tuberculosis targeted towards both the diphosphate binding site and an adjacent hydrophobic subsite
Nilov D.K., Gushchina I.V., Shcherbakova T.A., Baldin S.M., Švedas V.K.
Abstract

Transketolase from Mycobacterium tuberculosis (mbTK) is involved in the pentose phosphate pathway essential for bacterial survival and thus constitutes an attractive target for the antituberculosis therapy. We found a new class of active site-targeted furan sulfonate inhibitors of mbTK that are capable of binding to both the thiamine diphosphate cofactor subsite and adjacent hydrophobic subsite Ile211-Leu402-Phe464, thereby suppressing enzyme activity. The most potent compound identified by computer screening, STK106769, was found to inhibit mbTK with IC50 of 7 µM and suppress the growth of M. tuberculosis H37Rv strain. The hydrophobic subsite Ile211-Leu402-Phe464 of mbTK is substituted by significantly more polar residues in homologous human TK, which is an important factor determining the selectivity of binding of TK inhibitors.

Biohimiâ. 2025;90(2):288-293
pages 288-293 views
Alteration of the JNK signaling pathway in the hippocampus associated with age and development of AD-like pathology, and impact of IQ-1S
Muraleva N.A., Zhdankina A.A., Khlebnikov A.I., Kolosova N.G.
Abstract

Alzheimer’s disease (AD) is a multifactorial neurodegenerative disorder that is the leading cause of senile dementia. Age is a key risk factor for the most common (>95%) sporadic form of AD; there are no effective methods for its prevention or treatment. Growing evidence indicates that the development of AD and other neurodegenerative diseases is associated with activation of mitogen-activated protein kinase pathways, and the JNK signaling pathway is considered a potential target for the prevention and treatment of AD, although information on changes in its activity during ontogenesis is extremely limited. The aim of this study was to compare age-related changes in the activity of the JNK signaling pathway in the hippocampus of Wistar rats and OXYS rats, which spontaneously develop all the key features of AD, and to evaluate the effect of a selective JNK3 inhibitor [sodium salt of 11H-indeno[1,2-b]quinoxalin-11-one oxime (IQ-1S)]. The ability of IQ-1S to suppress accelerated aging of the OXYS rat brain has been proven previously, but its effect on JNK activity has not been studied. In the present study, we showed that with age, the activity of the JNK signaling pathway increases in the hippocampus of rats of both lines. At the same time, the manifestation and active progression of AD signs in OXYS rats occur against the background of increased, compared to Wistar rats, phosphorylation of the key kinase of this signaling pathway – JNK3 and its target proteins, which allows us to consider JNK3 as a potential target for interventions aimed at preventing neurodegenerative processes. This is also supported by the fact that the neuroprotective effect of the selective JNK3 inhibitor IQ-1S, which we previously identified, and its ability to suppress the development of neurodegenerative processes in OXYS rats, is associated with a decrease in the level of phosphorylation of JNK3, c-Jun, APP and Tau in the hippocampus.

Biohimiâ. 2025;90(2):294-305
pages 294-305 views
Molecular biomarkers of neurodegeneration in amyotrophic lateral sclerosis
Shevchuk D.V., Tukhvatulin A.I., Dzharullaeva A.S., Berdalina I.A., Zakharova M.N.
Abstract

Amyotrophic lateral sclerosis (ALS) is the most prevalent motor neuron disease. However, definitive diagnosis can be delayed by up to 12 months due to the lack of specific and sensitive biomarkers for ALS. In our study, conducted for the first time on a large cohort of ALS patients (n = 100) within the Russian population, we assessed key biomarkers of neurodegenerative pathology, including β-amyloids (Aβ40 and Aβ42) and tau proteins (Tau-total and Tau-p181), as well as other pathogenetically relevant, promising biomarkers such as FGF-21, Kallikrein-6 (KLK-6), NCAM-1, Neurogranin (NRGN), TDP-43, Apolipoprotein E4, Clusterin (Apo J), Complement Factor H, Fetuin-A, α2-Macroglobulin, Apo AI, Apo CIII, Apo E, Complement C3, GDNF, sRAGE, and S100B protein. Significant differences between ALS patients and the control group were observed for Aβ40 (p = 0.044), Aβ42 (p < 0.001), FGF-21 (p < 0.001), Tau-total (p = 0.001), Tau-pT181 (p = 0.014), Clusterin (p < 0.001), Complement C3 (p = 0.001), and S100B (p = 0.024). A significant direct correlation was found between ALSFRS-R score and the concentrations of Aβ40 and Aβ42. Alterations in the complement system (Complement C3 and Complement Factor H) were identified, highlighting the critical role of neuroinflammatory processes in ALS pathogenesis. Additionally, increased levels of FGF-21 were observed in patients with the bulbar onset of ALS. The significant elevation in concentration of the chaperone protein clusterin in patients with rapid disease progression suggests its potential as a prognostic biomarker for motor neuron disease. Furthermore, its role in maintaining proteostasis could provide novel therapeutic targets for intervention.

Biohimiâ. 2025;90(2):306-320
pages 306-320 views
Induction of fibroblast-to-myofibroblast differentiation by alteration of cytoplasmic actin ratio
Levuschkina Y.G., Dugina V.B., Shagieva G.S., Boichuk S.V., Eremin I.I., Khromova N.V., Kopnin P.B.
Abstract

Myofibroblasts, which play a crucial role in the tumour microenvironment, represent a promising avenue for research in the field of oncotherapy. This study investigates the potential for induced differentiation of human fibroblasts into myofibroblasts through the downregulation of the γ-cytoplasmic actin (γ-CYA), which was achieved by RNA interference. A decrease in γ-CYA expression in human subcutaneous fibroblasts resulted in the upregulation of myofibroblast markers, including α-smooth muscle actin (α-SMA), ED-A FN, and type III collagen. These changes were accompanied by notable alterations in cellular morphology, characterised by a significant increase in cell area and formation of pronounced supermature focal adhesions. The downregulation of γ-CYA resulted in a compensatory increase in the expression of β-cytoplasmic actin and α-SMA, and the formation of characteristic α-SMA-positive stress fibers. In conclusion, our results demonstrate that a reduction in γ-CYA expression leads to myofibroblastic trans-differentiation of human subcutaneous fibroblasts.

Biohimiâ. 2025;90(2):321-331
pages 321-331 views

Согласие на обработку персональных данных с помощью сервиса «Яндекс.Метрика»

1. Я (далее – «Пользователь» или «Субъект персональных данных»), осуществляя использование сайта https://journals.rcsi.science/ (далее – «Сайт»), подтверждая свою полную дееспособность даю согласие на обработку персональных данных с использованием средств автоматизации Оператору - федеральному государственному бюджетному учреждению «Российский центр научной информации» (РЦНИ), далее – «Оператор», расположенному по адресу: 119991, г. Москва, Ленинский просп., д.32А, со следующими условиями.

2. Категории обрабатываемых данных: файлы «cookies» (куки-файлы). Файлы «cookie» – это небольшой текстовый файл, который веб-сервер может хранить в браузере Пользователя. Данные файлы веб-сервер загружает на устройство Пользователя при посещении им Сайта. При каждом следующем посещении Пользователем Сайта «cookie» файлы отправляются на Сайт Оператора. Данные файлы позволяют Сайту распознавать устройство Пользователя. Содержимое такого файла может как относиться, так и не относиться к персональным данным, в зависимости от того, содержит ли такой файл персональные данные или содержит обезличенные технические данные.

3. Цель обработки персональных данных: анализ пользовательской активности с помощью сервиса «Яндекс.Метрика».

4. Категории субъектов персональных данных: все Пользователи Сайта, которые дали согласие на обработку файлов «cookie».

5. Способы обработки: сбор, запись, систематизация, накопление, хранение, уточнение (обновление, изменение), извлечение, использование, передача (доступ, предоставление), блокирование, удаление, уничтожение персональных данных.

6. Срок обработки и хранения: до получения от Субъекта персональных данных требования о прекращении обработки/отзыва согласия.

7. Способ отзыва: заявление об отзыве в письменном виде путём его направления на адрес электронной почты Оператора: info@rcsi.science или путем письменного обращения по юридическому адресу: 119991, г. Москва, Ленинский просп., д.32А

8. Субъект персональных данных вправе запретить своему оборудованию прием этих данных или ограничить прием этих данных. При отказе от получения таких данных или при ограничении приема данных некоторые функции Сайта могут работать некорректно. Субъект персональных данных обязуется сам настроить свое оборудование таким способом, чтобы оно обеспечивало адекватный его желаниям режим работы и уровень защиты данных файлов «cookie», Оператор не предоставляет технологических и правовых консультаций на темы подобного характера.

9. Порядок уничтожения персональных данных при достижении цели их обработки или при наступлении иных законных оснований определяется Оператором в соответствии с законодательством Российской Федерации.

10. Я согласен/согласна квалифицировать в качестве своей простой электронной подписи под настоящим Согласием и под Политикой обработки персональных данных выполнение мною следующего действия на сайте: https://journals.rcsi.science/ нажатие мною на интерфейсе с текстом: «Сайт использует сервис «Яндекс.Метрика» (который использует файлы «cookie») на элемент с текстом «Принять и продолжить».