Molecular Biology

ISSN (print): 0026-8984

Media registration certificate: No. 0110239 dated 02/08/1993

Founder: Russian Academy of Sciences

Editor-in-Chief Makarov Alexander Alexandrovich

Number of issues per year: 6

Indexation: RISC, list of Higher Attestation Commissions, CrossRef, White List (level 3), Scopus

"Molekulârnaâ biologiâ" covers a wide scope of problems related to molecular, cell and computational biology including genomics, proteomics, bioinformatics, molecular virology and immunology, molecular development biology, and molecular evolution. Molecular Biology publishes reviews, mini-reviews, experimental and theoretical works, short communications. Annualy, the journal publishes special issues devoted to most rapidly developing branches of physical-chemical biology and to the most outstanding scientists on the occasion of their anniversary birthdays. The authors of the journal are from Russia and other countries of the World.
"Molekulârnaâ biologiâ" is indexed/abstracted in Science Citation Index Expanded (SciSearch), Journal Citation Reports/Science Edition, SCOPUS, Chemical Abstracts Service (CAS), Google Scholar, EBSCO Discovery Service, CSA, CAB International, Academic OneFile, Academic Search, AGRICOLA, Biological Abstracts, Biological and Agricultural Index, BIOSIS, CAB Abstracts, CSA Environmental Sciences, EMBiology, Expanded Academic, Global Health, Health Reference Center Academic, Highbeam, INIS Atomindex, OCLC, OmniFile, Science Select, SCImago, Summon by ProQuest, Zoological Record, Microbiology Abstracts Section B: Health & Safety Science Abstracts, Virology and AIDS Abstracts.

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Vol 59, No 6 (2025)

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ОБЗОРЫ

Recombinase-Based Engineering of Plant Genomes in the Era of Genome Editing
Rozov S.M., Deineko E.V.
Abstract
The rapidly evolving CRISPR/Cas-based genome editing technologies, which have dominated nearly all areas of molecular biology over the past decade, still face several unresolved challenges. One of the major limitations of current genome editing tools is the low efficiency of targeted long-sequence insertions. This issue is particularly critical in plant systems, where genome editing efficiency is hindered by specific cellular characteristics. Site-specific recombinases (SSRs), which have long been employed in genetic engineering to mediate various genomic rearrangements – including deletions, duplications, insertions, and inversions – are limited in their application by the requirement for preexisting recombination recognition sites in the genome. However, CRISPR/Cas and recombinase tools complement each other, and their combined use offers a powerful strategy to overcome key limitations of genome editing. The discovery of CRISPR-associated transposons such as CAST and OMEGA, which naturally utilize their own recombinases, marks a significant advance in genome engineering, providing an elegant example of the natural convergence between CRISPR and recombinase technologies.
Molecular Biology. 2025;59(6):873-890
pages 873-890 views
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Gut microbiota in Colorectal Cancer Carcinogenesis: Evolution of Hypotheses
Glazunova E.V., Kurnosov A.S., Molodtsova P.A., Moskalenko A.M., Makarov V.V., Zlobovskaya O.A.
Abstract
Colorectal cancer remains one of the leading causes of cancer-related mortality, highlighting the importance of optimizing approaches for its early diagnosis and therapy. One promising area in this field is the study of the gut microbiome’s role in the initiation and progression of colorectal cancer. This review examines three main theories explaining the microbiota’s contribution to carcinogenesis: the "Alpha-bug" theory, the "Keystone pathogen" hypothesis, and the "Driver–Passenger" model. The review analyzes data on the mechanisms of microbiota interaction with tumor cells, including inflammation induction, genotoxicity, and disruption of the intestinal barrier function. The review also presents research findings demonstrating that some microorganisms, previously considered markers of late-stage disease, may possess pro-oncogenic properties, refining existing carcinogenesis models. The presented data suggest that the microbiota and its dysbiotic alterations could be considered potential targets for colorectal cancer diagnosis and therapy.
Molecular Biology. 2025;59(6):891–908
pages 891–908 views
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Novel Approaches to anti-EGFR Therapy
Dudkina E.V., Nadyrova A.I., Luginskaya S.A., Kosnyrev A.S., Ulyanova V.V., Ilinskaya O.N.
Abstract
Epidermal growth factor receptor (EGFR) is one of the most studied proteins in the world. A genuine interest in EGFR is related to its key role in the main conserved signalling pathways responsible for cell growth, survival, and proliferation. Dysregulation of these signalling pathways leads to malignant transformation, promotion of tumour progression, cell migration and invasion. In this regard, EGFR is considered as one of the main targets for anticancer drugs development. Despite several generations of novel anti-EGFR drugs have been successfully developed, acquisition of drug resistance, as well as the mutation status of downstream effector protein KRAS, significantly reduce tumour response to the therapy. This review focuses on the current approaches of anti-EGFR therapy. Here, we will describe drugs aimed at blocking EGFR-mediated signalling, such as monoclonal antibodies, tyrosine kinase inhibitors. Mechanisms of acquired resistance to anti-EGFR therapy will be reviewed, and combination treatment strategies will be proposed. Finally, we will discuss promising antitumor agents including immunotoxins and ribonucleases (RNases) of various origins.
Molecular Biology. 2025;59(6):909-927
pages 909-927 views
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ГЕНОМИКА. ТРАНСКРИПТОМИКА

Personalised Pharmacotherapy with Sertraline in Patients with Anxiety—Depressive Disorder Based on Omics Biomarkers
Gareeva A.E., Nasibullin T.R., Pozdnyakov S.A., Borodina L.S., Timerbulatov I.F., Baymeeva N.V., Bagaev D.E., Smirnov V.V.
Abstract
Sertraline, a selective serotonin reuptake inhibitor, is widely used as a first-line drug for anxiety and depressive disorders. Clinical efficacy and adverse reactions observed with antidepressants are closely related to the concentration of the drug in the patient’s blood, but the vast majority of antidepressants demonstrate significant pharmacokinetic variability, leading to pronounced interindividual differences in the steady-state concentration of the drug in the blood and its efficacy even with the same dosing regimen. In this regard, it becomes obvious that genetic markers alone are not enough to obtain the most complete profile of the efficacy and safety of a drug; a combination of genotyping methods with omics biomarkers is necessary. As a result of examination of patients diagnosed with mixed anxiety-depressive disorder (F41.2), residents of the Republic of Bashkortostan, it was found that polymorphic variants rs16947 (CYP2D6*2), rs389209 (CYP2D6*4), rs1065852 (CYP2D6*10) of the CYP2D6 gene do not have a significant effect on the activity of CYP2D6. Genetically determined variations in the activity of the CYP2D6 isoenzyme lead to differences in the metabolism of sertraline and its active metabolite N-desmethylsertraline in different patients, which causes variability in their concentrations in blood plasma. A statistically significant increase in the plasma concentrations of sertraline and N-desmethylsertraline was found in patients carrying slow allelic variants rs3892097, rs1065852, rs16947 of the CYP2D6 gene. A statistically significant moderate inverse correlation was found between the dose and the metabolic ratio C6-HO-THBC/CP. The results obtained are preliminary, which makes it necessary to continue the study with an expanded sample size.
Molecular Biology. 2025;59(6):928-937
pages 928-937 views
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МОЛЕКУЛЯРНАЯ БИОЛОГИЯ КЛЕТКИ

Benzopyran Derivative Improves Synaptic Plasticity, Exploration Interest and Alleviates Amyloidogenesis and Astrogliosis in 5xFAD Mice
Zernov N., Melenteva D.M., Popugaeva E.A.
Abstract
Current Alzheimer’s disease (AD) therapies offer only symptomatic relief and fail to halt disease progression, underscoring the urgent need for novel therapeutic strategies. We have previously shown that selective positive allosteric modulator of TRPC6, benzopyran derivative (C20), exhibits synaptoprotective properties at nanomolar concentrations, restores synaptic plasticity in 5xFAD mice, and enhances hippocampus-dependent memory. Here, we further evaluate the preclinical efficacy and safety of C20, focusing on its effects on chronic toxicity, mutagenicity, amyloidosis, astrogliosis, synaptic plasticity, and behavior in a transgenic AD model. Chronic and acute toxicity studies were performed on female wild type mice. The Ames test was conducted using Salmonella typhimurium and E. coli strains to evaluate the mutagenic potential of C20. 8 months old 5xFAD were used as model of AD. Electrophysiological recordings were applied to study long term potentiation in hippocampal slices of 5xFAD mice following intraperitoneal injections of C20. Behavioral testing included the open field test. Immunohistochemical analyses were performed to quantify amyloid plaques and astrogliosis in the hippocampus. Chronic and acute toxicity studies revealed no significant adverse effects on mice weight and survival, indicating that C20 is well-tolerated at the tested dose. The Ames test confirmed that C20 is almost non-mutagenic. Behavioral testing demonstrated that C20-treated mice exhibited increased exploration in the open field test. Immunohistochemical analyses detected a significant reduction in amyloid plaques and astrogliosis. Our findings suggest that C20 is a safe and effective therapeutic candidate for AD, with the potential to restore synaptic plasticity, improve cognitive function, and reduce pathological hallmarks of the disease.
Molecular Biology. 2025;59(6):938–956
pages 938–956 views
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Effect of the Histone Lysine Methyltransferase G9a Inhibitor on the Lifespan and Radioresistance of Drosophila melanogaster
Timusheva N.S., Shaposhnikov M.V., Proshkina E.N., Moskalev A.A.
Abstract

The enzyme lysine methyltransferase G9a is an important regulator of transcription of various genes and cellular processes, but its role in determining aging and radioresistance of an organism has not been well studied. In this work, the effect of UNC0646, a selective G9a inhibitor, on the lifespan of Drosophila melanogaster and its resistance to γ-radiation and paraquat was investigated. UNC0646 at the concentrations of 0.1–100 μM exerted a geroprotective effect on females, causing an increase in the average lifespan by 1.6–13.9% (p < 0.05). At the same time, after consuming this substance for two weeks, a decrease in Drosophila resistance to γ-radiation was observed. The positive effect of the drug on the lifespan of females may be due to the activation of genes of DNA damage response and repair (D-Gadd45, mei-9, spn-B, Ku80) and proteostasis genes (Hsp27, Hsp68, Atg1, Ire1).

Molecular Biology. 2025;59(6):957–970
pages 957–970 views
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The Role of NOX2-Mediated Oxidative Stress in Initiation of Acute Amyloid Toxicity
Osypov A.A., Mukhina K.A., Lyubanskaya A.D., Nikiforova A.B., Korchagina V.M., Mitkevich V.A., Popova I.Y.
Abstract
Although the role of NADPH oxidase 2 (NOX2) in the development of Alzheimer’s disease (AD) is widely recognized, its contribution to the initial stages of amyloid-induced pathology remains unclear. Intraventricular administration of β-amyloid (Aβ) causes acute amyloid toxicity, leading to neurodegenerative changes similar to AD. The acute phase, lasting several days, is a critical time window for studying early pathological mechanisms. In this work, we assessed the level of oxidative stress in the brain of BALB/c mice at the early stages of amyloid toxicity and the role of NOX2 in these processes. Analysis of key markers of oxidative stress in various fractions of brain homogenate on day 4 after Aβ administration showed that individual parameters demonstrated only a tendency to change, without reaching statistical significance. However, the principal component analysis (PCA) revealed a clear separation between the Aβ-treated and control groups, indicating the need for a comprehensive rather than isolated analysis of biochemical changes at early stages of pathology. It is noteworthy that the centroids of the groups in PCA were located along the same straight line, and the group receiving Aβ together with the NOX2 inhibitor occupied an intermediate position between the control and Aβ groups. This indicates a partial suppression of oxidative stress through NOX2. At the same time, the NOX2 inhibitor completely prevented Aβ-induced microgliosis in the hippocampus, confirming that the concentration used was sufficient to suppress NOX2-dependent microglial activation. The in vivo data demonstrate that oxidative stress induced by Aβ administration may be not entirely mediated by NOX2, although this mechanism plays an important role in the initiation of the pathological process in AD.
Molecular Biology. 2025;59(6):971–978
pages 971–978 views
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Newcastle Disease Virus Vaccine Strain H as a Potential Oncolytic Agent in Ovarian Cancer Therapy
Sarkisova V.A., Karshieva S.S., Makarova A.A., Neymysheva D.O., Chumakov P.M.
Abstract

Ovarian cancer remains one of the most lethal malignancies with a five-year survival rate around 20% at III–IV stages, which determines the urgent need to develop new therapeutic approaches. Newcastle disease virus (NDV) demonstrated considerable promise as an oncolytic agent, capable of selectively lysing tumor cells, suppressing the metastatic potential and stimulating anti-tumor immunity. Despite the established therapeutic potential, studies that investigate oncolytic properties of this virus within the context of ovarian cancer remain limited. In this work, we evaluated oncolytic activity of the NDV vaccine strain H in SC-OV-3, TOV-21G and OV-90 ovarian cancer cell lines. Such parameters as ability to support viral replication and cell viability after infection were investigated. As a result, all three lines were permissive to NDV-H infection. Therapeutic efficacy in vivo was assessed using a model of TOV-21G subcutaneous xenografts in BALB/c nude mice. Upon intravenous administration of the virus, a statistically significant reduction in tumor volume was observed compared to the control group. Based on these results, NDV-H strain can be considered as a potential oncolytic agent for the treatment of ovarian cancer.

Molecular Biology. 2025;59(6):979–987
pages 979–987 views
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Molecular and Genetic Analysis of a Rare Primary Culture of Head and Neck Paraganglioma
Snezhkina A.V., Fedorova M.S., Pavlov V.S., Pudova E.A., Katunina I.V., Kalinin D.V., Kobelyatskaya A.A., Kudryavtseva A.V.
Abstract
Head and neck paragangliomas (HNPGLs) are rare neuroendocrine tumors that originate in the parasympathetic paraganglia of the head and neck. The diagnosis of these tumors is challenging, and the therapeutic options are limited. The study of HNPGLs is fraught with challenges at every stage. One of the main problems is the absence of HNPGL cell lines in cell repositories, which is associated with the difficulty of their culturing and low division rate. In this regard, neither functional nor preclinical studies are available for this category of tumors. This significantly slows down the study of the molecular mechanisms of HNPGL pathogenesis and the development of effective therapeutic approaches. Here, we investigated the molecular genetic characteristics of the primary HNPGL culture were. Using the single-cell RNA sequencing method, expression patterns were analyzed, and cell types were annotated. The results demonstrated that the HNPGL primary culture cells were optimally divided into three clusters, had different degrees of differentiation, expressing neural tissue cell and stem cell markers. Exome sequencing revealed genetic abnormalities in the HNPGL culture, including mutations in the IGSF3, DHH, EXOSC8, SERPINA1, TYR and NQO1 genes, aneuploidy, as well as multiple chromosomal duplications and deletions. These results enhance our knowledge of the molecular genetic features of successfully cultured HNPGL tumor cells.
Molecular Biology. 2025;59(6):988–1001
pages 988–1001 views
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МЕТОДЫ

Comparative Evaluation of DNA Extraction Methods from Fecal Samples: Statistical Analysis of Commercial Kits and Laboratory Protocols Using Real-Time PCR Data
Kurnosov A.S., Linde N.N., Molodtsova P.A., Glazunova E.V., Moskalenko A.M., Sheptulina A.F., Bodunova N.A., Zlobovskaya O.A.
Abstract

Emergence of new data on the association between composition of the intestinal microbiota and various human diseases have generated increasing interest in its investigation. In this context, selection of the DNA extraction method represents a critical stage in experimental design, significantly affecting the reliability and reproducibility of results. This study presents a comparative analysis of 12 DNA extraction methods applied to 46 fecal samples, including 9 commercial kits and 3 laboratory protocols. We evaluated taxonomic representation, including Gram-positive (Lactobacillaceae, Coprococcus spp., Streptococcus sp., Clostridium leptum) and Gram-negative bacteria (Enterobacteriaceae, Akkermansia muciniphila, Fusobacterium nucleatum, Bacteroides fragilis). Extraction efficiency was assessed by DNA yield, expressed in GE/μL of eluate or in GE/g of feces, as well as by the frequency of low-abundance taxa loss. Based on the lysis type, clustering of methods was demonstrated: mechanical lysis provided stable and high DNA yields, particularly for Gram-positive bacteria, while chemical and enzymatic methods showed lower efficiency. We determined that lysis type and preliminary whole-fecal sample preparation are the key factors affecting DNA extraction efficiency and preservation of the native taxonomic profile. The best results were demonstrated by the QIAamp® PowerFecal® Pro DNA Kit (Qiagen) and the combination of AmpliTest UniProb + AmpliTest RIBO-prep kits (Centre for Strategic Planning, of the Federal medical and biological agency, Russia), both of which outperformed other methods in terms of DNA yield. The QIAamp® Fast DNA Stool Mini Kit (Qiagen) showed minimal losses of low-abundance taxa. These findings can be used for the standardization of extraction methodologies and the development of domestic protocols.

Molecular Biology. 2025;59(6):1002-1021
pages 1002-1021 views
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Simultaneous Incorporation of Different Cy5-Labeled Deoxypyrimidine Nucleotides into the Synthesized DNA Chain
Monakova P.M., Shershov V.E., Surzhikov S.A., Grechishnikova I.V., Lapa S.A., Chudinov A.V.
Abstract
In PCR with Taq polymerase on the Staphylococcus aureus genomic DNA template, the substrate properties of eight fluorescently labeled deoxyuridine and deoxycytidine triphosphates (Cy5-dUTP and Cy5-dCTP), which are dU-dC pairs with similar cyanine substituents, was compared during simultaneous introduction of the such pairs in PCR. The different Cy5-dUTP and Cy5-dCTP pairs differed from each other in that each of them had substituents with different linker lengths between the nitrogenous base and the fluorophore, as well as the linker lengths between the quaternary ammonium group and the second heterocycle of the Cy5 fluorophore. The amplification efficiency, as well as the yield of the product, and the density of label incorporation were determined. It was found that with the simultaneous introduction of Cy5-modified dU and dC into the reaction at equimolar concentrations, the inhibitory effect was not directly proportional to the concentration, in contrast to that with separate (individual) introduction of fluorescently labeled dNTPs. This allows one to use the simultaneous introduction of Cy5-modified dU and dC into PCR to increase sensitivity in methods based on the detection of a fluorescent signal, for example, in DNA-microarray technology.
Molecular Biology. 2025;59(6):1022-1028
pages 1022-1028 views
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