Biochemistry
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
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Vol 90, No 6 (2025)
Articles
OT REDAKTsII GENETIChESKIE TEKhNOLOGII V MEDITsINE, SEL'SKOM KhOZYaYSTVE I BIOTEKhNOLOGII
Biochemistry. 2025;90(6):693-694
693-694
THE ROLE OF m6A-RNA METHYLATION IN BLADDER CANCER DEVELOPMENT, PROGRESSION, AND TREATMENT RESPONSE
Abstract
Bladder cancer (BCa) remains a significant clinical challenge, characterized by high recurrence rates and variable responses to immunotherapy and chemotherapy. Recent studies have highlighted the role of N6-methyladenosine (m6A) RNA modification in regulating various cellular processes, including tumor progression and drug resistance. This review examines the impact of m6A methylation on BCa pathogenesis, with a particular focus on the role of m6A pathway factors and m6A-modi-fied RNAs in tumorigenesis, proliferation, invasion and migration processes. Moreover, mechanisms of m6A-mediated chemotherapeutic resistance in BCa cells are evaluated, including single nucleotide polymorphisms in m6A-associated patterns. Significant advances in high-throughput analysis of m6A methylation enabled development of novel m6A-based biomarkers for risk assessment and early diagnosis of BCa, prediction of cancer relapse, and treatment response. In this manuscript, the prospects of m6A-based molecular diagnostics in BCa are outlined.
Biochemistry. 2025;90(6):695-719
695-719
DIAGNOSTIC AND PROGNOSTIC POTENTIAL OF CIRCULATING microRNAS miR-1301-3p, miR-106A-5p, miR-129-5p, miR-3613-3p, miR-647 IN GASTRIC CANCER
Abstract
Gastric cancer (GC) is one of the most common malignant tumors worldwide and ranks fifth in the structure of cancer mortality. MicroRNAs are involved in the pathogenesis and progression of GC as epigenetic factors, and are considered as potential noninvasive markers. We selected microRNAs involved in the regulation of epigenetic mechanisms in GC (miR-1301-3p, miR-106a-5p, miR-129-5p, miR-3613-3p, miR-647) and analyzed their expression in plasma of GC patients. To assess their diagnostic and prognostic potential, we estimated correlations of differential expression with the clinical and pathological characteristics of GC tumors. The study included 65 plasma samples from GC patients and 48 plasma samples obtained from individuals without tumor lesions, which were used as a control group. The expression was analyzed by using the reverse transcription polymerase chain reaction (RT-PCR) method. When comparing the expression levels of selected microRNAs in the plasma of GC patients and the control group, significant differences were found for miR-1301-3p (p = 0.04), miR-106a-5p (p = 0.029), miR-129-5p (p < 0.0001), miR-647 (p < 0.0001). MiR-129-5p expression was significantly associated with the prevalence of a primary tumor (p = 0.002), with the development of metastases to regional lymph nodes (p = 0.003) and distant metastases (p = 0.003), as well as a late clinical stage (p = 0.003). There was a significant correlation between miR-3613-3p expression and the clinical stage of GC (p = 0.049). ROC analysis revealed that combining miR-106a-5p, miR-129-5p, miR-1301-3p and miR-647 improves the diagnostic and prognostic properties of a potential panel of markers.
Biochemistry. 2025;90(6):720-732
720-732
TRANSCRIPTIONAL BIOMARKERS IN DIAGNOSTICS OF GENETIC DISEASES: POSSIBILITIES, PROBLEMS AND PROSPECTS OF APPLICATION
Abstract
Quantitative analysis of gene transcription is widely used in various fields of biology, and in medicine it is used for diagnostics and profiling of genetic diseases. Recently, transcriptome studies using large-scale next-generation sequencing have become very popular. Transcriptome studies allow us to establish which cellular processes are active at a given time, to identify transcriptome dynamics in various tissues or conditions, for example, during ontogenesis or physiological adaptation, and to identify differentially expressed genes in case of disease. A significant change in the transcription level of one or more genes in a pathological condition may be sufficient for diagnosis, that is, it can serve as a transcriptional biomarker of the disease. However, in some cases, a change in the transcription level can be an indicator of mutations, including those leading to splicing disorders, transcriptional activity of mobile elements and pseudogenes. The review considers cases in which the transcription level may be useful for identifying the genetic causes of a disease, and discusses the issues that should be taken into account when using transcription as a diagnostic marker. In the future, it can be expected that specialized target panels based on transcription analysis will be used not only as a diagnostic and prognostic tool, but also as a predictor of structural abnormalities in the genome, which will contribute to the development of new effective strategies for the treatment of genetic diseases.
Biochemistry. 2025;90(6):733-751
733-751
TELOMERE LENGTH AND TELOMERASE ACTIVITY AS BIOMARKERS FOR DIAGNOSTICS AND PROGNOSIS OF PATHOLOGICAL DISORDERS
Abstract
Telomere biology research remains a hot topic. Analysis of several thousand clinical samples from healthy individuals performed in recent years has shown that the telomere length (TL) of peripheral blood leukocytes correlates with the TL of human internal organ cells and reflects their condition, decreases under the influence of damaging factors and can serve as an indicator of health status. A decrease in TL leads to proliferation arrest and is considered as an indicator of replicative aging of proliferating cells, and a decrease in TL of peripheral blood leukocytes is considered as an indicator of aging. Novel fundamental research data enabled to formulate the concepts about the role of the enzyme CST-Polymerase alpha/primase in the complementary C-strand synthesis after completion of the 3‘G overhang synthesis by telomerase during telomere replication. The discovery of telomeric TERRA RNA and its role in the regulation of telomerase activity (TA) and alternative lengthening of telomeres, as well as the possibility of TERRA translation, provided evidence of the complex epigenetic regulation of TL maintenance. The published data analysis allows concluding that telomeres are dynamic structures and that TL undergoes significant changes under the influence of damaging factors and is determined not only by the chronological age, but by the total effect of exposure to all exogenous and endogenous damaging factors during the life. An inheritable decrease in TL due to mutations in the genes of proteins that determine the telomere structure and participate in the telomere replication, primarily the proteins of the shelterin complex, the CST complex and telomerase, has been found in a number of hereditary diseases - telomeropathies. Analysis of TL and TA is of great importance for the diagnosis of telomeropathies and may be useful in cancer diagnostics, and analysis of TL - for monitoring the health status, including exposure to ionizing radiation and space flight factors, together with the prediction of individual sensitivity to the action of damaging factors of different nature. The modern advanced genetic technologies for the analysis of TL and TA are available for use in clinical and epidemiological studies, are actively used in the telomeropathies diagnostics and astronauts’ health monitoring, and continue to improve.
Biochemistry. 2025;90(6):752-780
752-780
SELECTION OF UTRs IN mRNA-BASED GENE THERAPY AND VACCINES
Abstract
The untranslated regions (UTRs) of messenger RNAs (mRNAs) play a crucial role in regulating translational efficiency, stability, and tissue-specific expression. The review describes various applications and challenges of UTR design in the development of gene therapy and mRNA-based therapeutics. UTRs affect critical biological functions, such as mRNA stability, modulation of protein synthesis, and attenuation of immune response. Incorporating tissue-specific microRNA (miRNA)-binding sites into 3‘ UTRs might improve precise targeting of transgene expression and minimize off-target effects. Nucleotide modifications (pseudouridine, N1-methyladenosine, and N4-acetylcytidine) in mRNA and UTRs in particular, improve mRNA stability and translational efficiency. At the same time, several challenges remain, such as lack of consensus on UTRs best suited for certain biomedical applications. Current efforts are focused on integrating high-throughput screening, computational modeling, and experimental validation to refine UTR-based therapeutic strategies. The review presents current information on the design of UTRs and their role in therapeutic applications, with special focus on the possibilities and limitations of existing approaches.
Biochemistry. 2025;90(6):781-811
781-811
MULTIEPITOPE mRNA VACCINE mRNA-mEp21-FL-IDT PROVIDES EFFECTIVE PROTECTION AGAINST M. tuberculosis
Abstract
Tuberculosis is a leading bacterial infection in terms of lethality. The development of new tuberculosis vaccines may reduce the number of new cases and deaths from it. One of the most promising areas of vaccination is represented by mRNA vaccines, which have already proven their high effectiveness against COVID-19 and other viral infections. In our study, we developed four new multiepitope mRNA antituberculosis vaccines by modern immunoinformatic methods; the vaccines differ from each other in sequences of encoded adjuvants and codon composition. Their immunogenicity and protectivity were tested in experiments on mice. Most of the developed mRNA vaccines have led to the formation of both cellular and humoral immunity. Meanwhile, the adaptive response was stronger in the case of vaccines with adjuvant RpfE. Nonetheless, the best protective response was elicited by the mRNA-mEp21-FL-IDT vaccine (with adjuvant FL), which decreased mycobacterial load in the lungs after infection of mice with M. tuberculosis and increased animal survival. Altogether, our results indicate that the mRNA-mEp21-FL-IDT vaccine, developed by mRNA immu-noinformatic methods, provides effective protection comparable to that seen after BCG vaccination.
Biochemistry. 2025;90(6):812-832
812-832
THE SELECTION OF OPTIMAL pegRNAs TO ENHANCE THE EFFICIENCY OF PRIME EDITING IN AT-RICH GENOME REGIONS
Abstract
Prime editing is a highly promising strategy for treating hereditary disorders due to its superior efficiency and safety profile compared to conventional CRISPR-Cas9 systems. This study is dedicated to development of a causal therapy for cystic fibrosis by targeting the F508del variant in the CFTR gene using prime editing, as this specific deletion accounts for a substantial proportion of cystic fibrosis cases. While prime editing has shown remarkable precision in introducing targeted genetic modifications, its application in AT-rich genomic regions, such as the one containing the F508del variant, remains challenging. To overcome this limitation, we systematically evaluated 24 pegRNAs designed for two distinct prime editing systems, PEmax and PE2-NG. The correction efficiency of the F508del variant reached 2.81% in basal lung cells from homozygous F508del patients, without normalization for transfection efficiency. However, the average transfection efficiency was only 11.9%, emphasizing the critical need for advancements in delivery methodologies. These findings highlight the potential of prime editing as a therapeutic approach for cystic fibrosis, while also underscoring the necessity for further optimization of both editing constructs and delivery vectors to achieve clinically relevant correction levels.
Biochemistry. 2025;90(6):833-846
833-846
PROGRESS IN CRISPR/Cas13-MEDIATED SUPPRESSION OF INFLUENZA A AND SARS-CoV-2 VIRUS INFECTION IN in vitro AND in vivo MODELS
Abstract
The worldwide number of deaths from complications caused by severe influenza and COVID-19 is about 1 million cases annually. The development of effective antiviral therapy strategies for the disease treatment is one of the most important tasks. The use of the CRISPR/Cas13 system, which specifically degrades viral RNA and significantly reduces the titer of the virus, can be a solution of this problem. Despite the recent discovery, Cas13 nucleases have already shown their high efficiency in suppressing viral transcripts in cell cultures. Recent advances in mRNA technology and improvements in non-viral delivery systems have made it possible to effectively use CRISPR/Cas13 in animal models as well. In this review, we have analyzed the experimental in vitro and in vivo studies on the use of CRISPR/Cas13 systems as antiviral agent in cell cultures and animals and discussed the main directions for improving the CRISPR/Cas13 system. These data allow us to understand the prospects and limitations of further use of CRISPR/Cas13 in the treatment of viral diseases.
Biochemistry. 2025;90(6):847-866
847-866
BIOTECHNOLOGIES OF PLANT RESISTANCE TO VIRUSES: CRISPR-Cas OR RNA INTERFERENCE
Abstract
Recently developed genetic technologies of gene editing (CRISPR-Cas) and RNA interference (RNAi) have already led to significant progress in almost all areas of life sciences, including biotechnology and medicine, and are now becoming increasingly popular in plant biology. In this review, we describe the basic principles of these two technologies and methods of their application on model plants and crops for the control of viral diseases. Examples of the antiviral effect of these technologies aimed at direct suppression of viral genomes of DNA and RNA-containing viruses, as well as suppression of the activity of host plant genes that increase susceptibility to viruses, are provided. The review contains a detailed comparison of the effectiveness of RNAi and CRISPR-Cas in protecting plants from viruses. The advantages and disadvantages of these technologies as well as the factors limiting their use in practice and ways to overcome them are discussed in detail.
Biochemistry. 2025;90(6):867-883
867-883
DESIGNING A THERMOSTABLE MINI-INTEIN FOR INTEIN-MEDIATED PURIFICATION OF RECOMBINANT PROTEINS AND PEPTIDES
Abstract
This paper reports design of a thermostable temperature-activated mini-intein based on the full-length intein DnaE1 from Thermus thermophilus HB27 (TthDnaE1). We performed rational design of three mini-inteins TthDnaE1 Δ272, Δ280 and Δ287 through deletion mutations in the full-length intein sequence. Two mini-inteins (Δ272 and Δ280) were capable of efficient protein splicing at temperatures above 50°C. The most active mini-intein with the Δ280 deletion was chosen as the basis for further design of a self-cleaving carrier of affinity tags through single-point mutagenesis. We performed the C1A, D405G and C1A/D405G mutations, which were proposed to eliminate the intein’s capability of N-terminal extein cleavage and extein ligation. As a result, the mini-intein Δ280 with double mutation C1A/D405G displayed the highest efficiency of C-terminal extein cleavage at its temperature optimum around 60°C. Thus, we constructed thermostable temperature-activated mini-inteins capable of efficient protein splicing or cleavage of C-terminal extein. The engineered TthDnaE1 Δ280 C1A/D405G mini-intein can serve as basis for the development of new expression system for intein-mediated production of pharmaceutical recombinant proteins and peptides.
Biochemistry. 2025;90(6):884-895
884-895