Cellular senescence is characterized by irreversible cell-cycle arrest, with cells remaining viable and metabolically active. This state features a proinflammatory senescence-associated secretory phenotype (SASP) that can harm neighboring tissues. Accumulation of senescent cells accelerates age-related physiological decline and associated pathologies. Furthermore, cellular senescence is implicated in various physiological processes, including embryonic development, wound healing, tumor progression, and immune response regulation. The complexity of the aging process arises from its diverse underlying mechanisms, potential reversibility, and intrinsic heterogeneity. Experimental gerontology focuses on identifying pathogenic modulators that regulate the formation and accumulation of senescent cells, as well as investigating their impact on tissue function. Within the field of experimental gerontology, considerable attention is devoted to identifying pathogenic modulators that regulate the formation and accumulation of senescent cells, as well as to investigating their impact on tissue function. Of particular interest is the characterization of novel molecular mechanisms that govern cellular aging. Key pathogenic molecular pathways include the p53-dependent senescence pathway, the p16INK4a/pRb pathway, and non-canonical pathways like IFIH1-MAVS, which contribute to oxidative stress, DNA damage, activation of SASP, and other cellular dysfunction. This study critically examines how viral and bacterial agents induce cellular senescence, particularly in vitro, reviewing the regulatory mechanisms involved. It discusses genetic variants affecting infection susceptibility and categorizes senescence markers. Investigating the molecular mechanisms underlying cellular aging presents promising avenues for the development of targeted and effective therapeutic interventions. Such strategies may include the selective induction of senescence in cancer cells, suppression of senescence to mitigate age-related diseases, or the comprehensive modulation of aging processes to optimize clinical outcomes.

Telomeres are specialized nucleoprotein complexes at the physical ends of linear chromosomes of most eukaryotes that represent a key structural element in genome stability regulation. One of the most important characteristics determining the protective capacity of telomeres is telomere length (TL). In Arabidopsis thaliana, telomere length varies among ecotypes, which may be considered as an adaptive mechanism to various environmental and stress conditions, including phytopathogenic infections. However, the mechanisms of TL regulation under biotic stress remain unclear. Here, we show the results of our study of the TL changes in A. thaliana plants under the Pseudomonas syringae pv. tomato DC3000 infection. In the study, we used natural ecotypes Col-0 (medium telomere length) and Sf-2 (long telomeres), as well as mutant plant lines with disordered and wild-type telomere length phenotypes, oli5- 2^–/– and nop2c-2^–/–, respectively. It was found that susceptibility to the phytopathogen varies in plants: the line with short telomeres, oli5-2^–/–, showed the highest sensitivity compared to the WT and nop2c-2^–/–. Sf-2 plants possessed the highest resistance to the infection. Significant shortening of TL on the third day after infection was found on the short arm of chromosome 4 of infected nop2c-2^–/– plants, whereas TL of infected oli5-2^–/– plants slightly decreased on the third day and increased on the seventh day after infection. The most resistant line Sf-2 retained TL on the third and seventh days after infection but significantly lost it on the 18th day. So, it was shown for the first time that phytopathogenic infection affects telomere length in plants, which opens a new direction in the study of plant telomere regulation under biotic stress. 

Karyotypes of seven Picea species distributed across Eurasia and East Asia were analyzed using fluorescence in situ hybridization (FISH) and DAPI fluorescent staining. For P. meyeri and P. purpurea, the 5S and 45S rDNA sites were mapped here for the first time, while karyotypes of P. abies, P. obovata, P. schrenkiana, P. crassifolia, and P. omorika were examined from new locations. All the species studied had a similar distribution of 5S rDNA loci on both arms of the large metacentric chromosome III: a more intense signal was observed in the middle of the long arm, partially overlapping with the 45S rDNA signal, and a minor 5S rDNA site was localized terminally on the short arm. The distribution of 5S rDNA loci varied in the karyotypes of the studied species: from 7 to 9 pairs of chromosomes carried 45S rDNA signals of varying intensity. Strong (major) signals were localized intercalarily and coincided with persistent secondary constrictions. Their number per haploid genome was as follows: 8 in P. omorika, 6 in P. abies and P. obovata, and 5 in P. schrenkiana, P. crassifolia, P. purpurea, and P. meyeri. We also detected several minor 45S rDNA sites on the Picea chromosomes that had not been previously described in the literature. Supernumerary (B) chromosomes found in some seedlings of P. obovata, P. meyeri, and P. purpurea did not carry 45S and 5S rDNA loci. Intensely fluorescent DAPI-positive bands were observed in the intercalary regions of the spruce chromosomes, and the centromere regions of certain chromosomes were also stained. Several constant DAPI-positive blocks were identified on chromosomes I, III, and X, with similar locations across all studied species. Fluorescence in situ hybridization with 45S and 5S rDNA probes in combination with DAPI staining allowed us to identify virtually all homologous chromosomes and compare karyotypes of different species. The intra- and interspecific karyotypic diversity in the genus Picea is discussed considering the distribution of 5S and 45S rDNA loci and DAPI signals.

The variability of nucleotide sequences of complete mitochondrial genomes in the Shors, a Turkic-speaking people from the Altai–Sayan region, was studied. The Shors exhibit a high level of nucleotide diversity due to the presence of two components of the East and West Eurasian origin in their gene pool (79.5 and 20.5 %, respectively). However, a relatively low level of mtDNA haplotype diversity was found among the Shors, which is associated with the high prevalence of certain identical mitochondrial haplotypes. Multidimensional scaling of interpopulation genetic distances indicates that the Shors fall in between East Asian ethnic groups and indigenous East Siberian peoples. By examining the polymorphism of whole mitochondrial genomes in individuals with the same hypervariable segment 1 haplotype belonging to haplogroup F1b1, found in ~37 % of the Shors, we identified six mtDNA haplotypes belonging to haplogroups F1b1-b1 and F1b1-b2. Phylogeographic analysis shows that the Shor mitochondrial gene pool is characterized by a high frequency (65.9 %) of mtDNA haplogroups found solely in the Altai–Sayan region: A-a1c1a, B4b1a3a1a, C4a1a4a1a, C4e, C5c*, D4b1a2a1a, D4m2a2, D5c1a2b, F1b1-b1, F1b1-b2, F2b1b1, and H8b1a. According to molecular dating results, the evolutionary age of these mtDNA haplogroups varies from 0.9 to 5.0 thousand years. All of the mtDNA haplogroups listed are of East Asian origin, except for the West Eurasian H8b1a. The isolated evolution of mitochondrial haplogroups specific to the peoples of the Altai–Sayan region is assumed to have been facilitated by their isolation from East Asian neighbors. This isolation occurred during the Bronze Age, when the Afanasyevo culture formed as a result of the mixing of indigenous populations and migrants – representatives of the Yamnaya culture, which existed in the Urals and Volga regions. In the absence of a significant influx of additional East Asian mtDNA haplotypes to the populations of the Altai–Sayan region over several thousand years, it appears that existing genetic lineages of East Asian origin diversified.

X-chromosomal STR markers (X-STR) are informative tools for kinship reconstruction, particularly in cases  where standard autosomal panels have limited discriminatory power: when reconstructing kinship between full sisters, paternal half-sisters, paternal grandmother and granddaughter, maternal aunt and niece. However, the use of X-STR markers in forensic genetics requires consideration of linkage disequilibrium structure and the use of haplotype frequencies in calculating the likelihood ratio (LR). In this work, the genetic structure of Forest and Tundra Nenets populations was assessed using 16 X-STR markers in order to obtain reference values. A sample of 504 Nenets males was analyzed, divided into subethnic groups (Forest and Tundra Nenets), phratries of Tundra Nenets (Haryuchi and Vanuito), as well as geographical local groups (individuals living in the Antipayutinskaya, Gydan and Nakhodka tundras). No statistically significant differences were found between the samples, and the pairwise Fst values (exact test) did not exceed 0.01. The Nenets population demonstrated an intermediate level of genetic diversity typical of Indigenous  Siberian populations. The loci DXS8377 (He = 0.910) and DXS10079 (He = 0.839) were found to be the most polymorphic in the Nenets population. Of the 16 markers, 13 were highly informative (PIC > 0.5). The combined power of exclusion (CPE) was 0.99996, which indicates that the panel is highly informative for reconstructing kinship relationships. Pairwise analysis of linkage disequilibrium (LD) revealed statistically significant deviations for 46 pairs of markers out of 120; however, the r² coefficient for all pairs of alleles did not exceed 0.09, which indicates a weak correlation between alleles. This study provides the reference data of allele and genotype frequencies recommended for use in assessing the likelihood ratio in the reconstruction of kinship relationships. The obtained reference data will contribute to improving the reliability and efficiency of forensic genetic analyses in the Russian Federation. 

The Phanagoria settlement, located on the Taman Peninsula, is a unique archaeological site. The history of the ancient city spans approximately 15 centuries, making Phanagoria a witness to many historical events, including those related to the early history of the Old Rus’ state. The early medieval period of Phanagoria’s history is of particular interest due to its insufficient study. The Phanagoria Expedition of the Institute of Archaeology of the Russian Academy of Sciences, in collaboration with the Phanagoria Museum-Reserve, studied the city’s cultural strata from the 7th–10th centuries. This period of the urban center’s existence is closely linked to the history of the Khazar Khaganate and culminates in the city’s destruction as a result of an enemy attack. During excavations, skeletal remains bearing signs of violent death were discovered. Anthropological analysis revealed Mongoloid features of the individuals discovered. This paper presents the results of a bioinformatics-based analysis of whole-genome sequences from the remains of three individuals from  a Khazar cultural layer. Radiocarbon dating was performed for two individuals. High mitochondrial DNA coverage  (43- to 96-fold) confirmed its low level of contamination, and determined the mitochondrial chromosome haplogroup. High genome coverage confirmed the authenticity of the analyzed ancient DNA and allowed the determination of the individuals’ sex and Y-chromosome haplogroup. Population analysis was performed using PCA, ancestral component analysis, using ADMIXTURE, and allele frequency correlation analysis, using the f3 statistic. Whole-genome data analysis of the three samples demonstrated the genetic proximity of the studied individuals to the modern Turkic-speaking population of Central Asia, as well as to early medieval nomadic groups of the Eurasian steppe, Hungarian Avars, and Mongols. Principal component analysis revealed the presence of Asian and European genetic components in the genomes of the studied samples. Our study suggests that the genetic profile of the individuals studied was formed by the mixing of the gene pools of people from the eastern regions of the Eurasian Steppe and populations of Western Eurasia. The Asian components are related to those of medieval groups of Mongols and Avars.

Rapid progress in both molecular diagnostics tools and targeted therapy for cystic fibrosis (CF) requires clear understanding of CFTR mutation spectrum in population constantly living in any large region of any country. There are still no published results of comprehensive genetic study of CF patients from the Yugra region (Western Siberian part of Russia). Three-step molecular genetic approach was used for gDNA samples derived from a group of 54 CF patients living in the Yugra region: (1) AFLP/RFLP was used for the panel of 35 major CFTR mutations; (2) NGS, for full sequencing of exons and exon-intron boundaries of CFTR gene; and (3) the MLPA technique, to search for large gene rearrangements. The search of major CFTR mutations in multiethnic Yugra population accounted for only 76.6 % of all CF-causing mutations. Most common were variants F508del (rs113993960), 1677delTA (rs121908776), CFTRdele2,3, E92K (rs121908751), R1066C (rs78194216). Genomic DNA samples from 19 CF patients from the tested group in which only one mutant allele was identified were analyzed by the NGS approach followed by MLPA. This allowed to reveal 19 rare pathogenic CFTR variants, including five new variants absent in CF mutation databases. Generally, three-tier molecular genetics approach applied for the first time for a Yugra-originated cohort of CF patients allowed to find 12 missense mutations, 9 nonsense ones, 6 in/dels, 4 splice-site variants, 1 CNV. Three alleles remained unidentified. Deciphering the genetic background for CF patients living in Yugra allowed to support rational administration of CFTR modulators with profound clinical effect. The need to develop a region-specific testing panel for common CFTR mutations is demonstrated.

Bronchial asthma (BA) is a heterogeneous disease, the development of which is determined by a complex interaction of genetic factors and environmental factors. Despite significant progress in understanding the molecular mechanisms of the disease, population-specific genetic characteristics, especially in multi-ethnic regions of Russia, remain understudied. The relevance of this study is determined by the need to identify ethnicity-specific genetic markers to improve approaches for personalized prediction of the risk of developing BA and its severity. The aim of the work was to conduct a comparative analysis of haplotypic combinations in the IL13 (rs20541, rs1800925, rs1295686) and ADAM33 (rs2280090, rs2787094, rs44707) genes between ethnic groups to identify potential population-specific genetic markers at BA-associated loci. The study involved 524 adolescents aged 12 to 18 years from Krasnoyarsk, Kyzyl and Abakan with verified ethnicity (Slavs – 293, Tuvans – 158, Khakass – 73). DNA was isolated from saliva samples followed by genotyping of polymorphic loci of the IL13 (rs20541, rs1800925, rs1295686) and ADAM33 (rs2280090, rs2787094, rs44707) genes using real-time PCR. It was found that rare variants of IL13 polymorphisms were more common in Russians than in Tuvans and the Khakass. The ATC haplotype of IL13 is 2–3 times more common among the Khakass and Tuvans than in Russians. In the Russian population, the GAC haplotype of the ADAM33 gene, containing rare alleles of all the polymorphisms studied, is detected significantly more often. The data obtained emphasize the relevance of haplotype analysis and the importance of taking into account ethnogeographical features when assessing the genetic risks of BA.

It is known that the pathogenesis of common diseases (CDs) is determined by a complex and nonlinear interaction of genetic predisposition, epigenetic modifications, and environmental factors. However, in addition to inherited genetic variants, somatic mutations play a key role in the pathological phenotype, shaping cell-type-specific genetic landscapes and influencing regional predisposition of target organs, age of onset, and variability in clinical manifestations. Thus, according to current concepts, CDs develop as a result of the combined influence of inherited germline variants and somatic mutations acquired during life, the interaction of which is realized through cell-specific molecular networks. Therefore, this review sequentially examines the main factors, classical and modern models of complex pathological phenotypes, as well as the achievements and prospects of analyzing inherited genetic variants in relation to CDs. The role of somatic mutations in the development of pathology is discussed using the example of atherosclerosis ontogenesis and the concept of atherooncology through the assessment of somatic genomic variability in smooth muscle cells of atherosclerotic plaques, where the sequential accumulation of “driver” mutations confers a selective advantage and triggers clonal evolution in the tissue microenvironment. Special attention is given to the concept of “paradominant” inheritance – a special form of nonMendelian transmission of complex traits that combines inherited predisposition and somatic mutations that arise early in ontogenesis. Based on an analysis of current data, we propose an integrative hypothesis postulating that inherited genetic variants form a body-wide predisposition to CDs, while somatic mutations, arising and selectively increasing in specific cellular compartments of target organs, are critical events explaining the regional specificity, temporal dynamics (age of onset), and variability in the severity of the clinical phenotype. A new paradigm for predictive medicine for CDs is based on a comprehensive characterization of the continuum of genetic variants (inherited and somatic), an analysis of their interactions with cell-specific molecular networks, and a transition from population-based risk assessments to causal models of individual pathogenesis.

Familial hypercholesterolemia (FH) is an autosomal codominant disorder characterized by impaired clearance of low-density lipoproteins from the bloodstream, markedly elevated plasma total cholesterol and low density lipoprotein cholesterol levels, and early onset of atherosclerosis and cardiovascular disease. FH is one of the most common monogenic disorders in humans. The majority of FH cases are caused by pathogenic variants in three genes: LDLR (OMIM: 143890), APOB (OMIM: 107730), and PCSK9 (OMIM: 607786). More than 80 % of FH cases are associated with mutations in the LDLR gene, located on chromosome 19. In 25–75 % of patients with a clinical FH phenotype, no pathogenic variant is identified in these genes. Whole-exome sequencing and targeted gene panel sequencing of the LDLR, APOB, PCSK9, and LDLRAP1 genes were performed in patients with an FH phenotype, followed by confirmation of the identified variants by Sanger sequencing. Three unrelated probands were found to carry intronic LDLR variants for which functional evidence was previously unavailable. The aim of this study was to functionally assess in vitro the effects of three intronic LDLR variants (NM_000527.5: c.940+3_940+6del, c.941-3C>G, and c.2389+5G>A) on pre-mRNA splicing using a minigene assay. Minigene constructs encompassing target exons with flanking intronic sequences were generated and transfected into the HEK293 and HeLa cell lines. The deleterious effect of all three variants on pre-mRNA splicing was confirmed. The fournucleotide deletion c.940+3_940+6del resulted in two aberrant transcripts: inclusion of six nucleotides from intron 6 and complete retention of the minigene intronic sequence. The c.941-3C>G variant caused loss of the canonical acceptor splice site and activation of a cryptic site, with inclusion of intronic nucleotides from intron 6. The c.2389+5G>A variant resulted in exon 16 skipping. Functional in vitro analysis is a key tool for the molecular verification of intronic variants of uncertain clinical significance and, in conjunction with clinical data, supports the establishment of a definitive molecular diagnosis.

Pathogenic variants in the SLC26A4 gene (solute carrier family 26, member 4) are a common cause of inherited hearing loss. The SLC26A4 gene encodes the transmembrane protein pendrin, a member of the SLC26 anion transporter family, with predominant expression in the inner ear, thyroid, and kidney tissues. Pathogenic SLC26A4 variants cause nonsyndromic recessive hearing loss (DFNB4) and Pendred syndrome (sensorineural hearing loss and thyroid dysfunction). In many studies analyzing the SLC26A4 gene, along with patients who have two recessive pathogenic SLC26A4 variants (M2 patients) and an accurate molecular genetic diagnosis can be made, a group of patients with only one pathogenic SLC26A4 variant (M1 patients) is often identified, which creates a diagnostic problem. The presence of M1 patients may reflect copy number variations (CNVs, deletions/duplications) in the SLC26A4 gene that are not detected by routine diagnostic methods. The aim of the study is to search for deletions/duplications in the SLC26A4 gene using the MLPA (Multiplex Ligation-dependent Probe Amplification) method in thirteen patients belonging to the indigenous people of the Tyva Republic (Southern Siberia), in whom only one pathogenic SLC26A4 variant (M1 patients) was identified during the study of the etiology of hereditary hearing loss. As a result of MLPA analysis and molecular cloning in DNA samples of three M1 patients from two related Tuvinian families, a novel variant was revealed – tandem duplication of twelve nucleotides (c.1185_1196dup) in exon 10 of the SLC26A4 gene. This variant is an in-frame insertion resulting in the inclusion of four additional amino acid residues Gly-Phe-Phe-Ser (p.(Gly396_Ser399dup)) in a highly conserved region of the pendrin protein. Most predictive programs predict the damaging effect of the c.1185_1196dup variant on the structure and function of the pendrin protein. The pathogenicity of the c.1185_1196dup variant is supported by its segregation with hearing pathology in the pedigree of patients in whom it was found in a compound heterozygous state with pathogenic SLC26A4 variants, as well as its absence in a control sample of Tuvinians and in the world genomic databases. Functional in vitro studies are needed to confirm the potentially deleterious effects of the novel c.1185_1196dup (p.(Gly396_Ser399dup)) variant and its association with hearing pathology. 

Age-related macular degeneration (AMD) is a progressive disease that leads to blindness and is the cause of visual impairment in an aging population. Apolipoprotein E (ApoE) is one of the key proteins in lipoprotein metabolism. ApoE is expressed in the retina and is found in drusen in AMD patients. ApoE isoforms are significant genetic determinants of AMD risk (ε2 > ε3 > ε4), wherein the effects of APOE alleles vary by ethnic group. APOE genotype may also influence response to treatment. Here we examine the effect of APOE alleles on the risk of neovascular AMD and response to anti-VEGF treatment in patients from the population of Western Siberia. Genotyping of the rs429358 and rs7412 polymorphisms of the APOE gene was carried out in patients with neovascular AMD (n = 315) and the control group (n = 317) using allele-specific PCR. To assess the association of APOE alleles with treatment response, 275 patients were categorized into three groups of treatment response (good, weak, no response) after three loading injections of aflibercept. We revealed a significant association between the ε2 allele and neovascular AMD: carriers of ε2 had a 1.5- fold higher risk of AMD compared with carriers of other allelic variants (OR = 1.536; 95% CI: 1.075–2.195). The results indicate a moderate association of the ε2 allele with the development of neovascular AMD in the Russian population. However, no association was found between APOE genotype and short-term response to anti-VEGF therapy. 

RNA interference is an evolutionarily conserved mechanism of post-transcriptional gene expression regulation present in all living organisms. It is highly relevant to multiple areas of molecular medicine, including diagnostics and novel immunomodulatory approaches. Recent studies have increasingly highlighted the role of extracellular vesicles and their cargo in parasite-host interactions. The trematode Opisthorchis felineus, which parasitizes the human biliary tract, causes opisthorchiasis, a disease associated with chronic inflammation and other hepatobiliary injuries. The long-term survival of the parasite is likely linked to modulation of host immune response. Nevertheless, the mechanism by which liver fluke vesicles affect human immune cells remains unclear. The aim of this study was to identify potential human gene targets of tRNA-derived small RNAs and to assess their enrichment among differentially expressed genes (DEGs) in the transcriptome of THP-1 human monocytes. Target prediction for eight most abundant O. felineus tRNA fragments identified 1,299 potential target genes in human monocytes. Seven cDNA libraries prepared from THP-1 monocytes  before and after treatment with vesicles from adult O. felineus were sequenced using paired-end 2 × 150 bp sequencing (DNBseq, BGI), yielding 43.8 million reads per library. Among 1484 DEGs, 159 predicted targets of tRNA-derived small RNAs showed significant expression changes upon vesicle treatment. These genes were associated with pathways involved in cell-cycle regulation and cell death, including DNA integrity control (M16357), G1/S transition (M2074), apoptosis (M15303), and programmed cell death (M27436), as well as immune-related pathways, including the monocyte pathway (M4956), mononuclear macrophage differentiation (M25144), MHC-I antigen presentation (M1066), and proteasomemediated antigen processing (M1070). These findings suggests that O. felineus tRNA-derived small RNAs may contribute to the regulation of these processes in human monocytes.