The placenta has a unique hypomethylated genome. Due to this feature of the placenta, there is a potential possibility of using regulatory elements derived from retroviruses and retrotransposons, which are suppressed by DNA methylation in the adult body. In addition, there is an abnormal increase in the level of methylation of the LINE-1 retrotransposon in the chorionic trophoblast in spontaneous abortions with both normal karyotype and aneuploidy on different chromosomes, which may be associated with impaired gene transcription using LINE-1 regulatory elements. To date, 988 genes that can be expressed from alternative LINE-1 promoters have been identified. Using the STRING tool, genes (NUP153 and YWHAB) were selected, the products of which have significant functional relationships with proteins highly expressed in the placenta and involved in trophoblast differentiation. This study aimed to analyze the expression of the NUP153 and YWHAB genes, highly active in the placenta, from canonical and alternative LINE-1 promoters in the germinal part of the placenta of spontaneous and induced abortions. Gene expression analysis was performed using real-time PCR in chorionic villi and extraembryonic mesoderm of induced abortions (n = 10), adult lymphocytes (n = 10), spontaneous abortions with normal karyotype (n = 10), and with the most frequent aneuploidies in the first trimester of pregnancy (trisomy 16 (n = 8) and monosomy X (n = 6)). The LINE-1 methylation index was assessed in the chorionic villi of spontaneous abortions using targeted bisulfite massive parallel sequencing. The level of expression of both genes from canonical promoters was higher in blood lymphocytes than in placental tissues (p < 0.05). However, the expression level of the NUP153 gene from the alternative LINE-1 promoter was 17 times higher in chorionic villi and 23 times higher in extraembryonic mesoderm than in lymphocytes (p < 0.05). The expression level of NUP153 and YWHAB from canonical promoters was higher in the group of spontaneous abortions with monosomy X compared to all other groups (p < 0.05). The LINE-1 methylation index negatively correlated with the level of gene expression from both canonical (NUP153 – R = –0.59, YWHAB – R = –0.52, p < 0.05) and alternative LINE-1 promoters (NUP153 – R = –0.46, YWHAB – R = –0.66, p < 0.05). Thus, the observed increase in the LINE-1 methylation index in the placenta of spontaneous abortions is associated with the level of expression of the NUP153 and YWHAB genes not only from alternative but also from canonical promoters, which can subsequently lead to negative consequences for normal embryogenesis.

Relevance. Abnormal epigenetic regulation of genes responsible for the development of the embryo and placenta is associated with many pregnancy pathologies. Aim. The aim of this work was to analyze the prevalence of abnormal methylation of the PRDM16 and PTPRN2 genes in chorionic villi of spontaneous abortions with normal karyotype and with the most frequent aneuploidies (trisomy 16 and monosomy X). Materials and Methods. The methylation profile was evaluated using targeted bisulfite massive parallel sequencing in chorionic villi of induced abortions (n = 10), spontaneous abortions with normal karyotype (n = 39), trisomy 16 (n = 17) and monosomy X (n = 20) and peripheral blood lymphocytes of healthy volunteers (n = 6). Results and Discussion. In analyzed genes, differential methylation of individual CpG sites was found in chorionic villi of spontaneous abortions. Despite the absence of significant differences between the groups in the average level of methylation in analyzed gene regions, abnormal methylation of the PRDM16 and PTPRN2 genes were detected for 33 % and 5 % of spontaneous abortions, respectively, indicating a high incidence of epigenetic abnormalities in these genes in the chorionic villi of spontaneous abortions. The level of methylation of the PRDM16 gene significantly correlated with the level of methylation of the retrotransposon LINE-1, which indicates the generalized nature of methylation disorders in spontaneous abortions. Finally, the level of methylation of the PTPRN2 gene depended on the age of mothers of spontaneous abortions with monosomy X, which raises the question of the influence of maternal factors on the methylation profile in this group of spontaneous abortions. Conclusion. The results indicate that epigenetic disorders of the PRDM16 gene may be associated with spontaneous termination of pregnancy in the first trimester.

Background. DNA methylation regulates numerous biological processes, mediating normal development. Alterations in methylation patterns are associated with multiple pathological conditions like hereditary diseases and cancer, making them valuable clinical biomarkers for patient stratification, disease monitoring, early diagnosis, and prediction of response to therapy. Highly targeted, high-throughput methodologies focusing on critical genomic loci enable precise identification of distinct methylation signatures. the aim of the study was to analyze and summarize literature data describing the use of high-throughput DNA methylation analysis technologies, including those based on targeted approaches. Material and Methods . A systematic analysis of literature data was conducted using the PubMed, Web of Science, and Scopus databases, focusing on the characteristics of high-throughput DNA methylation analysis used in cancer and some genetic diseases. A total of 113 sources were analyzed, chronologically covering the period from 2000 to June 2025, 32 of which were used to write the review. Results. The existing technologies for high-throughput methylome analysis, DNA conversion methods, and their advantages and limitations were summarized. In addition, the current targeted enrichment methods, their strengths and weaknesses, and potential applications in scientific and diagnostic practice were discussed. Conclusion. DNA methylation analysis has evolved from a basic research tool into a cornerstone of translational medicine, particularly in oncology. Modern methylome analysis techniques facilitate the discovery of epigenetic markers critical for diagnosing diseases, assessing prognosis, guiding therapy selection, and identifying molecular targets for targeted drugs. Targeted DNA enrichment increases analytical precision and sensitivity while reducing costs. Furthermore, specialized strategies permit targeted analysis even with challenging samples. Combined with the flexibility to focus on specific genomic regions, these advantages make targeted approaches viable not only in academic research but also in routine clinical diagnostics.

CHD2-related neurodevelopmental disorders are increasingly recognized as a distinct group of epileptic encephalopathies with heterogeneous clinical manifestations. Here, we report a 12-year-old female patient with pharmacoresistant epilepsy, mild cognitive impairment (IQ = 56), and extraneurological features including grade II kyphoscoliosis and planovalgus foot deformity. Video-EEG monitoring revealed a phenotype consistent with Jeavons syndrome, characterized by daily eyelid myoclonia with absences and marked photosensitivity with an eye closure sensitivity (ECS) phenomenon. Molecular genetic testing via whole-exome and Sanger sequencing identified two novel variants in the CHD2 gene (NM_001271.4): c.1634T>G (p.Leu545Arg) and c.3810G>C (p.Leu1270Phe). Long-read nanopore sequencing confirmed their de novo status and cis-positioning on the paternal allele. Structural bioinformatic analysis using AlphaFold3, FoldX/mCSM (v5.0 package), UCSF ChimeraX (v1.10.1), and PyMOL (v3.1.8) demonstrated that both variants individually destabilize the CHD2 protein, with a cumulative destabilizing effect when combined: p.Leu545Arg affects the ATP-binding domain, whereas p.Leu1270Phe disrupts hydrophobic packing within the C-terminal DNA-binding domain. These findings suggest accelerated protein degradation as a potential disease mechanism. Our data support the pathogenicity of these heterozygous cis-variants and implicate CHD2 haploinsufficiency as the leading etiopathogenic mechanism, though distinct domain-specific effects of each substitution may also contribute to the complex molecular synergy observed in this case.

A personalized approach is a priority in the diagnosis and treatment of cancer. Accurate diagnostic tests for assessing the tumor’s molecular characteristics and optimizing the treatment strategy are essential for effective personalized treatment. Multigene NGS panels simultaneously detect a variety of genetic disorders, including single nucleotide substitutions, insertions and deletions, DNA copy number variations, translocations, microsatellite instability, and tumor mutational burden. This is crucial for selecting targeted therapy and immunotherapy, assessing prognosis, and monitoring the progression of cancer. This review discusses the evolution of precision oncology in the 21st century, the possibilities and advantages of NGS in molecular oncology, the technical and analytical characteristics of various multigene NGS panels with both amplification-based and hybridization-based enrichment, and their clinical applications in molecular diagnostics. The review focuses specifically on existing Russian and international NGS technologies. It examines available Russian and international multigene NGS panels, including problems of their application in routine cancer care in Russia.

Miscarriage is potentially associated with abnormal epigenetic regulation of genes responsible for the development of the embryo and placenta. The aim of this work was to analyze the methylation level of various subfamilies of the LINE-1 retrotransposon, which makes up about 17% of the entire genome, in chorionic villi of spontaneous abortions of the first trimester of pregnancy with different karyotypes, including the most common aneuploidies. The methylation profile in the LINE-1 retrotransposon promoter was analyzed using targeted bisulfite massive parallel sequencing in chorionic villi of induced abortions (n = 39), spontaneous abortions with normal karyotype (n = 173), trisomy 16 (n = 62) and monosomy X (n = 46), and peripheral blood lymphocytes of healthy volunteers (n = 17). The level of methylation of the LINE-1 retrotransposon subfamilies in the control groups of adult lymphocytes and chorionic villi of induced abortions was the highest for evolutionarily young L1HS subfamilies, lower for the more ancient L1PA2 and L1PA3 subfamilies, and the lowest for the even more ancient L1PA4 subfamily. In the groups of spontaneous abortions, an increased level of LINE-1 methylation was observed, and this effect was more pronounced for the older LINE-1 subfamilies. The revealed patterns indicate less control over the older subfamilies of the LINE-1 retrotransposon in the human genome, which can potentially be used as regulatory elements for nearby genes involved in embryonic development. An increase in the level of methylation of such sequences can disrupt the development of the placenta and embryo and make a certain contribution to miscarriage.