Abstract—Identification of the hereditary basis of preeclampsia remains a relevant area for medical genetics. Despite numerous attempts to search for the main predetermining factors, due to the multifactorial nature of the preeclampsia no generally accepted hypotheses for the pathogenesis of this pregnancy complication exists. One of the progressive approaches to the study of complex diseases is an analysis of gene–gene interactions, which makes it possible to isolate factors that can determine a high or low risk of predisposition within the pathology from a large array of combinations. In the presented work, analysis of gene–gene interactions was used to create a model that predicts the risk of severe preeclampsia and find key combinations of genes predisposing one to the development of preeclampsia in the Russian population. For the first time the prognostic potential of combinations of the rs3774298 BCL6 and rs2071045 LEP loci in the development of a severe form of preeclampsia (OR = 2.97) was demonstrated. Additionally, it was found that the rs3774298 polymorphic variant of the BCL6 gene is located in a functionally active region of the genome located in the binding site of the transcription factor CTCF, which can function as both a transcription activator and a repressor. This emphasizes the role of cell regulatory systems in the mechanisms of the formation and course of preeclampsia.

Abstract—Fetal growth restriction is a complication of pregnancy that is defined as the inability of the fetus to realize its genetically determined growth potential. Despite the high social and medical significance of this problem the exact pathogenesis of fetal growth restriction is not known. Therefore, the analysis of the molecular genetics mechanisms of this pathology within the framework of approaches using modern high-performance technologies of next generation sequencing is of undoubted interest. In this review we focused on the analysis of data obtained in studies of the genetics component of fetal growth restriction. The authors of these studies used next generation sequencing technologies and carried out whole transcriptome profiling. The results of the gene expression genome-wide analysis in placental tissue allow us to identify 1430 differentially expressed genes between fetal growth restriction and normal pregnancy, of which only 1

We aimed to explore the potential link of maternal age at menarche (mAAM) gene polymorphisms with risk of the fetal growth restriction (FGR). This case (FGR)–control (FGR free) study included 904 women (273 FGR and 631 control) in the third trimester of gestation examined/treated in the Departments of Obstetrics. For single nucleotide polymorphism (SNP) multiplex genotyping, 50 candidate loci of mAAM were chosen. The relationship of mAAM SNPs and FGR was appreciated by regression procedures (logistic/model-based multifactor dimensionality reduction [MB-MDR]) with subsequent in silico assessment of the assumed functionality pithy of FGR-related loci. Three mAAM-appertain loci were FGR-linked to genes such as KISS1 (rs7538038) (effect allele G-odds ratio (OR)allelic = 0.63/pperm = 0.0003; ORadditive = 0.61/pperm = 0.001; ORdominant = 0.56/pperm = 0.001), NKX2-1 (rs999460) (effect allele A-ORallelic = 1.37/pperm = 0.003; ORadditive = 1.45/pperm = 0.002; ORrecessive = 2.41/pperm = 0.0002), GPRC5B (rs12444979) (effect allele T-ORallelic = 1.67/pperm = 0.0003; ORdominant = 1.59/pperm = 0.011; ORadditive = 1.56/pperm = 0.009). The haplotype ACA FSHB gene (rs555621*rs11031010*rs1782507) was FRG-correlated (OR = 0.71/pperm = 0.05). Ten FGR-implicated interworking models were founded for 13 SNPs (pperm ≤ 0.001). The rs999460 NKX2-1 and rs12444979 GPRC5B interplays significantly influenced the FGR risk (these SNPs were present in 50% of models). FGR-related mAAM-appertain 15 polymorphic variants and 350 linked SNPs were functionally momentous in relation to 39 genes participating in the regulation of hormone levels, the ovulation cycle process, male gonad development and vitamin D metabolism. Thus, this study showed, for the first time, that the mAAM-appertain genes determine FGR risk.

At present, transcriptomics is one of the fastest developing fields of molecular biology, which allows to obtain detailed information about the functional activity of the genome in both normal and pathological conditions. We used modern transcriptomic technologies to comprehensively characterize the whole genome gene expression profile of human placental syncytiotrophoblast cells (STB) in physiological pregnancy and preeclampsia (PE). As a result of our analysis, we identified 26 differentially expressed genes (DEGs) in the STB cells between healthy and diseased states. The cluster of DEGs contains not only well-known candidate genes identified earlier in many foreign whole genome studies of the placenta (for example, LEP , INHBA , and FLT1 ) but also new genes ( AC098613.1 , AC087857.1 , FCRLB , TENM4 , PTP4A1P7 , LINC01225 , etc.) that can be considered as new biological markers of PE and are of interest for further study. Functional enrichment annotation indicated that most of the DEGs were implicated in the signaling pathways of regulation of hormonal secretion, MAPK cascade, ERK1 and ERK2 cascade, positive regulation of cell adhesion, and proliferation of endothelial cells. These processes may be associated with the development of PE at the level of STB cells. Additionally, we revealed that alternative splicing of the FLT1 gene indicates the important role of this RNA processing mechanism in the pathogenetics of PE due to a significant increase in the transcriptional diversity of genes in STB cells. The expression level of the transcript encoding the protein isoform FLT-1 e15a was significantly increased in patients with PE compared to the control group. This study expands understanding of the molecular mechanisms involved in PE and can serve as a basis for development of preventive, prognostic, and therapeutic strategies in the field of personalized obstetrics.

Autism spectrum disorder (ASD) is a developmental disorder characterized by the early onset of problems with communication, learning, and behavior. The syndromic form of ASD is caused by monogenic mutations. When it is not possible to find genetic or other known mechanisms, the term “idiopathic autism” is used. A significant part of both syndromic and idiopathic autism is associated with translational deregulation dependent on the mechanistic target of rapamycin (mTOR). In this review, we present both bioinformatic and experimental data that link the mTOR signaling pathway to maternal autoantibody related autism and childhood autoimmune neuropsychiatric disorders such as Sydenham’s chorea and pediatric autoimmune neuropsychiatric disorder associated with streptococcal infections (PANDAS). The need for ASD subtyping and the prospects of mechanism-based therapy with inhibitors of the mTOR signaling pathway are also discussed.

Преэклампсия (ПЭ) − тяжелая акушерская патология, ежегодно затрагивающая до 8% всех беременностей. К настоящему времени проведены многочисленные генетические исследования с использованием как кандидатного, так и полногеномного подходов, чтобы раскрыть генетическую основу ПЭ. Эти работы выявили ряд многообещающих генов-кандидатов ПЭ, включая локус STOX1. В представленной работе проведён анализ роли наследственной вариабельности гена STOX1 в формировании предрасположенности к ПЭ в различных этнических группах России. Обнаруженные нами ассоциации генотипов локуса STOX1 с ПЭ характеризуются популяционной специфичностью: у русских установлены рисковые генотипы полиморфных маркеров rs4746796 и rs7095976, в якутской этнической выборке был выявлен протективный генотип аллельного варианта rs1694505. Preeclampsia (PE) is a severe obstetric pathology that affects up to 8% of all pregnancies per year. By now numerous genetic studies have been conducted using both candidate and genome-wide approaches to reveal the genetic basis of PE. Therefore, a number of promising candidate genes for PE, including the STOX1 locus, were identified. In this article, the role of heritable variation of the STOX1 gene in the formation of predisposition to PE in various ethnic groups of Russia was analyzed. The associations of genotypes of the STOX1 locus with PE that we found were characterized by population specificity. Genotypes of polymorphic markers rs4746796 and rs7095976 with risk effect were identified in Russians. The protective genotype of the rs1694505 allele variant was revealed in the Yakut ethnicity.

In this study, the association between maternal age at menarche (AAM)-related polymorphisms and offspring birth weight (BW) was studied. The work was performed on a sample of 716 pregnant women and their newborns. All pregnant women underwent genotyping of 50 SNPs of AAM candidate genes. Regression methods (linear and Model-Based Multifactor Dimensionality Reduction (MB-MDR)) with permutation procedures (the indicator pperm was calculated) were used to identify the correlation between SNPs and newborn weight (transformed BW values were analyzed) and in silico bioinformatic examination was applied to assess the intended functionality of BW-associated loci. Four AAM-related genetic variants were BW-associated including genes such as POMC (rs7589318) (βadditive = 0.202/pperm = 0.015), KDM3B (rs757647) (βrecessive = 0.323/pperm = 0.005), INHBA (rs1079866) (βadditive = 0.110/pperm = 0.014) and NKX2-1 (rs999460) (βrecessive = −0.176/pperm = 0.015). Ten BW-significant models of interSNPs interactions (pperm ≤ 0.001) were identified for 20 polymorphisms. SNPs rs7538038 KISS1, rs713586 RBJ, rs12324955 FTO and rs713586 RBJ–rs12324955 FTO two-locus interaction were included in the largest number of BW-associated models (30% models each). BW-associated AAM-linked 22 SNPs and 350 proxy loci were functionally related to 49 genes relevant to pathways such as the hormone biosynthesis/process and female/male gonad development. In conclusion, maternal AMM-related genes polymorphism is associated with the offspring BW.

The associations of genes differentially expressed in the placenta with the risk of preeclampsia in women in Central Russia were studied. The study was conducted on a sample of 366 pregnant women with preeclampsia and 631 women in the control group. All pregnant women underwent typing of nine specially selected SNPs of genes differentially expressed in the placenta. Associations of SNPs of candidate genes with preeclampsia were assessed using logistic regression. For polymorphisms that showed associations with PE, their functional effects were assessed in silico . It was established that the G allele rs36011588 TMEM136 was a protective factor (OR = 0.65), and the CA haplotype of the rs2532058–rs66707428 PPP1R12C was a risk factor (OR = 1.21) for the development of preeclampsia. The associations of these SNPs with developing preeclampsia may be due to their important epigenetic significance: they are located at the sites of modified histones in the regions of promoters and enhancers, in DNase-hypersensitive sites, in binding sites for regulatory proteins, and in the binding domains for transcription factors. Also, these loci are associated with the level of transcription and alternative splicing in tissues pathogenetically significant for the development of preeclampsia.

Альтернативный сплайсинг (АС) мРНК является ключевым этапом посттранскрипционной регуляции экспрессии генов, который обеспечивает формирование тканеспецифичных и клеткоспецифичных изоформ РНК. Вероятно, этот механизм оказывает значительное влияние на развитие и функционирование плаценты. В качестве объекта исследования выбраны децидуальные клетки (ДК), которые играют важную роль в поддержании физиологической гестации. Проведено глубокое полнотранскриптомное секвенирование РНК ДК образцов плацентарной ткани, полученных от пациенток с физиологическом течением беременности, в ходе которого идентифицированы 151233 события АС в 352 генах. Примечательно, что только 130 генов характеризовались двумя и более событиями АС. Данные гены вовлечены в канонический сигнальный путь Wnt, регуляцию субстрат-зависимой миграции клеток, активацию андрогенных рецепторов, сплайсинг мРНК. Максимальное число альтернативных событий установлено для гена FN1, продукт которого ассоциирован с развитием преэклампсии и является скрининговым маркером преждевременных родов. Исследование продемонстрировало перспективность дальнейшего изучения распределения альтернативно сплайсированных изоформ гена FN1 в группе пациенток как с физиологической беременностью, так и в когорте с акушерской патологией. Alternative splicing (AS) of mRNA is a key stage of post-transcriptional regulation of gene expression, which ensures the expression of various isoforms of RNA. Probably, this mechanism plays an important role in the development and functioning of the placenta. Decidual cells (DC) were chosen as the object of research due to their key role in physiological pregnancy. Whole transcriptome sequencing of DC RNA of placental tissue samples obtained from patients with the physiological pregnancy was performed, during which 151233 AS events in 352 genes were identified. It is noteworthy that two or more AS events characterized only 130 genes. These genes are involved in the canonical Wnt signaling pathway, regulation of substrate-dependent cell migration, activation of androgen receptors, and mRNA splicing. The maximum number of alternative events per gene established for the FN1 gene, the product of which is associated with the development of preeclampsia and is a screening marker of premature birth. The study suggests the prospects for further exploring of the distribution of alternatively spliced isoforms of the FN1 gene in a cohort of patients with both physiological pregnancy and obstetric pathology.

Alternative splicing (AS) of RNA is a key step in the post-transcriptional regulation of gene expression. It provides transcriptional plasticity and control of the expression of RNA isoforms in a certain type of tissues and cells at a given time. Presumably, this mechanism plays an important role in the development and functioning of the placenta. The study carried out deep whole-transcriptome sequencing with a detailed analysis of alternative splicing events in decidual cells (DC) of placental tissue during the physiological course of pregnancy. In decidual cells, 149 067 AS events annotated in GENCODE v.26 were identified in 20 463 genes; 4038 of these genes were characterized by ten or more isoforms. Analysis of the network of reconstructed genes demonstrated a high degree of interactions between alternatively spliced genes and revealed regulatory relationships that ensure the coordinated expression of most of the central genes associated with the initiation and elongation of translation in eukaryotes and modulation of angiogenesis and cell adhesion mediated by DE-cadherin. The results obtained confirm the importance of alternative splicing, which significantly increases transcriptional diversity and represents an important mechanism of gene regulation in decidual cells. It should be noted that a number of genes susceptible to AS in DC are associated with pregnancy complications, and therefore it seems relevant to further study this mechanism of RNA processing in a cohort of patients with obstetric pathology.

Проведен репликативный анализ ассоциаций однонуклеотидных полиморфных вариантов 8 наиболее значимых генов-кандидатов преклампсии: rs1801133 гена MTHFR, rs1799963 гена F2, rs6025 гена F5, rs1799889 гена SERPINE1, rs1799983 и VNTR гена NOS3, rs3025000, rs3025010 и rs10434 гена VEGF, rs699 гена AGT, rs4646994 гена ACE. Полученные результаты показали ассоциацию с развитием данной патологии шести SNP пяти генов: rs1799889 гена SERPINE1 и rs1799983 гена NOS3 у бурятов, русских и якутов, VNTR гена NOS3 у бурятов, rs1801133 гена MTHFR, rs6025 гена F5 и rs3025010 гена VEGF у русских. We conducted a replicative associations analysis of the single-nucleotide polymorphisms of 8 most significant candidate genes of preeclampsia: rs1801133 in the MTHFR gene, rs1799963 in the F2 gene, rs6025 in the F5 gene, rs1799889 in the SERPINE1 gene, rs1799983 and VNTR in the NOS3 gene, rs3025000, rs3025010 and rs10434 in the VEGF gene, rs699 in the AGT gene, rs4646994 in the ACE gene. The results demonstrate а significant associations of preeclampsia with 5 SNP 6 genes: rs1799889 in the SERPINE1 gene and rs1799983 in the NOS3 gene in Buryats, Russians and Yakuts, VNTR in the NOS3 gene in Buryats, rs1801133 in the MTHFR gene, rs6025 in the F5 gene and rs3025010 in the VEGF gene in Russian.

Objective. To study the molecular mechanisms responsible for the development of diseases grouped within the great obstetrical syndromes (GOS) at the level of the transcriptome of human maternal placenta. Material and Methods. We gathered the results of genome-wide transcriptome studies of the human placental tissue using Gene Expression Omnibus (GEO) data repository for the following phenotypes: physiological pregnancy, preeclampsia (PE), premature birth, and intrauterine growth restriction (IUGR). Eleven data sets were selected and supplemented with our experimental data; a total of 481 samples of human placental tissue were included in the integrative analysis. Bioinformatic data processing and statistical analyses were performed in the R v3.6.1 software environment using the Bioconductor packages. The pooled dataset was used to search for common molecular targets for GOS via weighted gene co-expression network analysis (WGCNA). The functional annotation of genes and the resulting clusters was carried out with the DAVID database; protein-protein interaction network was built using the STRING software; and the hub genes for the network were identified using the MCC analysis with plugin cytoHubba in Cytoscape software 3.7.2. Results. We obtained a table of expression levels for 15,167 genes in 246 samples. Hierarchical clustering of this network allowed to find 55 modules of co-expressed genes in the group with PE, 109 modules in the group with PB, 75 modules in patients with IUGR, and 56 modules in the control group. The preservation analysis of co-expressed modules for the studied phenotypes suggested the presence of a common cluster comprising eight genes specific only for patients with PE and IUGR, as well as the module of 23 co-expressed genes typical only for patients with PB and IUGR. Protein-protein interaction network was built for these gene sets, and the SOD1, TXNRD1, and UBB genes were the central nodes in the network. Based on network topology evaluation with cytoHubba, six hub genes (rank ˂ 5) were identified as follows: SOD1, TKT, TXNRD1, GCLM, GOT1, and ACO1. Conclusion. The obtained results allowed to identify promising genetic markers for preeclampsia, intrauterine growth restriction, and miscarriage. Moreover, the study also made it possible to identify the most important overlapping molecular mechanisms of these diseases occurring in the placental tissue.

The advent of high-throughput sequencing technologies has expanded our understanding of the biological significance of non-coding regions of the genome. In recent years, more and more studies have been devoted to studying the role of noncoding RNAs in the development of diseases, as well as their participation in various cellular processes. Until now, all transcriptome studies of native placental tissue with the description of the noncoding RNA region were carried out without isolating individual cell populations. This approach, due to the high cellular heterogeneity of the placental tissue, significantly complicates the ability to determine the molecular-biological functions of individual cells and their role in the molecular pathogenesis of reproductive disorders. In this work, we propose a technique for obtaining total RNA from single decidual cells of frozen placental tissue obtained by laser-capture microdissection technology for transcriptome sequencing, including a cluster of noncoding RNAs. This technique can be successfully used to study the full-genome expression profile of other placental cell populations. The high accuracy of results on the transcriptome profiling of decidual cells obtained using the developed technique was additionally confirmed by an integrative analysis with the results of a 10x Genomics experiment.