Co-expression analysis of placental genes in the search for key signaling pathways and biomarkers of the great obstetrical syndromes

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.

Analysis of differential expression of lipid metabolism genes in atherosclerotic plaques in patients with coronary atherosclerosis

Aim. The goal of the study was to analyze the differential expression of lipid metabolism-related genes in the atherosclerotic plaques of different types in patients with coronary atherosclerosis.Material and Methods. The study was performed on the specimens of atherosclerotic plaques in 45–65-year-old patients with coronary atherosclerosis with stable exertional angina functional class II-IV without acute coronary syndrome. Coronary atherosclerosis was verified by coronary angiography. Atherosclerotic plaque tissue was sampled intraoperatively when indicated. Whole-genome sequencing of ribonucleic acid (RNA) was performed using the TruSeq RNA Sample Preparation Kit (Illumina, USA).Results. We analyzed the differences in the expression of 12 genes including LDLR, APOB, PCSK9, LDLRAP1, LIPA, STAP1, ABCA1, APOA1, APOE, LPL, SCARB1, and SREBF2 depending on the type of atherosclerotic plaques. The expression level of APOE gene was eight times higher in unstable atherosclerotic plaques of dystrophic-necrotic type (p < 0.0001). The expression levels of LDLR and APOB genes were eight times higher in stable atherosclerotic plaques (p < 0.0001). We did not find differences in the expression levels of the ABCG5, ABCG8, APOC3, CETP, CLPS, CYP7A1, and PNPLA5 genes.Conclusion. The study showed the differences in the activity of individual metabolism-related genes in the atherosclerotic plaques of different types in patients with coronary atherosclerosis. Obtained data may become the basis for the development of test systems aimed at predicting the development of atherosclerotic process and its complications.

The lineage of coronavirus SARS-CoV-2 of Russian origin: Genetic characteristics and correlations with clinical parameters and severity of coronavirus infection

The identification of new SARS-CoV-2 and human protein and gene targets, which may be markers of the severity and outcome of the disease, are extremely important during the COVID-19 pandemic. The goal of this study was to carry out genetic analysis of SARS-CoV-2 RNA samples to elucidate correlations of genetic parameters (SNPs) with clinical data and severity of COVID-19 infection.Material and Methods. The study included viral RNA samples isolated from 56 patients with COVID-19 infection who received treatment at the City Hospital No. 40 of St. Petersburg from 04/18/2020 to 04/18/2021. Patients underwent physical examination with the assessments of hemodynamic and respiratory parameters, clinical risk according to National Early Warning Score (NEWS), computed tomography (CT) of the chest, and laboratory studies including clinical blood analysis, assessment of ferritin, C-reactive protein (CRP), interleukin-6 (IL-6), lactate dehydrogenase (LDH), D-dimer, creatinine, and glucose levels. All patients tested positive for SARS-CoV-2 RNA by polymerase chain reaction (PCR). Single nucleotide polymorphisms (SNPs) in viral RNA were identified through the creation of cDNA libraries by targeted sequencing (MiSeq Illumina). Bioinformatic analysis of viral samples was performed using the viralrecon v2 pipeline with the further annotation via Pangolin and Nextlade. Sampled genomes were visualized using the Integrative Genomics Viewer (IGV) software. Statistical data processing (descriptive statistics and graphical analysis of data relationships from diff erent tables) was performed using a GraphPad device on the Prism 8.01 platform.Results. A comparative analysis of SNP frequencies in the virus genome in samples from deceased and discharged patients was carried out. The SNPs associated with risk of death (OR > 1), neutral SNPs (OR = 1), and protective SNPs (OR < 1) were identifi ed. Patient samples were infected with 14 lines of SARS-CoV-2, fi ve of which (B.1.1.129, B.1.1.407, B.1.1.373, B.1.1.397, and B.1.1.152) were of Russian origin. The SNPs in the samples infected with the strains of non-Russian origin were associated with an increased risk of mortality (OR = 2.267, 95% confi dence interval 0.1594-8.653) compared to the SNPs in the samples obtained from the group of patients infected with the strains of Russian origin. Positive correlations were identifi ed between the average SNP number, nonsynonymous SNPs, and S-protein SNPs with the degree of respiratory failure, total NEWS score, CT-based form of disease, duration of treatment with mechanical ventilation, disease outcome, levels of LDH, glucose, D-dimer, and ferritin, and RNA amount in the PCR test. S-protein SNPs negatively correlated with the leukocyte and neutrophil counts.

Associations of rs4244285 in the CYP2C19 gene with multifactorial diseases

Xenobiotic metabolism system in the current populations is involved in the biotransformation of a wide range of endogenous substrates and various xenobiotics, which can contribute to developing the diseases of various organ systems, and, in some cases, comorbid conditions where increased biotransformation system activity is observed. In this regard, it is of great interest to study the involvement of polymorphism in xenobiotic metabolism genes in the development of both isolated pathology and various comorbid conditions.Aim. The goal of study was to investigate the involvement of rs4244285 in the CYP2C19 gene in the development of isolated pathology and comorbidities.Material and Methods. The frequencies of alleles and genotypes were studied in groups of patients with comorbid conditions including groups of coronary artery disease (CAD) with hypertension (HTN) (CAD_HTN, n = 133) and bronchial asthma (BA) with HTN (BA_HTN, n = 178), in group of isolated BA (n = 135), and in the population sample of the city of Tomsk (n = 377). Association analysis covered three initial groups of patients (CAD, BA, and BA_HTN) and subgroups assigned based on the presence of absence of HTN diagnosis taking into account comorbid conditions both in patient samples and in population control.Results and Discussion. The study demonstrated the predisposing eff ect of GA genotype on the development of comorbid BA and HTN (OR = 1.94, p = 0.038) and comorbid CAD and HTN (OR = 2.26, p = 0.009) compared to isolated BA. The AA genotype was observed 3.98 times less often in HTN patients than in normotensive individuals. However, the diff erences did not reach the level of statistical signifi cance due to the low occurrence of this genotype.Conclusion. The obtained results may be explained by the involvement of CYP2C19-metabolites of arachidonic acid in the regulation of vascular tone, which requires further study.

Early and late outcomes of combined and staged surgeries in patients with concomitant atherosclerotic lesions of the coronary and brachiocephalic arteries

Objective. To study the early and late outcomes of surgical treatment of patients with concomitant atherosclerotic lesions of coronary and brachiocephalic arteries while choosing a treatment strategy based on the developed diff erentiated approach algorithm.Material and Methods. The study comprised 243 patients with combined atherosclerotic lesions of the coronary and carotid arteries examined during the period from 01.07.2014 to 01.01.2021. Patients underwent revascularization surgeries based on the algorithm for choosing the volume and stages of surgical intervention, which was previously developed in the Federal Center for Cardiovascular Surgery named after S.G. Sukhanov. A single-stage combined surgery of coronary artery bypass grafting (CABG) and carotid endarterectomy (CEE) was performed in 104 patients (42.8%); 139 patients (57.2%) received staged revascularization including 102 patients (73.4%) who received CABG as the fi rst step and 37 patients (26.6%) who received CEE as the fi rst step of surgery. The endpoints for both early and late results were death from all causes, stroke, transient ischemic attack (TIA), acute myocardial infarction (AMI), and combined endpoint that included all of the above. Average follow-up time was 41.1 ± 21.8 months.Results. No fatal outcomes were in any group during the early postoperative period. At the hospital stage, there were 5 cases (2.1%) of stroke, 1 case (0.4%) of TIA, and 3 cases (1.2%) of acute MI. Long-term results were evaluated in 225 patients (92.3%). The overall survival rate was 93.8%. There were 5 cases (2.4%) of MI, 11 cases (4.9%) of stroke, and 1 case (1.0%) of TIA. No signifi cant diff erences were observed in immediate and long-term endpoints between the groups of staged and combined interventions as compared to immediate (AMI: p = 0.680; TIA: p = 0.500; acute cerebrovascular events: p = 0.567; combined: p = 0.940) and long-term results (deaths: 0.860; AMI: p = 0.906; TIA: p = 0.528; acute cerebrovascular events: p = 0.378; combined: p = 0.669).Conclusion. Based on successful experience with treating the concomitant atherosclerotic lesions of the coronary and brachiocephalic arteries, the proposed algorithm allowed to perform safe procedures in both arterial basins and to achieve satisfactory results in in-hospital and long-term periods in the Federal Center for Cardiovascular Surgery named after S.G. Sukhanov (Perm).

Molecular genetic study of clinical and cognitive features of schizophrenia: No associations with genes SOD2, GSTO1, NQO1

The main features of schizophrenia are characterized by three domains of symptoms, including positive symptoms, negative symptoms, and cognitive defi cits, the overlap of which forms a polymorphism of clinical manifestations. Previous molecular genetic studies have found signifi cant genetic overlaps between the cognitive abilities and the risk of schizophrenia developing. Recent evidence suggests that oxidative stress may play an important role in the pathophysiology of schizophrenia.Aim. The aim of the study was to investigate the associations of polymorphisms of genes encoding the antioxidant enzymes SOD2, GSTO1, and NQO1 with clinical polymorphism of schizophrenia and the severity of cognitive deficit.Material and Methods. A comprehensive examination of 457 patients with a diagnosis of schizophrenia was carried out. Out of the total group of examined patients, cognitive functions were assessed using the BACS scale in 150 schizophrenic patients. The control group comprised 135 healthy individuals with age and gender corresponding to patient group. Their cognitive function was assessed. Genotyping of SOD2 (rs4880), GSTO1 (rs4925), and NQO1 (rs1800566) was done by realtime PCR.Results. When analyzing the distribution of genotypes and alleles of polymorphic variants of genes encoding the antioxidant enzymes SOD2, GSTO1, and NQO1, no associations between the studied loci and schizophrenia in the Russian population of the Siberian region were revealed. Also, no associations were found with clinical polymorphism of disease (disease course type, leading symptoms (positive or negative), and age of disease onset). The cognitive abilities of schizophrenic patients and healthy individuals were diff erent as expected, but no associations with genetic characteristics were found.Conclusion. In this work, we obtained negative results in regard to associations of polymorphic variants of genes encoding the antioxidant enzymes SOD2 (rs4880), GSTO1 (rs4925), and NQO1 (rs1800566) with the development of schizophrenia in the Russian population in the Siberian region, as well as with the severity of cognitive defi cit. The genetic profi le for the studied loci did not aff ect the clinical manifestations of disease in the examined sample.

Mitochondrial DNA polymorphism and myocardial ischemia: Association of haplogroup H with heart failure

The pathogenesis of atherosclerosis and ischemic heart disease is associated with oxidative stress and mitochondrial dysfunction. Mitochondrial DNA encodes subunits of mitochondrial respiratory chain and is highly polymorphic in human populations. Mitochondrial DNA can be considered a candidate genetic locus for predisposition to cardiovascular diseases.Aim. To analyze the associations of the mitochondrial genome polymorphism and chronic heart failure in ischemic heart disease.Material and Methods. The study included two groups of individuals: patients with a combination of ischemic heart disease and chronic heart failure (n = 175) and a population sample of residents of Tomsk (n = 424). Percentages of patients with chronic heart failure of NYHA classes II, III, and IV were 37%, 50%, and 13%, respectively. All patients underwent echocardiographic examination; body mass index and the lipid fractions in blood serum were determined. The average was 55.4 years in patients and 47.6 years in the population sample. Polymorphism of mtDNA was studied by sequencing the hypervariable segment of D-loop of mtDNA and subsequent classification of mtDNA haplotypes into the known haplogroups. The mtDNA haplogroup frequencies were compared between the samples using the Chi-square test. The associations of genotype with quantitative trait variability were analyzed by variance analysis.Results. Male patients showed a higher frequency of haplogroup H compared to the population (45.86% in patients and 35.4% in population) and a higher total frequency of haplogroup H subgroups except the most frequent subgroup H1 (36.94% and 25.22%, respectively). The values of significance level (p-value) and odds ratio (OR) were determined as follows: p = 0.04; odds ratio OR = 1.55 (95% confidence interval (CI) 1.02–2.34) for haplogroup H as a whole; p = 0.02; OR = 1.74 (95% CI 1.12–2.70) for haplogroup H without subgroup H1. Analysis of quantitative traits revealed the associations of the same genetic marker (mtDNA haplogroup H) with the levels of high-density lipoproteins (p = 0.03) and triglycerides (p = 0.02) in blood serum of men in the population sample.Conclusion. The obtained results suggested that the most frequent European mtDNA haplogroup H may be a risk factor for the complications of ischemic heart disease in men.

Polymorphism of folate metabolism genes and thrombotic complications in patients with functionally single ventricle

Aim. To analyze the relationships between the carriage of polymorphic variants in the folate metabolism genes and the development of thrombotic complications in patients with single ventricle (SV) during surgical treatment.Material and Methods. A total of 102 children with SV were examined in the performed research. All patients underwent surgical hemodynamic correction of congenital heart disease (CHD). According to a retrospective chart review, thrombosis was diagnosed in 12.7 % of the examined patients with SV. The analysis of polymorphism in the MTR A2756G enzyme gene revealed significant differences between the groups of patients with a history of thrombosis and without it.Results. We found that the risk of developing thrombosis was associated with the carriage of homozygous genotype 2756AA of the MTR enzyme gene (OR = 11.21; 95% CI: 1.39–89.96; p = 0.023).