Increasing evidence suggests that both coding and non-coding regions of sarcomeric protein genes can contribute to hypertrophic cardiomyopathy (HCM). Here, we introduce an experimental workflow (tested on four patients) for complete sequencing of the most common HCM genes (MYBPC3, MYH7, TPM1, TNNT2, and TNNI3) via long-range PCR, Oxford Nanopore Technology (ONT) sequencing, and bioinformatic analysis. We applied Illumina and Sanger sequencing to validate the results, FastQC, Qualimap, and MultiQC for quality evaluations, MiniMap2 to align data, Clair3 to call and phase variants, and Annovar’s tools and CADD to assess pathogenicity of variants. We could not amplify the region encompassing exons 6–12 of MYBPC3. A higher sequencing error rate was observed with ONT (6.86–6.92%) than with Illumina technology (1.14–1.35%), mostly for small indels. Pathogenic variant p.Gln1233Ter and benign polymorphism p.Arg326Gln in MYBPC3 in a heterozygous state were found in one patient. We demonstrated the ability of ONT to phase single-nucleotide variants, enabling direct haplotype determination for genes TNNT2 and TPM1. These findings highlight the importance of long-range PCR efficiency, as well as lower accuracy of variant calling by ONT than by Illumina technology; these differences should be clarified prior to clinical application of the ONT method.

The review provides information on the function of the FTO gene (known as the fat mass and obesity-associated gene) and the encoded enzyme, on the functional role of single nucleotide polymorphisms (SNPs) in coding and noncoding gene regions and the range of their competences, and on association of the FTO polymorphisms with diseases and traits. Factors that have modifying effect on the contribution of polymorphisms to the risk of disease development and trait variability are discussed. The FTO gene encodes alpha-ketoglutarate-dependent dioxygenase, which has a wide range of competences (including demethylation of RNA and single-stranded DNA), which are important for the functioning of the body. Nonsynonymous substitutions in the FTO gene lead to the development of orphan autosomal recessive disease (OMIM 612938). In the FTO noncoding regions, a wide range of variants has been detected, including those of regulatory importance (eQTL, sQTL, etc.). The competence of these variants extends to both FTO and neighboring genes (IRX3, IRX5, RPGRIP1L). Intronic polymorphisms of the FTO gene have been found to be associated with a wide range of multifactorial diseases and traits (obesity and related anthropometric traits, lipid metabolism markers, diabetes mellitus (type 2), coronary heart disease, metabolic syndrome, and other diseases). In the overwhelming majority of studies, the same allele variants are classified as risk ones; however, previously established associations of the FTO polymorphisms with diseases (traits) are demonstrated not in all populations. It is demonstrated that the effects of the FTO gene SNPs can be modified by exogenous and endogenous environmental factors, as well as lifestyle (including the type of diet, consumption of certain nutrients and medications, physical activity, etc.). Epigenetic factors (DNA methylation at CpG sites) are also important for regulating the level of FTO expression and the effects of individual SNPs. The accumulated data on the FTO structure and function, as well as the functional role of the encoded enzyme, make this gene attractive from the point of view of developing personalized approaches to healthcare.

In this study, we for the first time described the variability of methylation levels of 71 CpG sites in microRNA genes in leukocytes and blood vessels (coronary artery atherosclerotic plaques, intact internal thoracic arteries, and great saphenous veins) in patients with atherosclerosis using the Infinium HumanMethylation27 BeadChip microarray. Most of the analyzed CpG sites were characterized by the low variability, and most of these low-variable sites were hypomethylated in all tissue samples. CpG sites in coronary artery atherosclerotic plaques and leukocytes were similar in their methylation status. The highest variability of CpG methylation levels between different tissues was found for the CpG sites of the MIR10B gene; the methylation levels of these sites in leukocytes and atherosclerotic arteries were lower than in intact blood vessels. We also found that several cardiovascular disease risk factors, as well as medications, might affect methylation levels of CpG sites in microRNAs.

Cardiomyopathies are an actively investigated clinically and genetically heterogeneous group of myocardial pathologies. At present, it is acknowledged that along with genetic factors, epigenetic mechanisms can be of high value in determining both the risk of this pathology and the formation of clinical features of the disease. This review provides an analysis of studies examining histone modifications and chromatin remodeling, as well as alterations in DNA methylation in different forms of cardiomyopathies. Most of the studies in this field are focused on the analysis of the epigenomic profile of myocardial specimens from patients with dilated cardiomyopathy. The development of cardiomyopathy (dilated, hypertrophic, ischemic, restrictive, and arrhythmogenic) is accompanied by changes in the myocardium at the level of epigenetic processes, which leads to alterations in gene expression and an imbalance of metabolic pathways, including those pathogenetically important for the development of heart diseases. Cardiomyopathy genes (LMNA, TNNI3, ANKRD1, SLC25A4, EYA4, GATAD1, PRDM16, and DMD) are also involved in epigenetic alterations occurring in the myocardium. Epigenetic modifications, as well as enzymes that regulate epigenetic processes, are analyzed in terms of the prospects for their use to identify new molecular markers and metabolic pathways that are of value for cardiomyopathies, to develop diagnostic panels and new drugs. At the same time, high clinical and etiological heterogeneity of cardiomyopathies, a large number of diverse and interrelated epigenetic processes that occur both in physiologically normal state and in the disease pathogenesis point to the need to expand epigenetic studies in different forms of cardiomyopathies, including the level of epigenome, transcriptome, and epitranscriptome using omics approaches for the measurements of individual myocardial cells in humans and model animals, as well as in cell lines, in disease modeling.

The review focuses on the functional role of histamine and the genetic factors involved in maintaining the physiological level of this amine in the organism, as well as on the involvement of histamine

Neurogenic inflammation is a pathological process based on bidirectional interactions between cells of the nervous and immune systems as well as on a wide range of biologically active substances. Aim. Basing on scientific publications and information provided in databases, to analyze markers of neurogenic inflammation (biochemical, genetic) and characterize their involvement in the pathogenesis of diseases of various organ systems. Results. Neurogenic inflammation that occurs during the development of various diseases (asthma, urticaria, atopic dermatitis, psoriasis, rheumatoid arthritis, pain syndrome, interstitial cystitis, colitis, etc.) is characterized by common stages and pathophysiologically active substances. Mediators released by nerve cells (substance P, calcitonin gene-related peptide, vasoactive peptide), acting on specific receptors, contribute to mast cell degranulation with the release of a complex of biologically active substances (histamine, tryptase, nerve growth factor, etc.), which activate inflammatory processes. Biologically active substances and receptors significant for the development of neurogenic inflammation are under genetic control. At the same time, there are overlaps of the spectrum of diseases for which importance in the pathogenesis of neurogenic inflammation is proved and an association between variants of neurogenic inflammation genes. This makes it possible to conclude that the course of neurogenic inflammation will depend not only on the etiological factors, but also on the genetic features of key molecules involved in neurogenic inflammation processes. The similarity of the pathogenetic links of neurogenic inflammation (at the genetic and biochemical levels) in various pathologies may underlie the formation of comorbid conditions. Conclusion. Understanding the biochemical and genetic components of the development of neurogenic inflammation is of interest for prevention and treatment of diseases (including comorbid ones) based on this pathological process.