При развитии туберкулезной инфекции большую роль играет генетически опосредованная способность хозяина давать адекватный иммунный ответ на патоген. Полногеномные исследования ассоциаций, выполненные в различных популяциях, показали связь ряда хромосомных регионов с развитием туберкулеза (ТБ). Вместе с тем полная характеристика факторов генетической чувствительности к заболеванию остается пока нерешенной задачей, а выявленные ассоциации далеко не всегда повторяются при исследованиях в других популяциях. Проанализированы 45 одно-нуклеотидных полиморфных вариантов (SNP) у 768 человек, включая 323 больных туберкулезом и 445 здоровых индивидов. Анализ ассоциаций туберкулеза с генетическими маркерами проведен с помощью логистической регрессии. Для учета множественных сравнений использовали пермута-ции. Номинальная статистически значимая ассоциация с туберкулезом выявлена для двух SNP: rs10515787 (интронный вариант гена EBF1) и rs10956514 (интронный вариант гена ASAP1) (p = 0.005 и 0.049 соответственно); после проведения пермутационного теста сохранилась лишь одна из ассоциаций - для rs10515787 (p = 0.003). Таким образом, у русских г. Томска подтверждена ассоциация rs10515787 в гене EBF1 с развитием туберкулеза. Однако результаты настоящего исследования определяют редкий аллель A как рисковый для развития ТБ, в то время как в более раннем исследовании он указан в качестве протективного в отношении риска развития туберкулеза. Выявленная ""инверсия ассоциации"" представляет собой интересный факт, требующий дополнительных исследований.

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 and genes of the histamine pathway in the development of several common diseases. Histamine is a biogenic amine with a wide range of competencies, the physiological effects of which are realized with the help of four types of receptors (HRH1, HRH2, HRH3, and HRH4), characterized by tissue-specific expression. The key genes responsible for maintaining the physiological level of histamine are HDC (responsible for the synthesis of endogenous histamine), AOC1, HNMT, MAOB, and ALDH7A1 (involved in the degradation of histamine and its metabolites). However, in total, according to Gene Ontology, proteins and enzymes encoded by more than 200 genes are involved in the histamine pathway. Both temporal and chronic imbalances between the synthesis/intake of histamine and its degradation/metabolism in the human body (including those caused by specific genetic features) mediate the development of inflammatory manifestations with disturbance of the homeostasis of various organ systems (nervous, immune, endocrine, cardiovascular, etc.). Immunopathologic reactions mediated by histamine accompany the development of antigen-specific and nonspecific immediate and delayed-type hypersensitivity reactions of inflammation, effector immunocomplex reactions, autoimmune disorders, and cancer and, ultimately, can determine the comorbidity of common diseases. The review also provides information on the associations of the genes of the histamine pathway with common diseases (according to the studies using the candidate-gene approach and genome-wide association studies).

В обзоре представлены сведения о функциональной роли гистамина, генетических факторах, задействованных в поддержании физиологического уровня данного амина в организме, а также о вовлеченности гистамина и генов гистаминового метаболического пути в развитие некоторых заболеваний многофакторной природы. Гистамин - биогенный амин с широкой сферой компетенций, физиологические эффекты которого реализуются при помощи четырех типов рецепторов (HRH1, HRH2, HRH3 и HRH4), характеризующихся тканеспецифичной экспрессией. Ключевыми генами, ответственными за поддержание физиологического уровня гистамина, являются HDC (отвечает за синтез эндогенного гистамина), AOC1, HNMT, MAOB и ALDH7A1 (участвуют в процессах деградации гистамина и его метаболитов); но в общей сложности по данным ""Gene Ontology"" в метаболических путях гистамина задействованы белки и ферменты, кодируемые более 200 генами. Как временные, так и хронические нарушения баланса между синтезом/поступлением гистамина и его деградацией/метаболизмом в организме человека (в том числе и в результате генетических особенностей) опосредуют развитие воспалительных проявлений с нарушением гомеостаза различных систем органов (нервной, иммунной, эндокринной, сердечно-сосудистой и др.). Иммунопатологические реакции, опосредованные гистамином, сопровождают развитие антиген-специфической и неспецифической гиперчувствительности немедленного и замедленного типов воспаления, эффек-торные иммунокомплексные реакции, аутоиммунные расстройства, онкологию и в конечном итоге могут определять коморбидность многофакторных патологий. В обзоре также представлена информация об ассоциациях генов гистаминового метаболического пути с многофакторными заболеваниями (по данным работ с использованием кандидатного подхода и полногеномных ассоциативных исследований).

Comorbid states of diseases significantly complicate diagnosis and treatment. Molecular mechanisms of comorbid states of asthma and hypertension are still poorly understood. Prioritization is a way for identifying genes involved in complex phenotypic traits. Existing methods of prioritization consider genetic, expression and evolutionary data, molecular-genetic networks and other. In the case of molecular-genetic networks, as a rule, protein-protein interactions and KEGG networks are used. ANDSystem allows reconstructing associative gene networks, which include more than 20 types of interactions, including protein-protein interactions, expression regulation, transport, catalysis, etc. In this work, a set of genes has been prioritized to find genes potentially involved in asthma and hypertension comorbidity. The prioritization was carried out using well-known methods (ToppGene and Endeavor) and a cross-talk centrality criterion, calculated by analysis of associative gene networks from ANDSystem. The identified genes, including IL1A, CD40LG, STAT3, IL15, FAS, APP, TLR2, C3, IL13 and CXCL10, may be involved in the molecular mechanisms of comorbid asthma/hypertension. An analysis of the dynamics of the frequency of mentioning the most priority genes in scientific publications revealed that the top 100 priority genes are significantly enriched with genes with increased positive dynamics, which may be a positive sign for further studies of these genes.

One of the most common comorbid pathology is asthma and arterial hypertension. For experimental modeling of comorbidity we have used spontaneously hypertensive rats with ovalbumin (OVA)-induced asthma. Rats were randomly divided into three groups: control group, OVA-induced asthma group; OVA-induced asthma + IL10 shRNA interference group. Target gene (IL10) was predicted by ANDSystem. We have demonstrated that RNA-interference of IL10 affected cardiovascular (tested using Millar microcatheter system) as well as respiratory functions (tested using force-oscillation technique, Flexivent) in rats. We have shown that during RNA-interference of IL10 gene in vivo there were changes in both cardiac and lung function parameters. These changes in the cardiovascular parameters can be described as positive. But the more intensive heart workload can lead to exhaust and decompensation of the heart functions. Knockdown of IL10 gene in asthma modeling induces some positive changes in respiratory functions of asthmatic animals such as decreased elastance and increased compliance of the lungs, as well as less pronounced pathomorphological changes in the lung tissue. Thus, we provide the data about experimentally confirmed functionality changes of the target which was in silico predicted to be associated with both asthma and hypertension - in our new experimental model of comorbid pathology.

The prevalence of comorbid diseases poses a major health issue for millions of people worldwide and an enormous socio-economic burden for society. The molecular mechanisms for the development of comorbidities need to be investigated. For this purpose, a workflow system was developed to aggregate data on biomedical entities from heterogeneous data sources. The process of integrating and merging all data sources of the workflow system was implemented as a semi-automatic pipeline that provides the import, fusion, and analysis of the highly connected biomedical data in a Neo4j database GenCoNet. As a starting point, data on the common comorbid diseases essential hypertension and bronchial asthma was integrated. GenCoNet (https://genconet.kalis-amts.de) is a curated database that provides a better understanding of hereditary bases of comorbidities.

Comorbidity, a co-incidence of several disorders in an individual, is a common phenomenon. Their development is governed by multiple factors, including genetic variation. The current study was set up to look at associations between isolated and comorbid diseases of bronchial asthma and hypertension, on one hand, and single nucleotide polymorphisms associated with regulation of gene expression (eQTL), on the other hand. A total of 96 eQTL SNPs were genotyped in 587 Russian individuals. Bronchial asthma alone was found to be associated with rs1927914 (TLR4), rs1928298 (intergenic variant), and rs1980616 (SERPINA1); hypertension alone was found to be associated with rs11065987 (intergenic variant); rs2284033 (IL2RB), rs11191582 (NT5C2), and rs11669386 (CARD8); comorbidity between asthma and hypertension was found to be associated with rs1010461 (ANG/RNASE4), rs7038716, rs7026297 (LOC105376244), rs7025144 (intergenic variant), and rs2022318 (intergenic variant). The results suggest that genetic background of comorbidity of asthma and hypertension is different from genetic backgrounds of both diseases manifesting isolated.

Skin fibroblasts from a patient with neurodevelopmental and speech delay, anxiety disorder, macrocephaly, microorchidism, multiple anomalies of internal organs and ring chromosome 13 were reprogrammed into induced pluripotent stem cells (iPSCs) to generate a clonal stem cell line IMGTi003-A (iTAF6-6). IMGTi003-A pluripotency was demonstrated by three germ layer differentiation capacity in vitro, and this cell line had a mosaic karyotype with 46,XY,r(13) as a predominant cell subpopulation. IMGTi003-A line is a good model for studying of the mitotic instability of the ring chromosome 13.

Skin fibroblasts from a patient with intellectual disability and ring chromosome 22 were reprogrammed into induced pluripotent stem cells (iPSCs) to establish a clonal stem cell lines, IMGTi001-A (iTAF5-29) and IMGTi001-B (iTAF5-32). Because of ring chromosome mitotic instability these cell lines show mosaic karyotypes with 46,XX,r(22) in >83% cells, 45,XX,-22 as minor class and sporadically cells with other karyotypes. Differentiation in derivatives of all three germ layers was shown in teratoma assay for IMGTi001-A, and in embryoid bodies for both cell lines. To our knowledge, human iPSC lines with ring chromosome are described for the first time.

The application of array-based comparative genomic hybridization and next-generation sequencing has identified many chromosomal microdeletions and microduplications in patients with different pathological phenotypes. Different copy number variations are described within the short arm of chromosome 18 in patients with skin diseases. In particular, full or partial monosomy 18p has also been associated with keratosis pilaris. Here, for the first time, we report a young male patient with intellectual disability, diabetes mellitus (type I), and keratosis pilaris, who exhibited a de novo 45-kb microduplication of exons 4-22 of LAMA1, located at 18p11.31, and a 432-kb 18p11.32 microduplication of paternal origin containing the genes METTL4, NDC80, and CBX3P2 and exons 1-15 of the SMCHD1 gene. The microduplication of LAMA1 was identified in skin fibroblasts but not in lymphocytes, whereas the larger microduplication was present in both tissues. We propose LAMA1 as a novel candidate gene for keratosis pilaris. Although inherited from a healthy father, the 18p11.32 microduplication, which included relevant genes, could also contribute to phenotype manifestation.

Objective: To compare the genomic profiles of blastocoel fluid (BF), inner cell mass (ICM), and trophectoderm (TE) cells derived from the same blastocyst.

Design: Prospective study.

Setting: Academic and in vitro fertilization units.

Patient(s): Sixteen donated cryopreserved embryos at blastocyst stage.

Intervention(s): BF, TE, and ICM cells were retrieved from each blastocyst for chromosome analysis by means of next-generation sequencing (NGS).

Main outcome measure(s): Aneuploidy screening and assessment of mosaicism in BF, TE and ICM samples with subsequent comparison of genomic profiles between the three blastocyst compartments.

Result(s): Out of 16 blastocysts, 10 BF samples and 14 TE and ICM samples provided reliable NGS data for comprehensive chromosome analysis. Only 40.0% of BF-DNA karyotypes were fully concordant with TE or ICM, compared with 85.7% concordance between TE and ICM. In addition, BF-DNA was burdened with mosaic aneuploidies and the total number of affected chromosomes in BF was significantly higher compared with the TE and ICM.

Conclusion(s): BF-DNA can be successfully amplified and subjected to NGS, but owing to increased discordance with ICM and TE, BF does not adequately represent the status of the rest of the embryo. To overcome biologic and technical challenges associated with BF sampling and processing, blastocentesis would require improvement in both laboratory protocols and aneuploidy calling algorithms. Therefore, TE biopsy remains the most effective way to predict embryonic karyotype, and the use of BF as a single source of DNA for preimplantation genetic screening is not yet advised.

Background: Ring chromosome instability may influence a patient's phenotype and challenge its interpretation.

Results: Here, we report a 4-year-old girl with a compound phenotype. Cytogenetic analysis revealed her karyotype to be 46,XX,r(22). aCGH identified a 180 kb 22q13.32 duplication, a de novo 2.024 Mb subtelomeric 22q13.32-q13.33 deletion, which is associated with Phelan-McDermid syndrome, and a maternal single gene 382-kb TUSC7 deletion of uncertain clinical significance located in the region of the 3q13.31 deletion syndrome. All chromosomal aberrations were confirmed by real-time PCR in lymphocytes and detected in skin fibroblasts. The deletions were also found in the buccal epithelium. According to FISH analysis, 8% and 24% of the patient's lymphocytes and skin fibroblasts, respectively, had monosomy 22.

Conclusions: We believe that a combination of 22q13.32-q13.33 deletion and monosomy 22 in a portion of cells can better define the clinical phenotype of the patient. Importantly, the in vivo presence of monosomic cells indicates ring chromosome instability, which may favor karyotype correction that is significant for the development of chromosomal therapy protocols.

Ring chromosomes (RCs) are circular DNA molecules, which occur rarely in eukaryotic nuclear genomes. Lilian Vaughan Morgan first described them in the fruit fly. Human embryos very seldom have RCs, about 1:50,000. Carriers of RCs may have varying degrees of symptoms, from healthy phenotype to serious pathologies in physical and intellectual development. Many authors describe common symptoms of RC presence: short stature and some developmental delay that could be described as a “ring chromosome syndrome.” As a rule, RCs arise de novo through the end-joining of two DNA double-strand breaks, telomere-subtelomere junction, or inv dup del rearrangement in both meiosis and mitosis. There are family cases of RC inheritance. The presence of RCs causes numerous secondary chromosome rearrangements in vivo and in vitro. RCs can change their size, become lost, or increase their copy number and cause additional deletions, duplication, and translocations, affecting both RCs and other chromosomes. In this review, we examine RC inheritance, instability, mechanisms of formation, and potential clinical applications of artificially created RCs for large-scale chromosome rearrangement treatment.

This article contains data on the frequencies of alleles, genotypes and haplotypes of the single nucleotide polymorphisms (SNPs) rs2279590 and rs1532278 in the CLU gene in a cohort of normal elderly from the Russian population. The SNPs have been reported to be associated with Alzheimer's disease and cognitive functions in genome-wide and candidate genes association studies. Cognitive performance in sample set was estimated by the Montreal Cognitive Assessment (MoCA). The frequencies of alleles, genotypes and haplotypes of two SNPs were calculated in 3 groups: total sample set, sample set with MoCA score less than 21 (the first quartile) and group with MoCA score more than 24 (the fourth quartile).