Разработан метод мультиплексного генотипирования полиморфных маркеров генов, ассоциированных с когнитивными способностями и нейро-психиатрическими заболеваниями, основанный на многолокусной ПЦР и MALDI-TOF-масс-спектрометрии молекул ДНК. Охарактеризованы частоты 32 однонуклеотидных маркеров, локализованных в 24 генах, в выборке пожилых людей из русской популяции г. Томска. Полученные данные сопоставлены с данными для популяций из проекта «1000 геномов».

Specificity of the structure of gene pools of different ethno-territorial groups of the human population can underlie the epidemiological features of the spread of tuberculosis (TB) and the structure of the genetic component of the susceptibility to the disease. The variability of 62 genetic variants potentially associated with the risk of the development of TB in the Russian population of the city of Tomsk has been studied and the differentiation of various ethno-territorial groups of the world by these markers has been assessed. The studied sample comprised 445 Russian residents of the city of Tomsk without bronchopulmonary pathology. For comparison, the data on the variability of the genetic markers of interest in 26 populations from the 1000 Genomes Project was involved. In the Tomsk population, only the ancestral allele was found for seven of the 58 SNPs studied; the allele frequencies for 36 markers were within the limits of the values seen in other European populations; for 12 SNPs, the observed frequencies were closer to populations with a significant Mongoloid component. By the total of the SNPs, the Tomsk population, despite the geographical distance from the rest of the European populations, did not differ from them (in genetic distances and Gst statistics), although it had some features of the gene pool. Intergroup differentiation of the world populations by these SNPs reflects mainly interracial differences. The greatest differences in the genetic structure between the studied populations were seen for the markers localized in intergenic regions. Statistically significant differences were found when comparing the levels of the average expected heterozygosity between groups of “L4 carrier populations” of mycobacteria and “non-L4” populations, which indicates the impact of the prevalence of different pathogenic lineages of M. tuberculosis on the formation of population specificity of the allelic frequencies.

Специфичность структуры генофондов различных этно-территориальных групп населения может быть основой эпидемических особенностей распространения туберкулеза (ТБ) и структуры генетической компоненты подверженности данной патологии. Изучена вариабельность 62 потенциально значимых для развития ТБ генетических вариантов у русского населения г. Томска и дана оценка дифференциации по этим маркерам различных этно-территориальных групп мира. Изученная выборка представлена 445 русскими жителями г. Томска без бронхолегочной патологии. Для сравнения привлечены данные о вариабельности исследованных маркеров в 26 популяциях, охарактеризованных в проекте “1000 геномов”. В томской популяции для семи из 58 исследованных SNP обнаружен только анцестральный аллель; частоты аллелей для 36 маркеров находятся в границах значений, показанных для других европеоидных популяций; по 12 SNP зарегистрированные частоты были ближе к популяциям с существенной монголоидной компонентой. По совокупности полиморфных маркеров томская популяция, несмотря на географическую удаленность от остальных европеоидных популяций, не отличается от них (согласно расчетам генетических дистанций и Gst-статистики), хотя и имеет некоторые особенности генофонда. Межпопуляционная дифференциация популяций мира по этим SNP отражает главным образом межрасовые различия. Наибольшие различия по генетической структуре между популяциями показаны по маркерам, локализованным в межгенных регионах. Установлены статистически значимые различия при сравнении уровней средней ожидаемой гетерозиготности между группами “популяций-носителей линии L4” микобактерий и популяций “не-L4”, что свидетельствует о влиянии на формирование популяционной специфичности аллельных частот данных маркеров распространенности разных патогенных линий M. tuberculosis.

The genetically mediated ability of the host to provide an adequate immune response to the pathogen plays an important role in the development of tuberculosis infection. Genome-wide association studies performed in different populations revealed the association of a number of chromosomal regions with the development of tuberculosis (TB). At the same time, full characteristics of the factors of genetic susceptibility to the disease remains an unresolved problem, and the associations identified are not always reproduced in studies in other populations. A total of 45 single nucleotide polymorphisms (SNPs) were analyzed in 768 individuals, including 323 tuberculosis patients and 445 healthy individuals. Analysis of associations of tuberculosis with genetic markers was carried out using logistic regression. Permutations were used to account for multiple comparisons. Nominal statistically significant association with tuberculosis was detected for two SNPs, rs10515787 (intronic variant of the EBF1 gene) and rs10956514 (intronic variant of the ASAP1 gene) (p = 0.005 and 0.049, respectively). After the permutation test, only one of the associations was preserved, for rs10515787 (p = 0.003). Thus, in Russians from the city of Tomsk, the association of rs10515787 at the EBF1 gene with the development of tuberculosis was confirmed. However, the results of this study identify rare A allele as a risk factor for the development of TB, while in an earlier study, it was identified as being protective relative to the risk for developing of tuberculosis. The revealed “reverse association” is an interesting fact that requires further investigation.

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.