Combinations of proinflammatory cytokine genes and their interactions in Russian tuberculosis patients in the Chelyabinsk Region

Tuberculosis is a widespread infectious disease caused by M. tuberculosis, which is one of the leading causes of death  in the world.  According to numerous literature data,  this is a genetically determined disease, and genetical polymorphism is a mechanism that leads to progression from infection to clinical  manifestation. Susceptibility to infection correlates with different genes at several loci, and each individual gene plays a unique role. It is known, that  the analysis of individual polymorphic variants  of genes does not provide  a sufficiently complete picture of the  mechanisms of formation of a predisposition to multifactorial pathologies, such  as tuberculosis, since  their  development is based  on complex intergenic and  gene-environmental interactions, which  must  be taken  into  account when  predicting the  risk of developing active  forms of the  disease  and  its severity. The concept of the functioning of cytokines as biomarkers of tuberculosis suggests that their products and interactions play an important role in the immunopathogenesis of the disease, because they form a cytokine chain  with  unique  functions, where  the  removal  of any  link in the  chain  disrupts  the  entire  mechanism of the  immuno-inflammatory process.  IL-6, together with  TNFα and  IL-1β, initiate early  pro-inflammatory reactions in  tuberculosis, stimulating local  and  systemic  inflammatory reactions under  participation of all common pro-inflammatory mechanisms with further  transition to activation of acquired immunity. Earlier, we carried  out a set of studies to evaluate  the association of alleles and genotypes  of these cytokine genes with a predisposition/resistance to pulmonary tuberculosis in Russians  of the  Chelyabinsk region.  These  studies have resulted  into assessment of certain distribution patterns of IL-1β, TNFα, IL-6  alleles and their genotypes in pulmonary tuberculosis and its various clinical  forms. The following methods were used: isolation of DNA samples  from whole blood,  genotyping of the studied  gene polymorphisms using PCR  and RFLP techniques. In this study, we analyzed  the intergenic interactions of the genes for the pro-inflammatory cytokines IL-1β, TNFα, IL-6 using the method of reducing multifactor dimension in patients with pulmonary tuberculosis. The program designs optimal models  of combinations for the studied  genes and their  interactions in tuberculosis patients. As a result of this study, a three-locus model  IL-6  (-174)*С – IL-1β (+3953)*Т – IL-1β (+3953)*С was established, which was characterized by 100% reproducibility and prediction accuracy of 72%. Among the analyzed  polymorphisms, the  IL-6  (-174)*C polymorphism possessed  the  highest  predictive potential with 15.27%

INTERGENIC INTERACTIONS OF CYTOKINE GENES IL1, IL1RA, IL6, IL10 AND TNFА IN PATIENTS WITH IRRITABLE BOWEL SYNDROME AND ULCERATIVE COLITIS IN RUSSIAN POPULATION OF THE CHELYABINSK REGION

Сomplex intergenic interactions should be taken into account when predicting the risk of adverse course in a pathological process. This presumption is at the heart of evolving multifactorial diseases (ulcerative colitis and irritable bowel syndrome). A single genetic polymorphism seems to be a weak risk factor when predicting the disease evolution and it could not be used as a prognostic model for development of multifactorial pathologies, especially in cases of rare alleles. However, it is well known that the combination of unfavorable alleles of several genes with an additive effect is dangerous. Therefore, identification of such polymorphisms is very important.Previously we conducted a test panel, in order to evaluate associations of alleles and genotypes of some cytokine genes (IL1β, TNFα, IL1rа, IL10, IL6) with predisposal, or resistance for ulcerative colitis and irritable bowel syndrome in the Russian Chelyabinsk region. Distribution of alleles and genotypes of these genes have been assessed in irritation bowel disease (IBD) and ulcerative colitis (UC). The following methods were used: isolation of DNA samples from whole blood, genotyping of the studied gene polymorphisms with PCR, RFLP. A comparative analysis of intergenic interactions between the cytokine genes IL1β, TNFα, IL1ra, IL10, IL6 in the IBD and UC patients was carried out by the Multifactor Dimensionality Reduction method. The analysis is based on the use of polymorphic loci of IL1β, TNFα, IL1ra, IL10, IL6 combinations chosen for analysis of intergenic interactions, with respect to the risk for IBS and UC predisposition. As a result of this study, a fourlocus model IL1β(+3953)*Т/TNFα(-308)*A/IL10(-1082)*G/IL6(-174)*G was identified for IBS, which was characterized by 90% repeatability and prediction accuracy of 74.5%. This model of gene interactions between the cytokine IL1β, TNFα, IL1ra, IL10, IL6 genes had the greatest prediction potential (p < 0.001) in IBS, whereas the model for UC was not statistically significant. The following types of genetic interactions were established: synergism between the IL1β(+3953)*Т and TNFα(-308)*A loci, whereas IL6(-174)*G и IL10(-1082)*G, TNFα(-308)*A seem to be in antagonistic relationships. The study made it possible to establish that the -174G/C IL-6 polymorphism may play a central role and provide intergenic interactions with SNPs of IL1β, TNFα, IL10 for predisposal to irritable bowel syndrome in Chelyabinsk Region of Russia

Immunogenetic profile of MIC (A, B) HLA loci linked to MHC antigenic complex in Russians of the Chelyabinsk Region

The MIC genes are located on chromosome 6 in the class I major histocompatibility complex (MHC) region and encode a membrane-bound stress-inducible protein that acts as a ligand to stimulate the NKG2D activating receptor expressed on the surface of the most natural killer cells (NK). Currently, 7 MIC loci are known, of which only MICA and MICB encode proteins and show a significant allelic polymorphism. The MIC gene polymorphism and their location in the HLA region suggests presence of some ethnic and populational differences for the gene frequencies, linkage disequilibrium of distinct loci, and distribution of HLA-MIC haplotypes, thus making it possible to get information on genetic relationship of human populations. The aim of our study was to assess immunogenetic profile of Russian population in Chelyabinsk Region based on the non-classical HLA loci, i.e., MICA and MICB, in the context of worldwide population data. Methods of the study included immunogenetic typing of 100 donors identifying themselves as Russians, taken from the Registry of Stem Cell Donors at the Chelyabinsk Regional Blood Transfusion Station. The 2 loci (MICA and MICB) were typed at basic resolution, using PCR technique with sequence-specific primers (SSP-PCR). Gene frequencies (GF) were calculated using programs for immunogenetic research (Arlequin 3.5).Among Russian population from Chelyabinsk Region, the following characteristics of the MICA gene distributions were found: MICA *008, *002, *010, *009, frequency of > 7%; average frequencies, for MICA *004, *007, *018, *017; whereas MICA *027, *011, *006, *009:02, *049, *012, *016 was registered at a frequency of < 3.5%. MICB gene profile was as follows: MICB *005:02, *004, *002, *008 at a frequency of > 6%; at a frequency of 4% MICB *003, *005:03; MICB *005:01, * 005:04, * 009N, MICB *013, *014 at a frequency of0.5%. As based on calculated genetic distances (according to Ney) for the MICA locus, the dendrogram and scatter plot were designed by means of multidimensional scaling (MDS) method, presenting location of 30 world populations, including data on Russians in Chelyabinsk Region. The smallest genetic distances between the population of Russians from Chelyabinsk Region and other world populations were found between the population of Slovenia, as well as the USA population of European origin. As based on scatterplot obtained by the MDS approach for MICA gene frequencies, using the data of cluster analysis, we have found that the population of Russians from Chelyabinsk Region belongs to a cluster of typical European populations.The obtained patterns could be used for practical purposes to create a registry of stem cell donors in Russia. In addition, the data may be used as a control group for further research in the area of HLA-disease association, and could be also demanded by the specialists in population ethnogenesis

Room temperature chiral magnetic skyrmion in ultrathin magnetic nanostructures

Magnetic skyrmions are chiral spin structures with a whirling configuration. Their topological properties, nanometer size and the fact that they can be moved by small current densities have opened a new paradigm for the manipulation of magnetisation at the nanoscale. To date, chiral skyrmion structures have been experimentally demonstrated only in bulk materials and in epitaxial ultrathin films and under external magnetic field or at low temperature. Here, we report on the observation of stable skyrmions in sputtered ultrathin Pt/Co/MgO nanostructures, at room temperature and zero applied magnetic field. We use high lateral resolution X-ray magnetic circular dichroism microscopy to image their chiral N\'eel internal structure which we explain as due to the large strength of the Dzyaloshinskii-Moriya interaction as revealed by spin wave spectroscopy measurements. Our results are substantiated by micromagnetic simulations and numerical models, which allow the identification of the physical mechanisms governing the size and stability of the skyrmions.Comment: Submitted version. Extended version to appear in Nature Nanotechnolog

ПРИБОР НА ОСНОВЕ GaInAsSb СВЕТОДИОДОВ ДЛЯ ИЗМЕРЕНИЯ СОДЕРЖАНИЯ ВОДЫ В НЕФТИ

The main object of the work was developed the device based on GaInAsSb diodes for measurement water content in oil. Optical absorption method was used in this device. Three LEDs emitting in the range from 1.6 to 2.4 μm, and one wide-band GaSb/GaInAsSb/GaAlAsSb photodiode were used as sources of radiation and detectors.The device was developed on the basis of selective optical absorption method of detection for measuring water content in oil. As sources of radiation, LEDs emitting in the range from 1.6 to 2.4 μm were used. The results of the experiments showed that the method used makes it possible to measure the water concentration in oil in the range from 0.2 to 40% with an relative error of not more than 2 %.The technical requirements and operating parameters of the used light and photodiodes were established. Investigations of the dependence of the luminescence spectra of LEDs on temperature have shown the importance of using thermal control on the sources and detectors of radiation. The possibility of using one device for different types of oil, as well as oil products during preliminary calibration were shown in the paper. The importance of using a rotary pump for mixing and pumping the analyzed medium and a flow cell was established.Изготовление приборов на основе полупроводниковых излучателей является важным направлением применения оптического абсорбционного метода для детектирования жидких сред. Целью данной работы являлось создание прибора для измерения содержания воды в нефти на основе GaInAsSb светодиодов.Датчик измерения концентрации воды в нефти включает 3 светодиода на различные длины волн и один широкополосный фотоприемник. Использование светодиодов на основе GaInAsSb кристаллов позволило получить высокоэффективный и точный прибор для измерения концентрации воды в нефти. Предложен способ измерения анализируемой среды с помощью проточной кюветы, учитывающий неоднородность распределения водонефтяной эмульсии. Полный цикл измерения концентрации воды в нефти состоял в измерении поглощения излучения от каждого из трех светодиодов в течение 10 с, усреднении результатов и сравнении с калибровочной кривой.Разработан прибор на основе селективного оптического абсорбционного метода детектирования для измерения содержания воды в нефти. В качестве источников излучения использованы светодиоды, излучающие в диапазоне от 1,6 до 2,4 мкм. Результаты экспериментов показали, что используемый метод позволяет производить измерения концентрации воды в нефти в диапазоне от 0,2 до 40 % с погрешностью не более 2 %.Установлены технические требования и параметры работы используемых светои фотодиодов, а также необходимость использования проточной кюветы для анализируемой среды. Показана возможность использования одного прибора для различных сортов нефти, а также нефтепродуктов при проведении предварительной калибровки

Оценка влияния полиморфизмов генов-транспортеров (RFC1, MDR1) и GGH на эффективность метотрексата при ревматоидном артрите

The efficacy of methotrexate (MT) in patients with rheumatoid arthritis (RA) may be determined by genetic factors.Objective: to evaluate the isolated and combined effects of single nucleotide polymorphisms (SNPs) of membrane transporter proteins (RFC1 80G>A and MDR1 3435C>T) and the GGH -401C>T gamma-glutamyl hydrolase enzyme genes on the efficacy of MT in patients with RA.Material and methods. The study group consisted of 85 patients with a confirmed diagnosis of RA, who received therapy with MT starting at 10 mg/week and increasing in dose to a maximum of 25 mg/week. Efficacy was assessed after six months of treatment using the dynamics of the DAS28 index, identifying patients who responded and those who did not respond to MT therapy.Genotyping of RFC1, MDR1 and GGH gene polymorphisms was performed by real-time polymerase chain reaction. Three different approaches were used to analyze the results: 1) analysis for each of the genes; 2) logistic regression; and 3) multifactor dimensionality reduction (MDR).Results and discussion. Single gene analysis was used to determine the most likely predictors of non-response to therapy: 1) for GGH-401C>T, TT genotype (odds ratio, OR 5.09; 95% confidence interval, C11.11—23.3); 2) forMDR13435C>T, the TT genotype (OR 2.38; 95% CI0.89-6.37); 3) for RFC180G>A, not - AA genotype (OR 1.87; 95% CI 0.93-3.76).The logistic regression model showed a significant effect of homozygous genotype GGH -401TT on the efficacy of MT with low sensitivity of the method. The multifactorial dimensionality reduction results show a significant synergistic effect of the MT transport genes (MDR1, RFC1) and the GGH enzyme encoding the conversion of MT to the elimination form.Conclusion. Using various statistical methods, the following results were obtained: Single gene analysis revealed the most likely predictors of nonresponse to MT therapy: GGH -401C>T - TT genotype, MDR1 3435C>T - TT genotype, RFC1 80G>A - not-AA genotype; the method of multiple logistic regression allowed to determine the significant effect of GGH -401ТТ genotype on the effect of the drug with a low sensitivity of the method; the isolated effect of polymorphisms is probably less pronounced than their combined effect on the effectiveness of MT. SNP synergism is a major contributor to the development of treatment resistance. MDR is a promising method that can be used in the future to assess the impact of SNPs.Эффективность метотрексата (МТ) у больных ревматоидным артритом (РА) может определяться генетическими факторами.Цель исследования — оценить изолированное и совместное влияние однонуклеотидных полиморфизмов (SNP) генов мембранных белков-транспортеров (RFC1 80G>A и MDR1 3435C>T) и гена фермента гамма-глутамилгидролазы GGH -401C>T на эффективность МТ у больных РА.Материал и методы. Исследуемую группу составили 85 больных с достоверным диагнозом РА, которым проводилась терапия МТ начиная с 10 мг/нед с повышением дозы максимально до 25 мг/нед. Эффективность оценивалась после 6 мес лечения по динамике индекса DAS28, были определены пациенты, отвечающие и не отвечающие на терапию МТ.Генотипирование полиморфизмов генов RFC1, MDR1 и GGH выполнено методом полимеразной цепной реакции в режиме реального времени. Для анализа результатов использовались три различных подхода: 1) анализ по каждому из генов; 2) логистическая регрессия и 3) многофакторное снижение размерности (Multifactor Dimensionality Reduction, MDR).Результаты и обсуждение. С помощью анализа по отдельным генам идентифицированы наиболее вероятные предикторы отсутствия ответа на терапию: 1) для GGH-401C>T — генотип TT(отношение шансов, ОШ5,09; 95% Доверительный интервал, ДИ 1,11—23,3); 2) для MDR13435C>T-генотип TT(ОШ2,38; 95% ДИ0,89-6,37); 3) Для RFC180G>A - генотип не АА (ОШ 1,87; 95% ДИ 0,93-3,76).Модель логистической регрессии свидетельствует о значимом влиянии на эффективность МТ носительства гомозиготного генотипа GGH -401TT при низкой чувствительности метода. Результаты многофакторного снижения размерности демонстрируют значимое синергичное влияние генов транспорта МТ (MDR1, RFC1) и фермента GGH, кодирующего конверсию МТ в форму Для элиминации.Заключение. С помощью разных статистических методов получены следующие результаты: анализ по отдельным генам выявил наиболее вероятные предикторы отсутствия ответа на терапию МТ: GGH - 401C>T - генотип TT, MDR1 3435C>T - генотип TT, RFC1 80G>A - генотип не AA; метод множественной логистической регрессии позволил определить значимое влияние генотипа GGH - 401ТТ на эффект препарата при низкой чувствительности метода; изолированное влияние полиморфизмов, вероятно, менее выражено, чем их совместное воздействие на эффективность МТ. Синергизм SNP вносит большой вклад в формирование резистентности к терапии. MDR - перспективный метод, который может быть использован в дальнейшем для оценки влияния SNP

МЕДИКАМЕНТОЗНОЕ ЛЕЧЕНИЕ МУКОВИСЦИДОЗА В РОССИИ: АНАЛИЗ ДАННЫХ НАЦИОНАЛЬНОГО РЕГИСТРА (2014)

The aim of this study was to analyze drug therapy of patients with cystic fibrosis (CF) in Russia. Methods. Findings of the Russian National Register of CF patients, 2014, were used in this study. The 2014 Register included data for 2,131 patients (2,092 alive and 39 died) from 74 regions of Russia. The median age was 10.2 (15.2) years, 29.2% of patients were aged 18 years and older. We analyzed administration of bronchodilators, inhaled corticosteroids (ICS), systemic steroids, dornase alfa, hypertonic saline solution, macrolides, systemic and inhaled antibiotics, pancreatic enzymes, ursodeoxycholic acid, and fat-soluble vitamins. Results. Drug administration rates were as follows: bronchodilators, 65.9%; ICS, 21.7%; systemic steroids, 5.5%; macrolides, 32.4%; dornase-alfa, 92.8%; hypertonic saline solution, 45.9%; intravenous antibiotics, 62.3%; oral antibiotics, 73.3%; inhaled antibiotics, 41.3%; pancreatic enzymes, 93.3%; ursodeoxycholic acid, 91.4%; and fat-soluble vitamins, 88.3%. Conclusion. Compared to treatment of CF patients in the Western Europe, there is higher rate of administration of pancreatic enzymes, ursodeoxycholic acid, dornase alfa, hypertonic saline solution and intravenous antibiotics in Russia. Compared to treatment strategy in USA, there is higher rate of administration of pancreatic enzymes and lower rate of administration of bronchodilators, hypertonic saline solution and inhaled antibiotics in Russia. Муковисцидоз (МВ) – тяжелое мультисистемное заболевание, требующее комплексного медикаментозного и немедикаментозного лечения. Особенностям лекарственной терапии разнородных по числу и возрасту групп больных МВ, проживающих в разных регионах России, посвящено ограниченное число работ, однако общий анализ данных большой группы пациентов в рамках единого регистра ранее не проводился. Цель. Выявление особенностей медикаментозной терапии больных МВ в России по данным национального Регистра (2014). Материалы и методы. Использованы сведения о пациентах (n = 2 131; 2 092 живых и 39 умерших) из 74 регионов России, состоящих в национальном Регистре больных муковисцидозом (2014). Медиана возраста пациентов составила 10,2 (15,2) года, доля взрослых (не моложе 18 лет) – 29,2 %. Проанализирована частота назначения лекарственной терапии бронходилататорами, ингаляционными (иГКС) и системными (сГКС) глюкокортикостероидами (ГКС), дорназой альфа, гипертоническим раствором натрия хлорида, макролидами, системными и ингаляционными антибактериальными препаратами (АБП), панкреатическими ферментами, урсодезоксихолевой кислотой (УДХК), жирорастворимыми витаминами. Результаты. Частота применения медикаментозной терапии по России распределена следующим образом: бронходилататоры – 65,9 %; иГКС – 21,7 %; сГКС – 5,5 %; макролиды – 32,4 %; дорназа альфа – 92,8 %; гипертонический раствор натрия хлорида – 45,9 %; внутривенные АБП – 62,3 %; пероральные АБП – 73,3 %; ингаляционные АБП – 41,3 %; панкреатические ферменты – 93,3 %; УДХК – 91,4 %; жирорастворимые витамины – 88,3 %. Отмечено, что взрослым больным наиболее часто назначаются бронхолитические препараты, АБП и ГКС; реже применяются панкреатические ферменты и УДХК. Заключение. Среди особенностей терапии российских больных по сравнению со странами Западной Европы можно выделить высокую долю назначения панкреатических ферментов, УДХК, дорназы альфа, гипертонического раствора и внутривенных АБП. По сравнению с США чаще назначаются панкреатические ферменты, реже – бронходилататоры, гипертонический раствор натрия хлорида и ингаляционные АБП

DEVICE BASED ON GAINASSB LEDS FOR MEASUREMENT OF WATER CONCENTRATION IN OIL

The main object of the work was developed the device based on GaInAsSb diodes for measurement water content in oil. Optical absorption method was used in this device. Three LEDs emitting in the range from 1.6 to 2.4 μm, and one wide-band GaSb/GaInAsSb/GaAlAsSb photodiode were used as sources of radiation and detectors.The device was developed on the basis of selective optical absorption method of detection for measuring water content in oil. As sources of radiation, LEDs emitting in the range from 1.6 to 2.4 μm were used. The results of the experiments showed that the method used makes it possible to measure the water concentration in oil in the range from 0.2 to 40% with an relative error of not more than 2 %.The technical requirements and operating parameters of the used light and photodiodes were established. Investigations of the dependence of the luminescence spectra of LEDs on temperature have shown the importance of using thermal control on the sources and detectors of radiation. The possibility of using one device for different types of oil, as well as oil products during preliminary calibration were shown in the paper. The importance of using a rotary pump for mixing and pumping the analyzed medium and a flow cell was established