Age-related trajectories of DNA methylation network markers: a parenclitic network approach to a family-based cohort of patients with Down Syndrome

Despite the fact that the cause of Down Syndrome (DS) is well established, the underlying molecular mechanisms that contribute to the syndrome and the phenotype of accelerated aging remain largely unknown. DNA methylation profiles are largely altered in DS, but it remains unclear how different methylation regions and probes are structured into a network of interactions. We develop and generalize the Parenclitic Networks approach that enables finding correlations between distant CpG probes (which are not pronounced as stand-alone biomarkers) and quantifies hidden network changes in DNA methylation. DS and a familybased cohort (including healthy siblings and mothers of persons with DS) are used as a case study. Following this approach, we constructed parenclitic networks and obtained different signatures that indicate (i) differences between individuals with DS and healthy individuals; (ii) differences between young and old healthy individuals; (iii) differences between DS individuals and their age-matched siblings, and (iv) difference between DS and the adult population (their mothers). The Gene Ontology analysis showed that the CpG network approach is more powerful than the single CpG approach in identifying biological processes related to DS phenotype. This includes the processes occurring in the central nervous system, skeletal muscles, disorders in carbohydrate metabolism, cardiopathology, and oncogenes. Our open-source software implementation is accessible to all researchers. The software includes a complete workflow, which can be used to construct Parenclitic Networks with any machine learning algorithm as a kernel to build edges. We anticipate a broad applicability of the approach to other diseases

Прогнозирование степени перегрузки правых камер сердца у пациентов с острой массивной тромбоэмболией легочной артерии на основании результатов КТ-диагностики

The study group included 147 patients at the stage of preparation for emergency surgical treatment of acute massive PE in the period from March 2012 to December 2019 inclusive. As CT indicators of overload of the right chambers of the heart, the usual CT indicators that do not require the use of expert – class computed tomographs were taken – they were the superior vena cava, inferior vena cava, unpaired vein; reflux of the contrast drug into the inferior vena cava; reflux of the contrast drug into the hepatic veins. In the course of the study, a comparative analysis of the average pressure in the pulmonary artery with the above CT indicators was performed. The most stable statistical relationship with the indicators of mean pressure in the pulmonary artery was demonstrated by CT parameters – the diameter of the unpaired vein and the reflux of the contrast agent into the hepatic veins. Based on the results of the work, a method for calculating the actual values of the average pressure in the pulmonary artery based on the CT parameter of the diameter of the unpaired vein is proposed.В группу исследования вошло 147 пациентов на этапе подготовки к экстренному хирургическому лечению острой массивной тромбоэмболии легочной артерии (ТЭЛА) в период с марта 2012 г. по декабрь 2019 г. включительно. В качестве КТ-показателей перегрузки правых камер сердца взяты обычные КТ-показатели, не требующие использования компьютерных томографов экспертного класса, ими стали верхняя полая вена, нижняя полая вена, непарная вена; рефлюкс контрастного препарата в нижнюю полую вену; рефлюкс контрастного препарата в печеночные вены. В ходе исследования проведен сравнительный анализ среднего давления в легочной артерии с вышеуказанными КТ-показателями. Наиболее устойчивую статистическую взаимосвязь с показателями среднего давления в легочной артерии продемонстрировали КТ-параметры – диаметр непарной вены и рефлюкс контрастного препарата в печеночные вены. По результатам работы предложена методика расчета фактических значений среднего давления в легочной артерии на основании КТ-параметра “диаметр непарной вены”

Biocompatibility of Bare Nanoparticles Based on Silicon and Gold for Nervous Cells

This work aimed to investigate the biocompatibility of bare (ligand-free) lasersynthesized nanoparticles (NPs) based on silicon (Si) and gold (Au) with primary hippocampal cultures. 1%, 5% and 7% of culture medium were replaced by 0.1 mg/mL NP solution on day 14 of culture development in vitro. Our studies revealed that the NPs caused a dose-dependent cytotoxic effect, which was manifested by an increase the number of dead cells and a decrease of the spontaneous functional calcium activity of neural networks. Au NPs revealed less pronounced cytotoxic effect than Si ones and it can be explained by larger size and better solubility of Si NPs. Keywords: bare nanoparticles, primary hippocampal cultures, neurotoxicit

Cytokine profile in hospitalized patients with COVID-19 of different severity

Analysis of cytokine profile markers in conjunction with the clinical manifestations of coronavirus disease 2019 (COVID-19) can provide valuable information about the pathogenetic manifestations of the disease, and therefore, in the future, determine drugs that affect the cytokine storm and have an anti-inflammatory effect.Aim. To identify correlations between the parameters of the developed cytokine profile and the clinical course in hospitalized patients with COVID-19 of different severity.Material and methods. The study included 70 hospitalized patients with a confirmed diagnosis of COVID-19, with a mean age of 58 [50;69] years, including 40 men (57%) and 30 women (43%). The average lung involvement according to computed tomography (CT) at admission was CT-2 [1;3]. Peripheral venous blood was taken at admission, which averaged 7 [6; 8] days from the symptom onset. Standard biochemical parameters were studied, as well as 47 cytokines and chemokines using the Multiplex system (Merck KGaA, Darmstadt, Germany).Results. Correlations was found between the lung involvement degree and the level of IL-8 (r=0,31, p<0,05), IL-15 (r=0,35, p<0,05), IL-18 (r=0,31, p<0,05), MCP-1 (r=0,36, p<0,05), MIG (r=0,50, p<0,05), TNF-α (r=0,41, p<0,05). An inverse correlation was also found in the level of blood oxygen saturation with the same indicators as follows: IL-8 (r=-0,27, p<0,05), IL-15 (r=-0,34, p<0,05), IL-18 (r=-0,31, p<0,05), MCP-1 (r=-0,40, p<0,05), MIG (r=-0,56, p<0,05), TNF-α (r=-0,45, p<0,05). IL-6 levels were significantly elevated in patients with severe COVID-19 (CT3, CT4), while no increase in IL-6 was observed in patients with moderate disease (CT1, CT2). It is noteworthy that in patients with diabetes, the highest values of IL-12, IL-9 were recorded.Conclusion. Hyperinflammatory syndrome in severe COVID-19 is manifested by high levels of IL-6, MIG, MDC, MCP-1, M-CSF, TNF-α, β, IL-8, IL-18, IL-15. With the CT-1 and CT-2, an increase in only the level of IL-18, IL-8 is noted. The identified patterns prove and make it possible to explain a number of systemic inflammatory changes that occur with COVID-19

Intracellular Neuroprotective Mechanisms in Neuron-Glial Networks Mediated by Glial Cell Line-Derived Neurotrophic Factor.

peer reviewedGlial cell line-derived neurotrophic factor (GDNF) has a pronounced neuroprotective effect in various nervous system pathologies, including ischaemic brain damage and neurodegenerative diseases. In this work, we studied the effect of GDNF on the ultrastructure and functional activity of neuron-glial networks during acute hypoxic exposure, a key damaging factor in numerous brain pathologies. We analysed the molecular mechanisms most likely involved in the positive effects of GDNF. Hypoxia modelling was performed on day 14 of culturing primary hippocampal cells obtained from mouse embryos (E18). GDNF (1 ng/ml) was added to the culture medium 20 min before oxygen deprivation. Acute hypoxia-induced irreversible changes in the ultrastructure of neurons and astrocytes led to the loss of functional Сa(2+) activity and neural network disruption. Destructive changes in the mitochondrial apparatus and its functional activity characterized by an increase in the basal oxygen consumption rate and respiratory chain complex II activity during decreased stimulated respiration intensity were observed 24 hours after hypoxic injury. At a concentration of 1 ng/ml, GDNF maintained the functional metabolic network activity in primary hippocampal cultures and preserved the structure of the synaptic apparatus and number of mature chemical synapses, confirming its neuroprotective effect. GDNF maintained the normal structure of mitochondria in neuronal outgrowth but not in the soma. Analysis of the possible GDNF mechanism revealed that RET kinase, a component of the receptor complex, and the PI3K/Akt pathway are crucial for the neuroprotective effect of GDNF. The current study also revealed the role of GDNF in the regulation of HIF-1α transcription factor expression under hypoxic conditions

Белковый состав и функциональные показатели мембран эритроцитов при трансплантации печени и почки

Organ transplantation is an effective treatment for many end-stage diseases. However, reperfusion injury constitutes a major complication of transplantation, which is associated with microcirculatory disorders and aggregation of blood corpuscles. Red blood cells (RBC) play an essential role in maintaining hemodynamic and rheological properties of the blood. Moreover, the study of mechanisms of changes in RBC functional indices is an urgent task. The main indicator of RBC functioning is the stability of RBC membrane structure. The issue of RBC membrane modification in organ transplantation has not been studied so far. Objective: to study the protein composition of RBC membranes, their aggregation and electrokinetic parameters in liver and kidney recipients, as well as in related kidney and liver fragment donors before and after operation. Research materials. Blood of 12 kidney recipients and 5 related kidney donors, 8 liver recipients and 4 related liver fragment donors – 1–2 hours before surgery, 1 week, 1, 2, 7, 10, 12 months after surgery. The control group consisted of 8 healthy volunteers. Research methods. Protein separation was done by Laemmli electrophoresis. RBC electrophoretic mobility, which characterizes the electrokinetic properties of cells, was measured by microelectrophoresis. Aggregation was calculated microscopically by counting unaggregated RBCs. Obtained values were compared by Mann-Whitney U test. Results. Examination of the RBC membrane of kidney recipients revealed a significant decrease in the amount of Band 3 protein and glycophorin before and after transplantation. Band 3 protein levels reduced at 1 month, glycophorin reduced at 7 months after surgery, with a maximum decrease in these protein fractions by more than 50% by 7 days compared with control values. There was also a decrease in spectrin content for 2 months after surgery with a maximum decrease of 30% by 1 month. In liver recipients, analysis of RBC membrane proteins revealed a decrease in the amount of glycophorin before surgery and further decrease at 2 months of post-transplant period. The maximum decrease in this index was 72% by 7 days after surgery. In addition, there was a fall in spectrin and Band 3 protein levels at 1 month by more than 60% relative to the control values. In donors, there were changes in the protein fraction of RBC membranes in the long-term post-operative period: spectrin and Band 3 protein levels reduced by 2 times at month 2 in kidney donors, while glycophorin levels reduced by 2.3 times at month 1 after operation in liver donors. Similarly, both groups of donors had increased actin levels at month 1 after surgery. The revealed changes in protein levels in the protein phase of RBC membranes were combined with functional indices of RBCs. In kidney recipients, decreased RBC electrophoretic mobility and increased aggregation were detected at 2 months. In liver recipients, the changes in these indicators were at 1 month. A decrease in RBC electrophoretic mobility was detected in donors of both groups. Conclusion. Changes in RBC membrane electronegativity are associated with changes in glycophorin and Band 3 protein levels, whereas in RBC aggregation process in liver/kidney recipients, the structural and functional disorders in the interrelationships of such membrane proteins as spectrin, Band 3 protein, and glycophorin, are significant factors. Alteration of actin determines inhibition of RBC aggregation growth in donors.Трансплантация органов является эффективным методом лечения пациентов с терминальными стадиями ряда тяжелых заболеваний. Однако серьезным осложнением при трансплантации являются реперфузионные повреждения, которые связаны с микроциркуляторными нарушениями и агрегацией форменных элементов крови. Эритроциты играют существенную роль в поддержании гемодинамических и реологических свойств крови, и изучение механизмов изменения их функциональных показателей является актуальной задачей. Основным показателем функционирования эритроцита служит стабильность структуры мембраны. Вопрос о модификации эритроцитарной мембраны при трансплантации органов на сегодняшний день не исследован.Цель: изучение белкового состава мембран эритроцитов, их агрегационных и электрокинетических показателей у реципиентов печени и почки, а также родственных доноров почки и фрагмента печени до и в динамике послеоперационного периода.Материалы исследования. Кровь 12 реципиентов почки, 5 родственных доноров почки, 8 реципиентов печени и 4 родственных доноров фрагмента печени во временной динамике – за 1–2 часа до операции, через 1 неделю, 1, 2, 7, 10, 12 месяцев после операции. Группу контроля составили 8 здоровых добровольцев.Методы исследования. Разделение белков проводили методом электрофореза по Лэммли. Электрофоретическую подвижность эритроцитов, характеризующую электрокинетические свойства клеток, измеряли методом микроэлектрофореза. Агрегацию рассчитывали микроскопически, путем подсчета неагрегированных эритроцитов. Сравнение полученных величин проводили по U-критерию Манна–Уитни.Результаты. Исследование мембраны эритроцитов крови реципиентов почки выявило значимое снижение количества белка полосы 3 и гликофорина до и после проведения трансплантации. Уровень белка полосы 3 был снижен в течение 1 месяца, гликофорина – в течение 7 месяцев после операции с максимальным уменьшением данных фракций белков более чем на 50% к 7-м суткам относительно значений контроля. Также регистрировалось снижение содержания спектрина в течение 2 месяцев после операции с максимальным снижением на 30% к 1 месяцу. У реципиентов печени анализ белков мембраны эритроцитов выявил снижение количества гликофорина до операции и дальнейшее его уменьшение в течение 2 месяцев посттрасплантационного периода. Максимальное снижение показателя – на 72% – было отмечено к 7-м суткам после операции. Кроме того, наблюдалось снижение количества спектрина и белка полосы 3 в течение 1 месяца более чем на 60% относительно значений контроля. У доноров изменения в белковой фракции эритроцитарных мембран регистрировались в отдаленный период после операции: у доноров почки снижение в 2 раза количества спектрина и белка полосы 3 отмечалось на 2-й месяц, у доноров печени снижение гликофорина в 2,3 раза – к 1-му месяцу после операции. Также в обеих группах доноров регистрировался рост концентрации актина к 1-му месяцу после операции. Выявленные изменения количества белков в белковой фазе эритроцитарных мембран сочетались с функциональными показателями эритроцитов. У реципиентов почки снижение ЭФПЭ и увеличение агрегации наблюдалось в течение 2 месяцев, у реципиентов печени изменения данных показателей зафиксированы в течение 1 месяца. У доноров обеих групп было выявлено уменьшение ЭФПЭ.Заключение. Совокупность полученных результатов показала, что изменение электроотрицательности мембран эритроцитов сопряжено с изменением содержания гликофорина и белка полосы 3, тогда как в процессе агрегации эритроцитов у пациентов после трансплантации печени/почки значимыми факторами являются структурно-функциональные нарушения взаимосвязей таких мембранных белков, как спектрин, белок полосы 3, гликофорин. Изменение актина определяет сдерживание роста агрегации эритроцитов у доноров

Age-related trajectories of DNA methylation network markers: A parenclitic network approach to a family-based cohort of patients with Down Syndrome

Despite the fact that the cause of Down Syndrome (DS) is well established, the underlying molecular mechanisms that contribute to the syndrome and the phenotype of accelerated aging remain largely unknown. DNA methylation profiles are largely altered in DS, but it remains unclear how different methylation regions and probes are structured into a network of interactions. We develop and generalize the Parenclitic Networks approach that enables finding correlations between distant CpG probes (which are not pronounced as stand-alone biomarkers) and quantifies hidden network changes in DNA methylation. DS and a family-based cohort (including healthy siblings and mothers of persons with DS) are used as a case study. Following this approach, we constructed parenclitic networks and obtained different signatures that indicate (i) differences between individuals with DS and healthy individuals; (ii) differences between young and old healthy individuals; (iii) differences between DS individuals and their age-matched siblings, and (iv) difference between DS and the adult population (their mothers). The Gene Ontology analysis showed that the CpG network approach is more powerful than the single CpG approach in identifying biological processes related to DS phenotype. This includes the processes occurring in the central nervous system, skeletal muscles, disorders in carbohydrate metabolism, cardiopathology, and oncogenes. Our open-source software implementation is accessible to all researchers. The software includes a complete workflow, which can be used to construct Parenclitic Networks with any machine learning algorithm as a kernel to build edges. We anticipate a broad applicability of the approach to other diseases