This work demonstrates the use of a solid-state nanopore detector to monitor the activity of a single molecule of a model enzyme, horseradish peroxidase (HRP). This detector includes a measuring cell, which is divided into cis- and trans- chambers by a silicon nitride chip (SiN structure) with a nanopore of 5 nm in diameter. To entrap a single HRP molecule into the nanopore, an electrode had been placed into the cis-chamber; HRP solution was added into this chamber after application of a negative voltage. The reaction of the HRP substrate, 2,2-azino-bis(3-ethylbenzothiazoline-6-sulfonate) (ABTS), oxidation by the enzyme molecule was performed in the presence of hydrogen peroxide. During this reaction, the functioning of a single HRP molecule, entrapped in the nanopore, was monitored by recording the time dependence of the ion current flowing through the nanopore. The approach proposed in our work is applicable for further studies of functioning of various enzymes at the level of single molecules, and this is an important step in the development of single-molecule enzymology.

Cardiovascular disease (CVD) represents one of the main causes of mortality worldwide and nearly a half of it is related to ischemic heart disease (IHD). The article represents a comprehensive study on the diagnostics of IHD through the targeted metabolomic profiling and machine learning techniques. A total of 112 subjects were enrolled in the study, consisting of 76 IHD patients and 36 non-CVD subjects. Metabolomic profiling was conducted, involving the quantitative analysis of 87 endogenous metabolites in plasma. A novel regression method of age-adjustment correction of metabolomics data was developed. We identified 36 significantly changed metabolites which included increased cystathionine and dimethylglycine and the decreased ADMA and arginine. Tryptophan catabolism pathways showed significant alterations with increased levels of serotonin, intermediates of the kynurenine pathway and decreased intermediates of indole pathway. Amino acid profiles indicated elevated branched-chain amino acids and increased amino acid ratios. Short-chain acylcarnitines were reduced, while long-chain acylcarnitines were elevated. Based on these metabolites data, machine learning algorithms: logistic regression, support vector machine, decision trees, random forest, and gradient boosting, were used for IHD diagnostic models. Random forest demonstrated the highest accuracy with an AUC of 0.98. The metabolites Norepinephrine; Xanthurenic acid; Anthranilic acid; Serotonin; C6-DC; C14-OH; C16; C16-OH; GSG; Phenylalanine and Methionine were found to be significant and may serve as a novel preliminary panel for IHD diagnostics. Further studies are needed to confirm these findings.

Changes in information on the number of human proteoforms, post-translational modification (PTM) events, alternative splicing (AS), single-amino acid polymorphisms (SAP) associated with protein-coding genes in the neXtProt database have been retrospectively analyzed. In 2016, our group proposed three mathematical models for predicting the number of different proteins (proteoforms) in the human proteome. Eight years later, we compared the original data of the information resources and their contribution to the prediction results, correlating the differences with new approaches to experimental and bioinformatic analysis of protein modifications. The aim of this work is to update information on the status of records in the databases of identified proteoforms since 2016, as well as to identify trends in changes in the quantities of these records. According to various information models, modern experimental methods may identify from 5 to 125 million different proteoforms: the proteins formed due to alternative splicing, the implementation of single nucleotide polymorphisms at the proteomic level, and post-translational modifications in various combinations. This result reflects an increase in the size of the human proteome by 20 or more times over the past 8 years.

Aim. To investigate the state of the platelet and plasma components of hemostasis in patients with myocardial infarction with non-obstructive coronary arteries (MINOCA).Material and methods. The study included 42 patients with non-ST-segment elevation myocardial infarction (NSTEMI): MINOCA (n=24) and MI-CAD (n=18). Platelet aggregation ability in response to activation was evaluated using Solar AP2110 and LASCA aggregometers. Platelet functional activity and calcium signaling were assessed using flow cytometry methods. The plasma component of hemostasis, in addition to routine coagulation tests was evaluated using the global coagulation test "Thrombodynamics". The control groups for tests consisted of healthy volunteers.Results. When analyzing the ability of platelets to form aggregates by the aggregometry tests, it was found that platelets in the MINOCA group formed aggregates significantly worse upon ADP stimulation at various concentrations compared to the MI-CAD group. However, when platelets were stimulated with collagen, the opposite effect was observed: in the MI-CAD group, there was a noticeable decrease in aggregate formation in terms of light scattering amplitude compared to the MINOCA group. Flow cytometry using the functional platelet activity test protocol revealed that both groups showed a significantly increased platelet size after activation, reduced platelet granularity) both at rest and upon activation, significantly decreased number of procoagulant phosphatidylserine-positive platelets, and reduced dense granule release upon activation compared to healthy volunteers. The calcium signaling test showed a weakened calcium release in response to ADP in the MINOCA group compared to the MI-CAD group. In the study of the plasma component, no significant differences between the groups or deviations were found according to both routine tests and the "Thrombodynamics" test.Conclusion. Platelet activity did not differ significantly between the MINOCA and MI-CAD groups; however, in the MINOCA group, platelet activity was lower in some tests compared to the MI-CAD group. In the study of the plasma hemostasis component, normocoagulation was recorded in both groups.

Using analytical technologies it is possible now to measure the entire diversity of molecules even in a small amount of biological samples. Metabolomic technologies simultaneously analyze thousands of low-molecular substances in a single drop of blood. Such analytical performance opens new possibilities for clinical laboratory diagnostics, still relying on the measurement of only a limited number of clinically significant substances. However, there are objective difficulties hampering introduction of metabolomics into clinical practice. The Institute of Biomedical Chemistry (IBMC), consolidating the efforts of leading scientific and medical organizations, has achieved success in this area by developing a clinical blood metabogram (CBM). CBM opens opportunities to obtain overview on the state of the body with the detailed individual metabolic characteristics of the patient. A number of scientific studies have shown that the CBM is an effective tool for monitoring the state of the body, and based on the CBM patterns (signatures), it is possible to diagnose and monitor the treatment of many diseases. Today, the CBM creation determines the current state and prospects of clinical metabolomics in Russia. This article, dedicated to the 80th anniversary of IBMC, is a review of these achievements focused on a discussion of their implementation in clinical practice.

AbstractMyocardial infarction is a major cause of morbidity and mortality worldwide. Metabolomic investigations may be useful for understanding the pathogenesis of ST-segment elevation myocardial infarction (STEMI). STEMI patients were comprehensively examined via targeted metabolomic profiling, machine learning and weighted correlation network analysis. A total of 195 subjects, including 68 STEMI patients, 84 patients with stable angina pectoris (SAP) and 43 non-CVD patients, were enrolled in the study. Metabolomic profiling involving the quantitative analysis of 87 endogenous metabolites in plasma was conducted. This study is the first to perform targeted metabolomic profiling in patients with STEMI. We identified 36 significantly altered metabolites in STEMI patients. Increased levels of four amino acids, eight acylcarnitines, six metabolites of the NO–urea cycle and neurotransmitters, and three intermediates of tryptophan metabolism were detected. The following metabolites exhibited decreased levels: six amino acids, three acylcarnitines, three components of the NO–urea cycle and neurotransmitters, and three intermediates of tryptophan metabolism. We found that the significant changes in tryptophan metabolism observed in STEMI patients—the increase in anthranilic acid and tryptophol and decrease in xanthurenic acid and 3-OH-kynurenine—may play important roles in STEMI pathogenesis. On the basis of the differences in the constructed weighted correlation networks, new significant metabolite ratios were identified. Among the 22 significantly altered metabolite ratios identified, 13 were between STEMI patients and non-CVD patients, and 17 were between STEMI patients and SAP patients. Seven of these ratios were common to both comparisons (STEMI patients vs. non-CVD patients and STEMI patients vs. SAP patients). Additionally, two ratios were consistently observed among the STEMI, SAP and non-CVD groups (anthranilic acid: aspartic acid and GSG (glutamine: serine + glycine)). These findings provide new insight into the diagnosis and pathogenesis of STEMI.

A comparative analysis of the results of genomic, transcriptomic, and proteomic profiling of HepG2 cell line samples was carried out in the gene-centric mode. The traceability of changes associated with the presence of nonsynonymous single nucleotide substitutions and indels in the genome at the transcriptomic and proteomic levels was shown. At the transcriptomic level, most of the molecular events caused by aberrations at the genomic level are recorded. At the same time, only single proteoforms can be detected among those encoded by the selected mutant genes. This is probably associated with the methodological limitations of proteomic methods, which do not allow registration of proteoforms present in the sample at low concentrations. The results of the study are consistent with previously obtained data from other scientific groups and describe the fundamental methodological solutions required to decipher the molecular postgenomic portrait of biological samples with a resolution at the level of aberrant molecules.

Platelet-type bleeding disorder-20 is a rare inherited thrombocytopenia caused by mutations in the SLFN14 gene. We report a case of a female patient with SLFN14 mutation, macrothrombocytopenia, severe hemorrhagic syndrome and a positive family history who was followed up from the age of 17 to 19. The 3-year follow-up showed a tendency towards partial normalization of platelet counts (from 47 to 82 × 109/L) and morphology. Platelet size and granularity as well as the density of glycoprotein (GP) membrane receptors such as GP Ib/V/IX and GP IIb/IIIa decreased. GP IIb/IIIa activation was impaired and there were no positive changes over time. The dense granules indicators were stably elevated. The parameters of a-granules (assessed by P-selectin expression) did not differ from the control group. The proportion of procoagulant phosphatidylserine-positive platelets at rest was increased and the potential to form procoagulant platelets upon activation was reduced. As the patient grew older, her bleeding disorder symptoms abated and she showed a tendency towards normalization of platelet laboratory parameters. All investigations were performed after obtaining informed consent from the patient and her parents in accordance with the Declaration of Helsinki.

Using human chromosome 18 (Ch18) genes as an example, a PCR analysis of the interindividual variability of expression of 244 genes was performed in the liver tissue. Although the quantitative profiles of the Ch18 transcriptome, expressed as the number of cDNA copies per single cell, showed a high degree of correlation between donors (Pearson correlation coefficient r(p) ranged from 0.963 to 0.966), the expression of the significant number of genes (from 13% to 19%, depending on the method of experimental data normalization) varied by more than 4-fold when comparing donors pairwise. At the same time, the proportion of differentially expressed genes increased with a decrease in the level of their expression. It is shown that the higher quantitative variability of low-abundance transcripts has mainly biological rather than technical nature. Bioinformatic analysis of the interindividual variability of the differential expression of Ch18 genes in the human liver tissue did not reveal any statistically significant groups of genes related to certain biological processes. This obviously indicates a rather transient nature of the interindividual variability of Ch18 gene expression, probably reflecting the response of cells of an individual to specific external stimuli.

The analysis of cytochrome P450 transcripts was carried out by the nanopore sequencing in liver tissue samples of three donors and HepG2 line cells. It has been demonstrated that direct mRNA sequencing with a MinION nanopore sequencer (Oxford Nanopore Technologies) allows one to obtained quantitative profiles for transcripts (and their splice variants) of cytochrome P450 superfamily genes encoding isoforms involved in metabolism of the large (~80%) part of drugs. The splice variant profiles substantially differ for donors. The cytochrome P450 gene expression at the transcript level is significantly weaker in cells of the HepG2 line compared with that in the normal liver tissue. This limits the capability of the direct mRNA nanopore sequencing for studying alternative splicing of cytochrome P450 transcripts in HepG2 cells. Both quantitative and qualitative profiles of the cytochrome P450 gene expression at the transcript level are notably differ in human liver tissue and HepG2 cells.

Despite modern possibilities of laboratory diagnosis of hemorrhagic syndrome, in some patients, the causes of bleeding remain unspecified. Among these reasons, mild defects in the platelet link of hemostasis can potentially be hidden. The aim of the work is to identify the features of the function of the platelet hemostasis in children with unspecified hemorrhagic syndrome. This study is supported by the Independent Ethics Committee and approved by the Academic Council of the Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology. We examined 50 patients aged 2 to 17 years with various manifestations of bleeding and lack of laboratory data proving coagulopathy and/or thrombocytopenia; platelet cytofluorometry with activation was performed. The morphological characteristics of platelets in terms of size/granularity (FSC/SSC), the density of the CD62p receptor as a marker of a-granule secretion, and d-granules of platelets were assessed by the fluorescence of loaded mepacrine. Platelet activation was performed with a CRP + TRAP mixture. Comparison was carried out with the results of examination of 50 healthy children (control group - CG) aged 2 to 17 years. The severity of hemorrhagic syndrome was assessed using the standardized ISTH BAT score. The severity of hemorrhagic manifestations according to BAT ISTH score ranged from 2 to 6 points. As a result of the study, two groups of patients differing in the calculated parameter of the FSC/SSC ratio for non-activated platelets were identified. In the CG, the median FSC/SSC was 1.235 (from 1.1 to 1.4), in group 1 (n = 19), the median was 0.97 (from 0.9 to 1.05), and in group 2 (n = 31), the median was 1.24 (from 1.11 to 1.43). The number of platelets of the CG and the groups of patients did not differ significantly. A significant correlation between a decrease in the number of platelets and an increase in their size and granularity, while maintaining a high correlation between size and granularity was observed in groups of patients. In group 1, the overall granularity was increased regardless of the size and number of platelets, the volume of dense granules and membrane CD62p was increased, but the granular CD62p was decreased. The degranulation mechanism was not impaired in both groups of patients. Our results indicate convincingly the contribution of the storage pool and platelet morphology disorders to the development of hemorrhagic manifestations in children with unspecified hemorrhagic syndrome.

The mechanisms of hemorrhagic manifestations in patients with ANKRD26associated thrombocytopenia (ANKRD26-AT) are poorly understood. The aim of this work is to detect possible morpho-functional disorders of platelets in patients with mutations in the ANKRD26gene by flow cytometry with activation. The study was approved by the Independent Ethics Committee of the Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology. 8 children aged from 1.5 to 15 years were examined. The platelet count ranged from 29 to 172 thousand/μl, with a median of 60 thousand/μl. The severity of hemorrhagic manifestations was assessed on a standardized scale (Pediatric Bleeding Questionnaire, PBQ) and it ranged from 0 to 5 points, with a median of 3.5 points. Platelet activation was performed with a CRP + TRAP mixture. Comparison was carried out with the results of examination of 26 apparently healthy children (control group, CG) aged 2 to 15 years. When compared with CG, patients showed an increase in platelet size (FSC; p= 0.018) and granularity (SSC; p< 0.001) after activation. In contrast to the CG, the correlation between FSC and SSC of platelets in patients was not significant (cor. = 0.55; p= 0.15). Patients showed a high, significant relationship between the number and FSC of platelets (cor. = –0.93; p< 0.001), as well as an increased density of CD42b (p < 0.001) and a decrease in the proportion of procoagulant platelets (p= 0.01) after activation. The revealed changes indicate violations of the mechanisms of activation and shape changes of platelets in patients with ANKRD26-AT.

The proteomic composition of a biological sample serves as the most important feature of a biological object, and it allows discriminating normal and pathological conditions. Targeted mass spectrometric analysis, namely, multiple reaction monitoring (MRM) using synthetic isotopically-labeled internal standard (SIS), is the main alternative to the ELISA method for the analysis of diagnostically significant proteins. Based on the MRM results, a prototype test system has been developed; it employs the targeted mass spectrometric method for multiplex, quantitative analysis of FDA-verified proteins in whole blood plasma. Using this approach, it was possible to measure the content of 42 proteins in 31 samples in a concentration range spanning five orders of magnitude. The interindividual variability for 30 of the 42 registered proteins was less than 40%. The largest scatter was observed for haptoglobin (68%), immunoglobulin heavy constant delta IGHD (90%), angiotensin (72%), sex hormone-binding globulin SHBG (100%) and lipoprotein-(a) (136%). The obtained results on the concentration of proteins correlate with published data (Hortin et al., 2008, Clinical Chemistry, 54, 1608) with R2=0.84. The developed prototype test system based on targeted mass spectrometric analysis of proteins can be considered as an alternative to methods using monoclonal antibodies.

Information about the trends in studies of molecular profiles of healthy people has been obtained.

Human genome contains ca. 20,000 protein-coding genes that could be translated into millions of unique protein species (proteoforms). Proteoforms coded by a single gene often have different functions, which implies different protein partners. By interacting with each other, proteoforms create a network reflecting the dynamics of cellular processes in an organism. Perturbations of protein-protein interactions change the network topology, which often triggers pathological processes. Studying proteoforms is a relatively new research area in proteomics, and this is why there are comparatively few experimental studies on the interaction of proteoforms. Bioinformatics tools can facilitate such studies by providing valuable complementary information to the experimental data and, in particular, expanding the possibilities of the studies of proteoform interactions.

Studies of genomes and transcriptomes are performed using sequencers that read the sequence of nucleotide residues of genomic DNA, RNA, or complementary DNA (cDNA). The analysis consists of an experimental part (obtaining primary data) and bioinformatic processing of primary data. The bioinformatics part is performed with different sets of input parameters. The selection of the optimal values of the parameters, as a rule, requires significant computing power. The article describes a protocol for processing transcriptome data by virtual computers provided by the cloud platform Amazon Web Services (AWS) using the example of the recently emerging technology of long DNA and RNA sequences (Oxford Nanopore Technology). As a result, a virtual machine and instructions for its use have been developed, thus allowing a wide range of molecular biologists to independently process the results obtained using the "Oxford nanopore".

Programmed cell death of non-nucleated blood cells – platelets – could be associated with pathophysiology of oncologic and oncohematologic diseases. It contributes to both bleedings (caused by the thrombocytopenia, which is induced by elimination of the platelets) and thrombosis (caused by the processes of blood coagulation on the surface of phosphatidylserine exposing platelets). Here we characterized functional responses of platelets from the patients with various oncological disorders undergoing chemotherapy and compared them to the platelets from the healthy donors and platelets pre-incubated with apoptosis inducer ABT-737. Some patients exhibited diminished capability of platelets to aggregate. Immunophenotyping of these platelets revealed their pre-activation in comparison to the platelets from the healthy donors. Calcium signaling analysis revealed that in the patient-derived platelets, as well as in the apoptotic platelets, intracellular calcium levels were increased in resting cells. However, moderate level of this increase together with weak expression of phosphatidylserine allows us to assume that apoptotic processes in the circulating platelets from the patients are limited.

In the frame of the work, data on the implementation of metabolomics tests in medicine have been systematized. Based on the obtained data, a set of protocols was proposed, the sequential realization of which makes it possible to conduct a blood metabolome analysis for medical purposes. Using this analysis and the number of blood samples from healthy volunteers, a prototype of a healthy person's metabolomic image has been developed; it allows visually and digitally to assess the compliance of the human blood metabolome with the norm. At the same time, 99% of the metabolic processes reflected in the blood plasma are estimated. If abnormalities are detected, the metabolomic image allows to get the value of these deviations of metabolic processes in digital terms.