Flow cytometry for comprehensive assessment of platelet functional activity in response to ADP stimulation

OBJECTIVES

Flow cytometry with adenosine diphosphate (ADP) allows to characterize molecular changes of platelet function caused by this physiologically important activation, but the methodology has not been thoroughly investigated, standardized and characterized yet. We analyzed the influence of several major variables and chose optimal conditions for platelet function assessment.

METHODS

For activation, 2.5 μM CaCl2 , 5 μM ADP and antibodies were added to diluted blood and incubated for 15 min. We analyzed kinetics of antibody binding and effects of their addition sequence, agonist concentration, blood dilution, exogenous calcium addition and platelet fixation.

RESULTS

We tested our protocol on 11 healthy children, 22 healthy adult volunteers, 9 patients after a month on dual antiplatelet therapy after percutaneous coronary intervention (PCI), 7 adult patients and 14 children with immune thrombocytopenia (ITP). We found that our protocol is highly sensitive to ADP stimulation with low percentage of aggregates formation. The assay is also sensitive to platelet function inhibition in post-PCI patients. Finally, platelet preactivation with ITP plasma was stronger and caused increase in activation response to ADP stimulation compared to preactivation with low dose of ADP.

CONCLUSIONS

Our assay is sensitive to antiplatelet therapy and platelet preactivation in ITP patients under physiological conditions with minimal percentage of aggregates formation.

A novel preliminary metabolomic panel for IHD diagnostics and pathogenesis

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.

[Splice variants of mRNA of cytochrome P450 genes: analysis by the nanopore sequencing method in human liver tissue and HepG2 cell line]

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.

Healthy pediatric platelets are moderately hyporeactive in comparison with adults' platelets

Studies on platelet function in children older than neonatal period are few and their results are controversial. The pediatric platelets were alternatively reported to be more active or less active than adults' ones. We compared platelet function in the several age groups of children to adults and evaluated the age when platelet function reaches the adults' status. The study included 76 healthy children and 49 healthy adult volunteers. Types of platelet activation used included: collagen-related peptide (CRP) and PAR-1 activating peptide SFLLRN; SFLLRN, PAR-4 activating peptide AYPGKF and adenosine diphosphate (ADP); ADP. The parameters determined included forward (FSC) and side scatter (SSC), CD42b, CD61, CD62P, PAC-1, annexin V binding and mepacrine release levels. Resting pediatric platelets were similar to adults' platelets except for 1.2-fold decreased FSC and dense granules volume in youngest children, and 2.5-fold increased annexin V level in children aged 1-10 years. After CRP+SFLLRN stimulation, pediatric platelets had a 1.2-fold lower alpha- and 1.1-fold lower dense granule release than adults. For SFLLRN+AYPGKF+ADP stimulation, this was observed only for youngest children. The response to ADP stimulation was identical for pediatric platelets and adults. Pediatric platelets have lower granular release than adults' platelets, which persists until the age of 18.

[PCR analysis of the expression of chromosome 18 genes in human liver tissue: interindividual variability]

Using human chromosome 18 (Ch18) genes as an example, a PCR analysis of the interindividual variability of gene expression in liver tissue was performed. Although the quantitative profiles of the Ch18 transcriptome, expressed in the number of cDNA copies per single cell, showed a high degree of correlation between donors (Pearson correlation coefficients 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 is mainly not technical, but biological. Bioinformatic analysis of the interindividual variability of the differential expression of chromosome 18 genes in human liver tissue did not reveal any statistically significant groups of genes related to certain biological processes that indicated a rather transient nature of the interindividual variability of their expression, probably reflecting the response of cells of an individual to specific external stimuli.

Platelet function and bleeding at different phases of childhood immune thrombocytopenia

Immune thrombocytopenia (ITP) is believed to be associated with platelet function defects. However, their mechanisms are poorly understood, in particular with regard to differences between ITP phases, patient age, and therapy. We investigated platelet function and bleeding in children with either persistent or chronic ITP, with or without romiplostim therapy. The study included 151 children with ITP, of whom 56 had disease duration less than 12 months (grouped together as acute/persistent) and 95 were chronic. Samples of 57 healthy children were used as controls, while 5 patients with leukemia, 5 with aplastic anemia, 4 with MYH9-associated thrombocytopenia, and 7 with Wiskott-Aldrich syndrome were used as non-ITP thrombocytopenia controls. Whole blood flow cytometry revealed that platelets in both acute/persistent and chronic ITP were increased in size compared with healthy donors. They were also pre-activated as assessed by PAC1, CD62p, cytosolic calcium, and procoagulant platelet levels. This pattern was not observed in other childhood thrombocytopenias. Pre-activation by CD62p was higher in the bleeding group in the chronic ITP cohort only. Romiplostim treatment decreased size and pre-activation of the patient platelets, but not calcium. Our data suggest that increased size, pre-activation, and cytosolic calcium are common for all ITP platelets, but their association with bleeding could depend on the disease phase.

Programmed Cell Death and Functional Activity of Platelets in Case of Oncohematologic Diseases

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.

Platelet function and blood coagulation system status in childhood essential thrombocythemia

Childhood essential thrombocythemia (ET) is a rare chronic myeloproliferative disorder. The quality of life of ET patients may decrease as a result of ischemic and hemorrhagic complications of unclear origin. Our goal was to characterize the hemostatic system in children with ET. We genotyped and investigated blood samples from 20 children with ET in a prospective case series study using platelet aggregation, functional flow cytometry (FC) assay and standard clotting assays. Three children had a JAK2V617F mutation, 4 had mutations in CALR and 13 were triple-negative. Myelofibrosis in stage 1-2 was detected in 3 children. Three patients had bleeding episodes and seven had ischemic events. Aggregation in response to collagen, adenosine diphosphate, and ristomycin was decreased in all patients. In FC, significant changes in the whole patient group compared to the healthy children control group were decrease in the resting forward scatter and PAC1 binding (activated GPIIb/IIIa) level. For the activated platelets, dense granules release (by mepacrine), PAC1, and GPIIb/IIIa levels were significantly decreased. GPIb/V/IX, P-selectin, and phosphatidylserine levels manifested only moderate differences. Forward and side scatter changes in response to stimulation (representing shape change) and dense granules release were significantly lower in the 3 patients with bleeding than in the 17 patients without hemorrhage. Activated partial thromboplastin time was slightly prolonged, prothrombin index was slightly shortened and thrombin time was normal, while fibrinogen was mildly decreased in the ET patients. It could be concluded that the observed platelet function defects could be related to bleeding in ET, and be potentially used as a marker.

[Mass-spectrometric MRM analysis of FDA-verified proteins in the blood plasma of healthy volunteers]

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.

[Blood metabolome analysis for creating a digital image of a healthy person]

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.

Methods of Computational Interactomics for Investigating Interactions of Human Proteoforms

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.

[Medical subject headings for the scientific groups evolution analysis on the example of academician A.I. Archakov's scientific school]

This paper proposes a method of comparative analysis of scientific trajectories based on bibliographic profiles. The bibliographic profile ("meshprint") is a list of MeSH terms (key terms used to index articles in the PubMed), indicating the relative frequency of occurrence of each term in the scientist's articles. Comparison of personalized bibliographic profiles can be represented in the form of a semantic network, where the nodes are the names of scientists, and the relationships are proportional to the calculated measures of similarity of bibliographic profiles. The proposed method was used to analyze the semantic network of scientists united by the academic school of the academician A.I. Archakov. The results of the work allowed us to show the relationship between the scientific trajectories of one scientific school and to correlate the results with world trends.

Infradian and Ultradian Rhythms of Body Temperature Resumption during Hibernation

The rhythms of short-term arousal episodes, associated with normalization of low body temperature, were studied in hibernating Erinaceus roumanicus. The episodes of body temperature recovery during hibernation were 1.7 times more incident during the acrophase of 4.058-day rhythm of glucocorticoid hormones, detected previously, than during the batiphase of this rhythm. Ultradian rhythm of arousal episodes conformed to a 4-h biorhythm: the maximum number of body temperature resumption episodes was recorded at 00.00-01.00, 04.00-05.00, 08.00-09.00, 12.00-13.00, 16.00-17.00, and 20.00-21.00. These data indicated that in mammals the mechanisms of infradian and ultradian rhythm maintenance were stable and did not depend on body temperature or were determined by external factors with periods of 4.058 days and 4 h.

Flow cytometry for pediatric platelets

The ability of platelets to carry out their hemostatic function can be impaired in a wide range of inherited and acquired conditions: trauma, surgery, inflammation, pre-term birth, sepsis, hematological malignancies, solid tumors, chemotherapy, autoimmune disorders, and many others. Evaluation of this impairment is vitally important for research and clinical purposes. This problem is particularly pronounced in pediatric patients, where these conditions occur frequently, while blood volume and the choice of blood collection methods could be limited. Here we describe a simple flow cytometry-based screening method of comprehensive whole blood platelet function testing that was validated for a range of pediatric and adult samples (n = 31) in the hematology hospital setting including but not limited to: classic inherited platelet function disorders (Glanzmann's thrombasthenia; Bernard-Soulier, Wiscott-Aldrich, and Hermasky-Pudlak syndromes, MYH9-dependent thrombocytopenia), healthy and pre-term newborns, acute and chronic immune thrombocytopenia, chronic lympholeukemia, effects of therapy on platelet function, etc. The method output includes levels of forward and side scatter, levels of major adhesion and aggregation glycoproteins Ib and IIb-IIIa, active integrins' level based on PAC-1 binding, major alpha-granule component P-selectin, dense granule function based on mepacrine uptake and release, and procoagulant activity quantified as a percentage of annexin V-positive platelets. This analysis is performed for both resting and dual-agonist-stimulated platelets. Preanalytical and analytical variables are provided and discussed. Parameter distribution within the healthy donor population for adults (n = 72) and children (n = 17) is analyzed.

[Postgenomic Medicine: Alternative to Biomarkers]

In the article relevance of high-performance postgenomic technologies is tackled. The intrinsic problems of the implementation of genomics, proteomics and metabolomics in routine clinical practice are considered. Further development of postgenomic medicine requires severe change in the current research approaches. Avenue for development of such approaches are illustrated by metabolome research of human blood plasma. The postgenomic biomarkers are pictured as molecular iceberg, greater part of which is inaccessible for detection with measurement methods. Due to diversity of protein forms the spectrum of molecular markers will always evaluate in terms of incompleteness and inconsistence regardless of technological development level. These properties of «big data» are typical of data intensive domains. Special computational methods are essential for data intensive analytics and hardly suitable for the evidence-based medicine.

[Multiomics study of HepG2 cell line proteome]

Current proteomic studies are generally focused on the most abundant proteoforms encoded by canonical nucleic sequences. Transcriptomic and proteomic data, accumulated in a variety of postgenome sources and coupled with state-of-art analytical technologies, allow to start the identification of aberrant (non-canonical) proteoforms. The main sources of aberrant proteoforms are alternative splicing, single nucleotide polymorphism, and post-translational modifications. The aim of this work was to estimate the heterogeneity of HepG2 proteome. We suggested multiomics approach, which combines transcriptomic (RNAseq) and proteomic (2DE-MS/MS) methods, as a promising strategy to explore the proteome.

[PCR analysis of the absolute number of copies of human chromosome 18 transcripts in liver and HepG2 cells]

Using reverse transcription in conjunction with the quantitative real-time PCR or digital droplet PCR, the transcriptome profiling of human chromosome 18 has been carried out in liver hepatocytes and hepatoblastoma cells (HepG2 cell line) in terms of the absolute number of each transcript per cell. The transcript abundance varies within the range of 0.006 to 9635 and 0.011 to 4819 copies per cell for HepG2 cell line and hepatocytes, respectively. The expression profiles for genes of chromosome 18 in hepatocytes and HepG2 cells were found to significantly correlate: the Spearman's correlation coefficient was equal to 0.81. The distribution of frequency of transcripts over their abundance was bimodal for HepG2 cells and unimodal for liver hepatocytes. Bioinformatic analysis of the differential gene expression has revealed that genes of chromosome 18, overexpressed in HepG2 cells compared to hepatocytes, are associated with cell division and cell adhesion processes. It is assumed that the enhanced expression of those genes in HepG2 cells is related to the proliferation activity of cultured cells. The differences in transcriptome profiles have to be taken into account when modelling liver hepatocytes with cultured HepG2 cells.

[International criteria of the research activity of groups and individual scientists in biology and medicine]

Comparison data on results of efficiency of the research institutes (RI) of RAMS by international and own evaluation criteria of the research activity of above institutions in 2011 are presented. The consistency of international and own evaluation results was observed in 21RI (39%), the institutions-leaders found, and in 13 RI (24%) - less effective institutions. Thus, the use of own evaluation criteria only complicates the unbiased assessment of the Russia's position in the international scientific rating.

[Knowledge-based technologies in proteomics]

Proteomic technologies enable to identify thousands of proteins in biological samples. These data require appropriate means for storage, dissemination and analytical processing to decipher the new knowledge. Automatic processing of high-efficient experiment results is powered by the controlled vocabularies, such as Medical Subjects Headings and GeneOntology. While ontology and vocabularies undergo constant evolution, it is necessary to provide the centralized storage of proteomic data for further revision in accordance with the updated knowledge domain. Proteomic repositories like PRIDE, The Global Proteome Machine, PeptideAtlas etc. are available to harbor the wealth of mass spectral data and appropriate protein identifications. The existing repositories facilitate the development of knowledge extraction technologies to compare the list of identified proteins with the GeneOntology annotations, Medical Subjects Headings, metabolic and regulatory pathways. This paper reviews modern analytical tools that exploit the knowledge-based technologies for proteome research.

[Selection of the peptide mass tolerance value for the protein identification with peptide mass fingerprinting]

Peptide mass-fingerprint is widely used for protein identification while studying proteome with the use of 1D or 2D electrophoresis. Peptide mass tolerance indicates the fit of theoretical peptide mass with the experimental measurements, and choice of this parameter sufficiently influences the protein identification. The role of peptide mass tolerance was estimated by counting the number of identified proteins for the reference set of mass-spectra. The reference set of 400 Ultraflex (Bruker Daltonics, Germany) mass-spectra was obtained for the slices of 1D gel of liver microsomes. Using Mascot server for protein identification, the peptide mass tolerance value was varied in the range from 0.02 to 0.40 Da with a step 0.01 Da. Depending on the tolerance the number of identified protein changes up to 10 times. Maximal number of identified proteins was reported for the tolerance value of 0.15 Da (120 ppm), which is 1.5 - 2 times higher than the recommended values for such type of mass-spectrometers. The software program PMFScan was developed to obtain the dependence of number of identified proteins of the tolerance values.

[Knowledgebase as a tool for monitoring post-genomic medico-biological research]

On-going molecular biological researches are characterized by exponential increase in the amount of experimental data which dictates the necessity to develop relevant information technologies. The knowledge-based approach appears to be a most promising and flexible tool for analytical processing biomedical information that allows new relationships between study objects to be established. In this article we analyze the work of researchers based at the Institute of Biomedical Chemistry with the materials of the PubMed biomedical library. A list of publication IDs for a half-year period has been compiled to elucidate individual profiles of research activities. Statistical analysis of medical subject headings (MeSH) reveals typical profiles of research of interest for separate divisions of the Institute. The proposed approach may be recommended as a means for improving the efficiency and coordination of biomedical research.

[Construction of protein semantic networks using PubMed/MEDLINE]

Method is described to produce the protein semantic networks based on the information from PubMed/MEDLINE. In this work we used semantic score to assess the connectivity between two proteins based on the number of shared relevant or related articles. Using such score we created the semantic network for 150 human proteins belonging to different metabolic pathways. Analysis of the network has shown that proteins involved into the same molecular processes were separated into distinct subgraphs.

[Identification of differentially expressed proteins using automatic meta-analysis of proteomics-related articles]

We present here a new method for automatic meta-analysis of proteomic articles using assessment of frequency of individual protein names in the text. The list of all possible human protein names including synonyms was retrieved from UniProt knowledgebase. The retrieved names were searched in full-texts of peer-reviewed publications from electronic version of "Proteomics" journal and from PubMedCentral. In the automatic mode we have confirmed the earlier list of proteins [Petrak et al., Proteomics (2008) 8, 1744] most frequently reported as differentially expressed (DEPs) in human tissues. We have also verified, that the most recurrent proteins were reported in proteomic papers regardless of tissue, experimental goals or, to some extent, experimental methods employed. Frequently reported DEPs were: annexins, peroxiredoxins, alpha-enolase, triosephosphate isomerase, and HSP60. Besides, serum albumin, cathepsin D and vimentin were observed with relatively high frequency. The DEPs were reported in papers related to oncological, cardiovascular and neuronal diseases, and were involved in such biological processes as inflammation, cell regulation, immune responce and signal transduction. We conclude that automatic meta-analysis of proteomic papers enabled extraction of frequently reported proteins that are most likely the differentially expressed ones.

Electrochemical reduction of sterol-14α-demethylase from Mycobacterium tuberculosis (CYP51b1)

The electrochemical reduction of the heme protein sterol-14alpha-demethylase from Mycobacterium tuberculosis (CYP51b1, or further CYP51) was investigated. Direct electron transfer was demonstrated between CYP51 and graphite screen-printed electrodes modified with gold nanoparticles and with the membrane-like synthetic surfactant didodecyl dimethylammonium bromide. The formal potential of the Fe3+/Fe2+ pair, E(1/2), is equal to -273 mV (vs. Ag/AgCl). The cathodic current corresponding to the reduction of oxygen by immobilized heme protein was registered in the presence of oxygen. Addition of lanosterol, one of the substrates of the CYP51 family, to the oxygenated solution caused a concentration-dependent increase in the reduction current in voltammetric and amperometric experiments. Ketoconazole, an inhibitor of CYP51, inhibited the catalytic cathodic current in the presence of lanosterol. Electrochemical reduction of CYP51 may serve as an adequate alternative to the reconstituted system, which requires additional redox partners for the exhibition of catalytic activity of heme proteins of the cytochrome P450 superfamily.