[Metabolome profiling in the study of aging processes]. / Metabolomnoe profilirovanie v izuchenii protsessov stareniia.

Aging of a living organism is closely related to systemic metabolic changes. But due to the multilevel and network nature of metabolic pathways, it is difficult to understand these connections. Today, this problem is solved using one of the main approaches of metabolomics - untargeted metabolome profiling. The purpose of this publication is to systematize the results of metabolomic studies based on such profiling, both in animal models and in humans.

[Ten years of the Russian metabolomics: history of development and achievements]. / Desiat' let rossiiskoi metabolomike: istoriia razvitiia i osnovnye rezul'taty.

Metabolomics is one of the omics sciences, the technologies of which are widely used today in many life sciences. Its application influenced the discovery of new biomarkers of diseases, the description of biochemical processes occurring in many organisms, laid the basis for a new generation of clinical laboratory diagnostics. The purpose of this review is to show how metabolomics is represented in the studies of Russian scientists, to demonstrate the main directions and achievements of the Russian science in this field. The review also highlights the history of metabolomics, existing problems and the place of Russian metabolomics in their solution.

[Metabolomic blood test: purpose, implementation and interpretation of data]. / Metabolomnyi analiz krovi: naznachenie, realizatsiia, interpretatsiia dannykh.

The human body is an open system that receives a variety of xenobiotics in the course of dietary route or respiration and in the form of the drugs. As a lump sum scores of toxic and potentially toxic substances are detected in a human body that significantly affect health and human lifespan. There are also thousands of diseases, dozens of which latently occur in the body of each person. Traditional diagnosis is not able to screen all the variety of xenobiotics and potential human diseases. For this purpose metabolomic blood test is available which is of non-targeted (review) nature. The test can reveal all the diversity of low molecular weight substances in blood, including tens of thousands of xenobiotics and markers of different diseases. Detection of xenobiotics in the blood, directional detoxification and subsequent monitoring of "body's chemical purity" together with the control of "normality" of all biochemical processes in the organism, using metabolomics blood tests is a necessary and presumably a sufficient condition in the implementation of inherent human genotype longevity. This article describes the purpose, implementation and interpretation of metabolomic blood test facilitating the implementation of this method in the Russian Federation, in order to significantly increase the average life expectancy.

[Pharmacometabonomics - the novel way to personalized drug therapy]. / Farmakometabonomika ­ novyi podkhod k personalizatsii lekarstvennoi terapii.

The review is devoted to pharmacometabonomics - a new branch of science focused on personalization of drug therapy through the comprehensive analysis of metabolites of patient's biological fluids. It considers the history of pharmacometabonomic, positioning to other "-omic" sciences, and system approach, realized by this science, in determination of individual therapeutic dose of the drugs and also a technical implementation of pharmacometabonomic based on direct mass spectrometry of blood plasma metabolites. Special attention is paid to a comparative analysis of pharmacometabonomics and other main approaches to personalized therapy in the clinic, such as pharmacogenetics and therapeutic drug monitoring. Finally, prospects of pharmacometabonomics applications in clinical practice were also discussed.

[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 data¼ are typical of data intensive domains. Special computational methods are essential for data intensive analytics and hardly suitable for the evidence-based medicine.

[Mass spectrometry analysis of blood plasma lipidome as method of disease diagnostics, evuation of effectiveness and optimization of drug therapy].

A new method for the analysis of blood lipid based on direct mass spectrometry of lipophilic low molecular weight fraction of blood plasma has been considered. Such technique allows quantification of hundreds of various types of lipids and this changes existing concepts on diagnostics of lipid disorders and related diseases. The versatility and quickness of the method significantly simplify its wide use. This method is applicable for diagnostics of atherosclerosis, diabetes, cancer and other diseases. Detalization of plasma lipid composition at the molecular level by means of mass spectrometry allows to assess the effectiveness of therapy and to optimize the drug treatment of cardiovascular diseases by phospholipid preparations.

[Metabolic profiling of human blood].

Metabolomics is a novel "omics" branch of science intended for studying a comprehensive set of low molecular weight substances (metabolites) of various biological objects. Metabolite profiles represent a molecular phenotype of biological systems and reflect information encoded at the genome level and realized at the transcriptome and proteome levels. Analysis of human blood metabolic profile is universal and promising tool for clinical applications because it is a sensitive measure of both endogenous and exogenous (environmental) factors affected on the patient's organism. Technical implementation of metabolic profiling of blood and statistic analysis of metabolite profiles for effective diagnostics and risk assessments of diseases are discussed in this review.

[Mass spectrometry of blood low-molecular fraction as a method for unification of therapeutic drug monitoring].

The article describes a new therapeutic drug monitoring (TDM) method based on direct infusion of low-molecular fraction of blood into electrospray ionization source of mass spectrometer. This technique allows performing TDM of almost all drugs used in clinic. In article, the universality and high-throughput of the method, that significantly simplifies its wide application, have been shown. Moreover, the possibility of method application in most cases of drug therapy has been argued as a tool of control of drug doses, rationality of drug therapy, and the quality of the drugs themselves. In conclusion, the prospects for application of the method as primary means of improving the quality and personalization of drug therapy have been discussed.

[Metabolic fingerprinting of blood plasma for patients with prostate cancer].

Application of blood plasma metabolites fingerprinting for the diagnostic of the 2nd stage of prostate cancer has been investigated. The diagnostic sensitivity (95%), specificity (96.7%) and accuracy (95.7%) of the metabolic fingerprinting were much higher then those for PSA test (35%, 83.3% and 51.7%, respectively) for the same patients. Area under the ROC-curve (0.994) suggests that the proposed approach is effective and can be used for clinical applications.

[The pattern of centriole immunostaining for tyrosinated or acetylated alpha-tubulin changes during mitosis in 3T3 (A31) cells but not in SV40-3T3 cells].

Comparative electron microscopic analysis of the patterns of centriolar and cytoplasmic microtubules immunostaining for acetylated or tyrosinated alpha-tubulin was performed during the cell cycles of the mouse diploid 3T3 (A31) and virus-transformed heteroploid SV40-3T3 cell lines. It was shown that the pattern of centriole immunostaining changed during mitosis in control 3T3 (A31) cells, but not in tumorigenic SV40-3T3 cells. A sharp change in the pattern of centriole immunostaining was observed in those cell cycle periods when the protein organization of centrosome underwent changes during interphase/mitosis or mitosis/interphase transitions due to the rearrangement of microtubule system. A high level of centriole immunostaining for tyrosinated and acetylated alpha-tubulin was observed at all cell cycle stages with the exception of entering mitosis for the former and the end of mitosis for the latter.

[Mass spectrometry methods in metabolomics].

The review is devoted to metabolomics, a new and rapidly growing area directed to the comprehensive analysis of metabolites of biological objects. Metabolites are characterized by various physical and chemical properties, traditionally studied by methods of analytical chemistry focused on certain groups of chemical substances. However current progress of mass spectrometry has led to the formation of unified methods, such as metabolic fingerprinting and metabolomic profiling, which allow defining thousands of metabolites in one probe. The current review describes basic characteristics of these methods, ways of metabolite separation, and the analysis of metabolites by mass spectrometry. The examples shown in this review, allow to estimate these methods and to compare their advantages and disadvantages. Besides that, authors show the methods most frequently used in metabolomics for data processing and the required resources, such as software for mass spectra processing and metabolite search database. In the conclusion, general suggestions for successful metabolomic experiments are given.

Two-dimensional electrophoretic proteome study of serum thermostable fraction from patients with various tumor conditions.

One of the problems of plasma proteomics is a presence of large major components. In this work, we use the thermostable fraction as a way to deplete these major proteins. The thermostable fraction of serum samples from patients with ovarian, uterus, and breast cancers and benign ovarian tumor was analyzed using two-dimensional electrophoresis combined with MALDI-TOF(-TOF)-mass spectrometry. Of them, alpha-1-acid glycoprotein and clusterin are expressly down-regulated in breast cancer, whereas transthyretin is decreased specifically in ovarian cancer. Apolipoprotein A-I forms have decreased spot volumes, while haptoglobin alpha1, in contrast, is elevated in several tumors. These data are partly consistent with previous art studies on cancer proteomics, which involve mass-spectrometry-based serum profiling techniques. Serum thermostable fraction may be recommended as a good tool for medium and small protein proteome investigation, in particular, by 2D-electrophoresis.

Proteomic and biochemical analysis of the mouse liver microsomes.

The efficiency of the proteomic approach for the revelation of proteins, including components of the liver microsomal monooxygenase system (cytochromes b5 and P450) was demonstrated. The liver microsomes and their ghosts (i.e. membranes devoid of "ballast" proteins) were prepared from the control and phenobarbital-treated mice. Microsomes and their ghosts were characterized using the conventional biochemical assay and analysed by one- and two-dimensional electrophoresis (1-DE and 2-DE, respectively) coupled with MALDI-TOF peptide mass fingerprinting procedure. Catalytic activity of cytochromes P450 was measured using specific fluorogenic substrates for CYP1A, CYP2A, CYP2B and CYP2C families. The protein composition of control and phenobarbital-induced ghosts was analysed. The proteomic 2D-based protein separation method enabled us to reveal up to 1005 proteins, the majority of them being soluble. Among the 34 identified proteins, the cytochrome b5-like protein was revealed; however, cytochromes P450 appeared to be undetectable under 2-DE separation conditions. The separation of microsomal ghosts proteins by 1-DE, followed by mass-spectrometric analysis of bands from the 45 to 66 kDa gel range made it possible to identify hydrophobic proteins including cytochromes P450 (CYP2A4 and CYP2A5) and dimethylaniline monooxygenase. The high O-deethylation rate of 7-ethoxycoumarin-a substrate for rodent CYPs 2A and 2B, in particular for CYP2A5-was observed, in agreement with the results of mass-spectrometric identification. Collectively, the data obtained indicate that a combination of enzyme activity assays and various protein separation techniques coupled with mass-spectrometric protein identification allows a more comprehensive insight into the machinery of the cellular detoxifying system.

[Study of the mouse liver microsomes by the methods of proteome analysis]. / Issledovanie mikrosom kletok pecheni myshi metodami poreomnogo analiza.

Proteome maps of microsomes and their ghosts (i.e. membranes purified from "ballast" proteins) were obtained using highly purified mouse liver microsomes. Comparative analysis of protein composition of ghosts without and after the induction with phenobarbital (cytochromes P450 inducer) by using 1D- and 2D-electrophoresis and MALDI-TOF-mass-spectrometry revealed more than 30 new proteins, in the course of induction in the 45-60 kDa range (corresponding to the mol. weights of cytochromes P450). In the 17 kDa range (corresponding to the mol. wt. of cytochrome b5) there were 4 additional protein stains about 20 proteins disappeared over the entire electrophoregram). Separation of microsomal ghosts proteins by 1D electrophoresis followed by mass-spectrometric analysis allowed to identify cytochromes P450. The present investigation demonstrates the efficiency of different proteomic methods combination (1D- and 2D-electrophoresis, mass-spectrometry, bioinformatics and determination of the enzyme activities) for cytochromes P450 identification and elucidation of their functioning in different animal tissues and then extrapolating this approach to humans.

Comparative analysis of different typing methods for Helicobacter pylori clinical isolates.

The goal of the present work was to compare different techniques of molecular typing using as an example clinical isolates of Helicobacter pylori obtained from patients in different regions of Russia. DNA-macroarray genome scanning using individual genes was employed to set up our basic classification of isolates that did or did not contain pathogenicity islands. In parallel, DNA of the same isolates was used in the conventional random amplified polymorphic DNA (RAPD) PCR analysis, and the isolates were also genotyped (cagA, vacA, iceA, and babA status) and their proteomic maps were obtained by means of unidimensional SDS polyacrylamide gel electrophoresis (1D-SDS-PAGE) coupled with identification using peptide mass fingerprinting by MALDI-TOF mass spectrometry. A statistically significant correlation (coefficient of correlation r = 0.25, p = 0.005) was observed between the results of genome scanning and 1D-SDS-PAGE. No correlation was found between RAPD-PCR typing and genome scanning.

[Structural and functional characteristics of insulin and mechanism of its effect]. / Strukturno-funktsional'nye osobennosti insulina i mekhanizma ego deistviia.

On the basis of analysis of own and literature data on insulin-receptor interaction two centers responsible for receptor binding were identified on 3D-structure of insulin with receptor. Two extracellular domains of insulin receptor interact with these centers on insulin molecule. The comparative analysis of primary structures of the protein disulfide isomerase thioredoxine domains and C-terminal domain of the receptor suggests existence of the thioredoxine domain in the insulin receptor. In this connection the role of the thiol disulfide an exchange reaction is discussed in terms of insulin interaction with receptor followed by subsequent conformational changes in the receptor molecule and activation of the intercellular tyrosine kinase domain. It is supposed, that besides known mechanism of receptor mediated insulin signal transduction and tyrosine kinase activation, there is other mechanism of insulin intracellular signal transduction realised via cytosolic insulin-binding proteins. Major components of intercellular insulin signal transduction include: protein disulfide isomerase and insulin degrading enzyme. The importance of change of the intracellular insulin degradation rate for insulin signal transduction is discussed.

Comparative analysis of proteome maps of Helicobacter pylori clinical isolates.

The gram-negative bacterium Helicobacter pylori is found in human gastric mucosa. A widely distributed H. pylori infection is associated with chronic gastritis, gastric and duodenal ulcers, and malignant neoplasms. In this study proteome maps of four H. pylori clinical isolates derived from patients of two Russian regions (Moscow/Moscow Region and Novosibirsk) were obtained using 2D-electrophoresis and MALDI-TOF-mass-spectrometry. Variability of some H. pylori proteins and the level of their expression have been evaluated. These four isolates could be easily subdivided into two equal groups characterized by the close proteome profiles and the isolate from Moscow Region and the isolate from Novosibirsk constituted one group. The present study demonstrates the potential of proteome technology, which can be employed together with genome and transcriptome studies for the multiparameter typing of clinical isolates of pathogenic microorganisms.

New peptidomimetics of insulin.

New peptidomimetics that have been obtained in the course of our experimental work show distinct insulin-like activity both in vitro and in vivo. The first peptidomimetic (PM 1) is essentially a decapeptide in which sites of A (20-21) and B (19-26) chains of insulin are linked by the peptides bond (Cys-Gly-Glu-Arg-Gly-Phe-Phe-Tyr-Cys-Asn). The second peptidomimetic (PM 2) has similar set of amino acid residues, except that two aromatic amino acids corresponding to the residues of B chain of insulin (B24 and B26) have been replaced with their D optical isomers (Cys-Gly-Glu-Arg-Gly-DPhe-Phe-DTyr-Cys-Asn). The third peptidomimetic (PM 3) has been obtained through acylation of N-terminal of PM 1 by the use of palmitic acid. The peptidomimetic incorporating D aromatic amino acids (PM 2) was demonstrated to exhibit more pronounced hypoglycemic impact, while the acylation of decapeptide tends to prolong the effective time of peptidomimetic influence in vivo.

[The prolonged action of an insulin peptidomimetic by the substitution of L-amino acid for its D-isomer]. / Uvelichenie vremeni deistviia peptidomimetika insulina putem zameny L-aminokislotnykh ostatkov ikh D-opticheskimi izomerami.

The synthesized decapeptide represents functionally important site for binding to the insulin receptor. Amino acid residues at position, 1-8 correlate with B-chain of insulin at position B19-B26, and the residues at position 9-10 correlate with A-chain at position A20-A21. The new peptide was obtained by substitution of two aromatic L-amino acid residues (B24 and B26) for their D-optical isomers. These peptides were tested with cell cultures L929 and PC12 (glucose uptake). Increased concentration of peptides correlated with stimulation of glucose uptake by cells. Studies carried out on animals with streptosotocine-caused diabetes showed that, synthesized peptides were able to decrease glucose level in blood, but decapeptide with D amino acid showed a more pronounced effect compared to the decapeptide with L amino acid.

[Numerical euristic approach to the proteome map analysis]. / Chislenno-évristicheskii podkhod v analize proteomnykh kart.

The possibility of numerical-heuristic approach has been examined for proteome map analysis that realized by neural network processing of 2D protein electrophoregramms. The fetal alcohol syndrome was used to illustrate that this approach islatively effective for diagnostics of diseases.