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Metabolomics Community in Russia: History of Development, Key Participants, and Results

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Metabolomics Community in Russia: History of Development, Key Participants, and Results Review Metabolomics Community in Russia: History of Development, Key Participants, and Results Elena E. Balashova * , Dmitry L. Maslov and Oxana P. Trifonova Institute of Biomedical Chemistry, Pogodinskaya st.10, 119121 Moscow, Russia; [email protected] (D.L.M.); [email protected] (O.P.T.) * Correspondence: [email protected] Received: 12 September 2020; Accepted: 21 October 2020; Published: 25 October 2020 Abstract: Metabolomics is the latest trend in the “-omics” sciences, of which technologies are widely used today in all life sciences. Metabolomics gave impetus to the description of biochemical processes that occur in many organisms, search for new biomarkers of disease, and laid the foundation for new clinical laboratory diagnostics. The purpose of this review is to show how metabolomics is represented in Russian science, what main research areas were chosen, and to demonstrate the successes and main achievements of Russian scientists in this field. The review is dedicated to the 10th anniversary of Russian metabolomics and also touches on the history of the formation of Russian metabolomics and prospects for the future. Keywords: metabolomics; Russian science; mass spectrometry 1. Introduction Metabolomics is known as a science in which technology platforms are aimed at identifying and quantifying low molecular weight compounds (metabolites). Metabolites are substrates and products of almost all biochemical reactions taking place in the body, play a key role in energy generation, signal transmission in the cell, and carry information about the physiological state of a living organism and ongoing pathological processes [1–3]. Metabolomics is a relatively new science and the youngest of the triad of basic “-omics”, including genomics and proteomics, which systematically describe biological objects (Figure1). The term “metabolome” was first introduced in 1998, but the main development of metabolomics was observed after 2010 [4], largely due to the use of new, constantly improving high-performance analytical methods and comprehensive bioinformatics data processing [5,6]. Along with other “-omics”, metabolomics research focuses on directions where achievements can bring significant benefits to humanity. Generally, metabolomics studies are able to give a representation of the biochemical processes that underlie the body’s reaction to internal and external stimuli. BioTech 2020, 9, 20; doi:10.3390/biotech9040020 www.mdpi.com/journal/biotech BioTech 2020, 9, 20 2 of 15 BioTech 2020, 9, x FOR PEER REVIEW 2 of 15 Figure 1. The sequential interconnection of “-omes” in a living system, which reflects the flow of information encoded in genes to the molecular phenotype of an organism—a metabolome. Figure 1. The sequential interconnection of “-omes” in a living system, which reflects the flow of 2. Metabolomicsinformation in Russia encoded in genes to the molecular phenotype of an organism—a metabolome. The firstThe systemic term “metabolome” development was of “-omics”first introduced science in in1998, Russia but startedthe main in thedevelopment early 2000s of at the Institutemetabolomics of Biomedical was Chemistry observed after (IBMC) 2010 [4], in largely Moscow. due to By the that use time, of new, IBMC, constantly dealing improving with problemshigh- of biologicalperformance and medical analytical chemistry methods under and comprehensive the leadership bioinformatics of academician data proce ofssing the [5,6]. Russian Along Academy with of other “-omics”, metabolomics research focuses on directions where achievements can bring Sciences (RAS) Alexsander I. Archakov, was actively developing post-genomic technologies, such as significant benefits to humanity. Generally, metabolomics studies are able to give a representation of transcriptomicsthe biochemical and proteomics processes that [ 7underlie–13]. In the 2000, body’s the reaction first to in internal the country and external Department stimuli. of Proteomic Research and, in 2003, the “Human proteome” Core Facility was created at IBMC. That allowed to move on2. to Metabolomics the concept in of Russia systems biology, the working definition of which at that time was “the study of biology asThe an first integrated systemic systemdevelopment of genetic, of “-omics” protein, scienc metabolice in Russia events started thatin the are early constantly 2000s at the changing and interdependent”Institute of Biomedical [14]. That Chemistry is, the main(IBMC) task in Moscow. of Core By Facility that time, was IBMC, to obtain dealing and with integrate problems proteomics, of transcriptomics,biological andand metabolicmedical chemistry information under forthe aleadership more holistic of academician study of livingof the Russian organisms. Academy The technicalof base andSciences technological (RAS) Alexsander capabilities I. Archakov, accumulated was actively at the developing IBMC became post-genomic a growth technologies, point for such such as studies transcriptomics and proteomics [7–13]. In 2000, the first in the country Department of Proteomic and contributed to the opening of the first metabolomics laboratory in the country—“Laboratory of Research and, in 2003, the “Human proteome” Core Facility was created at IBMC. That allowed to mass spectrometrymove on to the metabolomic concept of systems diagnostics” biology, under the wo therking supervision definition of of which Dr. Petr at that G. Lokhov.time was After“the some time, variousstudy of metabolomic biology as an studiesintegrated of system biological of genetic, body protein, fluids metabolic were performed events that in are the constantly laboratory to characterizechanging biological and interdependent” objects at the [14]. molecular That is, the level main to task create of Core metabolites-based Facility was to obtain diagnostics. and integrate The main materialproteomics, of the study transcriptomics, was human and blood metabolic plasma, information widely usedfor a more in the holistic clinic study and of the living most organisms. informative in The technical base and technological capabilities accumulated at the IBMC became a growth point terms of laboratory diagnostics body fluid. The main method for studying plasma metabolites was for such studies and contributed to the opening of the first metabolomics laboratory in the country— mass spectrometry“Laboratory of analysis. mass spectrometry The first metabolomics metabolomic diagnostics” data obtained under in the the supervision laboratory of wasDr. Petr published G. in 2009–2010Lokhov. in the After journals some Metabolomicstime, various meandtabolomicBiomeditsinskaya studies of biological khimiya body[15– 17fluids]. were performed in In recentthe laboratory years, metabolomicsto characterize biological has been objects developing at the inmolecular various level fields to ofcreate Russian metabolites-based science. Scientists study thediagnostics. factors that The main increase material the of risk the ofstudy diseases was human in humans, blood plasma, the e widelyffects ofused environmental in the clinic and factors, the presence of pathological processes, the patient’s state and the effectiveness of drug therapy. In several research areas metabolomics approaches are used to better understand the mechanisms of pathological processes development and the aging process, in both humans and animals (Table1). BioTech 2020, 9, 20 3 of 15 Table 1. The use of metabolomics in various fields of science in Russia. Scientific Institutions on the Basis of Which Metabolomic Studies References Metabolomic Studies Are Conducted METABOLOMIC STUDIES OF HUMAN BLOOD Laboratory of mass spectrometry metabolomic [17] diagnostics, IBMC (Moscow) Prostate cancer together with: Endocrinology Research Center (Moscow) [18] − Impaired glucose tolerance National Medical Research Center of − [19,20] Oncology (Moscow) Lung cancer Metabolomic diagnostic signatures Institute of Developmental Biology − (Moscow) and Kazan State Medical [21] University (Kazan) Parkinson’s disease Scientific Research Institute of Nutrition − [22] (Moscow) Obesity Metabolomic profiling of Laboratory of mass spectrometry metabolomic [23–25] human blood diagnostics, IBMC (Moscow) Laboratory of mass spectrometry metabolomic Therapeutic drug monitoring [26,27] diagnostics, IBMC (Moscow) METABOLOMICS OF AGING PROCESSES Laboratory of mass spectrometry metabolomic [28,29] diagnostics, IBMC (Moscow) METABOLOMICS OF PATHOLOGICAL PROCESSES DEVELOPMENT Laboratory of proteomics and metabolomics, Cataract pathogenesis International Tomography Center, Siberian [30–32] Branch of RAS (Novosibirsk) Laboratory of clinical metabolomics, Tomsk State The metabolic basis of the host’s University (Tomsk) together with Central [33,34] response to helminth infection Research Laboratory, Siberian State Medical University (Tomsk) PLANT METABOLOMICS Saint Petersburg State University (Saint Metabolic processes occurring in Petersburg) together with Vavilov Research [35–38] potato plants Institute of Plant Industry (Saint Petersburg) and Komarov Botanical Institute (Saint Petersburg) Significant results were achieved at the International Tomography Center, Siberian Branch of RAS (Novosibirsk), where the Mass Spectrometric Research Center for Collective Use of the Siberian Branch of RAS was established in 2010 under the supervision of Dr. Yuri P. Tsentalovich. At the preliminary stage, the main task of the Research Center was development of modern mass spectrometers. In 2015, on the basis of the Research Center the laboratory of proteomics and metabolomics
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