Application of Clinical Blood Metabogram to Type 2 Diabetes Mellitus.

The clinical blood metabogram (CBM) was developed to match a tailored analysis of the blood metabolome to the time, cost, and reproducibility constraints of clinical laboratory testing. By analyzing the main blood metabolite groups, CBM offers clinically relevant information about the intake of low-molecular substances into the organism, humoral regulation, liver function, amino acid level, and the lipid and carbohydrate metabolism. The purpose of this work was to investigate the relevance of using the CBM in patients with diabetes mellitus. For this, a CBM was obtained for 18 healthy individuals, 12 individuals with prediabetes, and 64 individuals with type 2 diabetes mellitus, separated into groups according to fasting blood glucose and oral glucose tolerance tests. The results showed that the CBM reveals diabetes-associated metabolic alterations in the blood, including changes in the levels of carbohydrates, ketone bodies, eicosanoids, phospholipids, and amino acids, which are consistent with the scientific data available to date. The CBM enabled the separation of diabetic patients according to their metabolic metabotypes, providing both a general overview of their metabolic alterations and detailing their individual metabolic characteristics. It was concluded that the CBM is a precise and clinically applicable test for assessing an individual's metabolic status in diabetes mellitus for diagnostic and treatment purposes.

Linking Clinical Blood Metabogram and Gut Microbiota.

Recently, a clinical blood metabogram was developed as a fast, low-cost and reproducible test that allows the implementation of metabolomics in clinical practice. The components of the metabogram are functionally related groups of blood metabolites associated with humoral regulation, the metabolism of lipids, carbohydrates and amines, lipid intake into the organism, and liver function, thereby providing clinically relevant information. It is known that the gut microbiota affects the blood metabolome, and the components of the blood metabolome may affect the composition of the gut microbiota. Therefore, before using the metabogram in the clinic, the link between the metabogram components and the level of gut microorganisms should be established. For this purpose, the metabogram and microbiota data were obtained in this work for the same individuals. Metabograms of blood plasma were obtained by direct mass spectrometry of blood plasma, and the gut microbiome was determined by a culture-based method and real-time polymerase chain reaction (PCR). This study involved healthy volunteers and individuals with varying degrees of deviation in body weight (n = 44). A correlation analysis determined which metabogram components are linked to which gut microorganisms and the strength of this link. Moreover, diagnostic parameters (sensitivity, specificity and accuracy) confirmed the capacity of metabogram components to be used for diagnosing gut microbiota alterations. Therefore, the obtained results allow the use of the metabogram in a clinical setting, taking into account its relationship with gut microbiota.

Clinical Blood Metabogram: Application to Overweight and Obese Patients.

Recently, the concept of a mass spectrometric blood metabogram was introduced, which allows the analysis of the blood metabolome in terms of the time, cost, and reproducibility of clinical laboratory tests. It was demonstrated that the components of the metabogram are related groups of the blood metabolites associated with humoral regulation; the metabolism of lipids, carbohydrates, and amines; lipid intake into the organism; and liver function, thereby providing clinically relevant information. The purpose of this work was to evaluate the relevance of using the metabogram in a disease. To do this, the metabogram was used to analyze patients with various degrees of metabolic alterations associated with obesity. The study involved 20 healthy individuals, 20 overweight individuals, and 60 individuals with class 1, 2, or 3 obesity. The results showed that the metabogram revealed obesity-associated metabolic alterations, including changes in the blood levels of steroids, amino acids, fatty acids, and phospholipids, which are consistent with the available scientific data to date. Therefore, the metabogram allows testing of metabolically unhealthy overweight or obese patients, providing both a general overview of their metabolic alterations and detailing their individual characteristics. It was concluded that the metabogram is an accurate and clinically applicable test for assessing an individual's metabolic status in disease.

Cell Proteomic Footprinting: Advances in the Quality of Cellular and Cell-Derived Cancer Vaccines.

In omics sciences, many compounds are measured simultaneously in a sample in a single run. Such analytical performance opens up prospects for improving cellular cancer vaccines and other cell-based immunotherapeutics. This article provides an overview of proteomics technology, known as cell proteomic footprinting. The molecular phenotype of cells is highly variable, and their antigenic profile is affected by many factors, including cell isolation from the tissue, cell cultivation conditions, and storage procedures. This makes the therapeutic properties of cells, including those used in vaccines, unpredictable. Cell proteomic footprinting makes it possible to obtain controlled cell products. Namely, this technology facilitates the cell authentication and quality control of cells regarding their molecular phenotype, which is directly connected with the antigenic properties of cell products. Protocols for cell proteomic footprinting with their crucial moments, footprint processing, and recommendations for the implementation of this technology are described in this paper. The provided footprints in this paper and program source code for their processing contribute to the fast implementation of this technology in the development and manufacturing of cell-based immunotherapeutics.

Mass Spectrometric Blood Metabogram: Acquisition, Characterization, and Prospects for Application.

In metabolomics, many metabolites are measured simultaneously in a single run. Such analytical performance opens up prospects for clinical laboratory diagnostics. In this work, a mass spectrometric metabogram was developed as a simplified and clinically applicable way of measuring the blood plasma metabolome. To develop the metabogram, blood plasma samples from healthy male volunteers (n = 48) of approximately the same age, direct infusion mass spectrometry (DIMS) of the low molecular fraction of samples, and principal component analysis (PCA) of the mass spectra were used. The seven components of the metabogram defined by PCA, which cover ~70% of blood plasma metabolome variability, were characterized using a metabolite set enrichment analysis (MSEA) and clinical test results of participating volunteers. It has been established that the components of the metabogram are functionally related groups of the blood metabolome associated with regulation, lipid-carbohydrate, and lipid-amine blood components, eicosanoids, lipid intake into the organism, and liver function thereby providing a lot of clinically relevant information. Therefore, metabogram provides the possibility to apply the metabolomics performance in the clinic. The features of the metabogram are also discussed in comparison with the thin-layer chromatography and with the analysis of blood metabolome by liquid chromatography combined with mass spectrometry.

Current State and Future Perspectives on Personalized Metabolomics.

Metabolomics is one of the most promising 'omics' sciences for the implementation in medicine by developing new diagnostic tests and optimizing drug therapy. Since in metabolomics, the end products of the biochemical processes in an organism are studied, which are under the influence of both genetic and environmental factors, the metabolomics analysis can detect any changes associated with both lifestyle and pathological processes. Almost every case-controlled metabolomics study shows a high diagnostic accuracy. Taking into account that metabolomics processes are already described for most nosologies, there are prerequisites that a high-speed and comprehensive metabolite analysis will replace, in near future, the narrow range of chemical analyses used today, by the medical community. However, despite the promising perspectives of personalized metabolomics, there are currently no FDA-approved metabolomics tests. The well-known problem of complexity of personalized metabolomics data analysis and their interpretation for the end-users, in addition to a traditional need for analytical methods to address the quality control, standardization, and data treatment are reported in the review. Possible ways to solve the problems and change the situation with the introduction of metabolomics tests into clinical practice, are also discussed.

Potential Plasma Metabolite Biomarkers of Diabetic Nephropathy: Untargeted Metabolomics Study.

Diabetic nephropathy (DN) is one of the specific complications of diabetes mellitus and one of the leading kidney-related disorders, often requiring renal replacement therapy. Currently, the tests commonly used for the diagnosis of DN, albuminuria (AU) and glomerular filtration rate (GFR), have limited sensitivity and specificity and can usually be noted when typical morphological changes in the kidney have already been manifested. That is why the extreme urgency of the problem of early diagnosis of this disease exists. The untargeted metabolomics analysis of blood plasma samples from 80 patients with type 1 diabetes and early and late stages of DN according to GFR was performed using direct injection mass spectrometry and bioinformatics analysis for diagnosing signatures construction. Among the dysregulated metabolites, combinations of 15 compounds, including amino acids and derivatives, monosaccharides, organic acids, and uremic toxins were selected for signatures for DN diagnosis. The selected metabolite combinations have shown high performance for diagnosing of DN, especially for the late stage (up to 99%). Despite the metabolite signature determined for the early stage of DN being characterized by a diagnostic performance of 81%, these metabolites as potential biomarkers might be useful in the evaluation of treatment of the disease, especially at early stages that may reduce the risk of kidney failure development.

Metabolome Profiling in Aging Studies.

Organism aging is closely related to systemic metabolic changes. However, due to the multilevel and network nature of metabolic pathways, it is difficult to understand these connections. Today, scientists are trying to solve this problem using one of the main approaches of metabolomics-untargeted metabolome profiling. The purpose of this publication is to review metabolomic studies based on such profiling, both in animal models and in humans. This review describes metabolites that vary significantly across age groups and include carbohydrates, amino acids, carnitines, biogenic amines, and lipids. Metabolic pathways associated with the aging process are also shown, including those associated with amino acid, lipid, and energy metabolism. The presented data reveal the mechanisms of aging and can be used as a basis for monitoring biological age and predicting age-related diseases in the early stages of their development.

Metabolomic Markers for Predicting Preeclampsia in the First Trimester of Pregnancy: A Retrospective Study.

We sought to identify the characteristic metabolite profile of blood plasma samples obtained from patients with preeclampsia. Direct high-resolution mass spectrometry was used to analyze samples from 79 pregnant women, 34 of whom had preeclampsia. We performed a comparative analysis of the metabolite profiles and found that they differed between pregnant women with and without preeclampsia. Lipids and sugars were identified as components of the metabolite profile that are likely to be associated with the development of preeclampsia. While PE was established only in the third trimester, a set of metabolites specific for the third trimester, including 2-(acetylamino)-1,5-anhydro-2-deoxy-4-O-b-D-galactopyranosyl-D-arabino-Hex-1-enitol, N-Acetyl-D-glucosaminyldiphosphodolichol, Cer(d18:0/20:0), and allolithocholic acid, was already traced in the first trimester. These components are also likely involved in lipid metabolism disorders and the development of oxidative stress.

Blood Plasma Metabolome Profiling at Different Stages of Renal Cell Carcinoma.

Early diagnostics significantly improves the survival of patients with renal cell carcinoma (RCC), which is the prevailing type of adult kidney cancer. However, the absence of clinically obvious symptoms and effective screening strategies at the early stages result to disease progression and survival rate reducing. The study was focused on revealing of potential low molecular biomarkers for early-stage RCC. The untargeted direct injection mass spectrometry-based metabolite profiling of blood plasma samples from 51 non-cancer volunteers (control) and 78 patients with different RCC subtypes and stages (early stages of clear cell RCC (ccRCC), papillary RCC (pRCC), chromophobe RCC (chrRCC) and advanced stages of ccRCC) was performed. Comparative analysis of the blood plasma metabolites between the control and cancer groups provided the detection of metabolites associated with different tumor stages. The designed model based on the revealed metabolites demonstrated high diagnostic power and accuracy. Overall, using the metabolomics approach the study revealed the metabolites demonstrating a high value for design of plasma-based test to improve early ccRCC diagnosis.

Comparative Metabolomic Study of Drosophila Species with Different Lifespans.

The increase in life expectancy, leading to a rise in the proportion of older people, is accompanied by a prevalence of age-related disorders among the world population, the fight against which today is one of the leading biomedical challenges. Exploring the biological insights concerning the lifespan is one of the ways to provide a background for designing an effective treatment for the increase in healthy years of life. Untargeted direct injection mass spectrometry-based metabolite profiling of 12 species of Drosophila with significant variations in natural lifespans was conducted in this research. A cross-comparison study of metabolomic profiles revealed lifespan signatures of flies. These signatures indicate that lifespan extension is associated with the upregulation of amino acids, phospholipids, and carbohydrate metabolism. Such information provides a metabolome-level view on longevity and may provide a molecular measure of organism age in age-related studies.

Personal Metabolomics: A Global Challenge.

Today, the introduction of metabolomics, like other omics sciences, into clinical practice as a personal omics test that realizes the perfect analytical capabilities of this science has become an important subject. The assembled data show that the metabolome of biosamples is a collection of highly informative and accurate signatures of virtually all diseases that are widespread in the population. However, we have not seen the emergence of personalized metabolomics in clinical practice. This article analyzes the causes of this problem. The complexity of personal metabolic data analysis and its incompatibility with widely accepted data treatment in metabolomics are shown. As a result, the impossibility of translating metabolic signatures accumulated in databases into a personal test is revealed. Problem-solving strategies that may radically change the situation and realize the analytical capabilities of metabolomics in medical laboratory practice are discussed.

Metabolomic Laboratory-Developed Tests: Current Status and Perspectives.

Laboratory-developed tests (LDTs) are a subset of in vitro diagnostic devices, which the US Food and Drug Administration defines as "tests that are manufactured by and used within a single laboratory". The review describes the emergence and history of LDTs. The current state and development prospects of LDTs based on metabolomics are analyzed. By comparing LDTs with the scientific metabolomics study of human bio samples, the characteristic features of metabolomic LDT are shown, revealing its essence, strengths, and limitations. The possibilities for further developments and scaling of metabolomic LDTs and their potential significance for healthcare are discussed. The legal aspects of LDT regulation in the United States, European Union, and Singapore, demonstrating different approaches to this issue, are also provided. Based on the data presented in the review, recommendations were made on the feasibility and ways of further introducing metabolomic LDTs into practice.

Mass spectrometry-based metabolomics diagnostics - myth or reality?

ABSTACTIntroduction: Metabolomics, one of the most high-promising technologies, is the most recently developed post-genomics discipline for developing new diagnostic tests for future implementation in medicine. More than 2,000 scientific papers, using mass spectrometry-based (MS-based) metabolomics analysis for human disease diagnostics, have been published during the past two decades, and almost every metabolomics study shows high diagnostic accuracy. However, despite the great results and promising perspectives, there are currently no diagnostic tests based on metabolomics that have been approved and introduced into clinics.Areas covered: In this report, the advantages and challenges of MS-based metabolomics are discussed with a focus on its developing role in diagnostics, and the current trends in implementing metabolomics diagnostics in the clinic.Expert opinion: In the development of new clinical diagnostics tests, MS-based metabolomics has potential as both a preliminary discovery base for routine testing and a multi-test prototype, which is hoped to be introduced into clinical practice in the near future. A laboratory-developed test (LDT) is one possible way that multi-testing could be developed.

In Situ Mass Spectrometry Diagnostics of Impaired Glucose Tolerance Using Label-Free Metabolomic Signature.

In metabolomics, mass spectrometry is used to detect a large number of low-molecular substances in a single analysis. Such a capacity could have direct application in disease diagnostics. However, it is challenging because of the analysis complexity, and the search for a way to simplify it while maintaining the diagnostic capability is an urgent task. It has been proposed to use the metabolomic signature without complex data processing (mass peak detection, alignment, normalization, and identification of substances, as well as any complex statistical analysis) to make the analysis more simple and rapid. METHODS: A label-free approach was implemented in the metabolomic signature, which makes the measurement of the actual or conditional concentrations unnecessary, uses only mass peak relations, and minimizes mass spectra processing. The approach was tested on the diagnosis of impaired glucose tolerance (IGT). RESULTS: The label-free metabolic signature demonstrated a diagnostic accuracy for IGT equal to 88% (specificity 85%, sensitivity 90%, and area under receiver operating characteristic curve (AUC) of 0.91), which is considered to be a good quality for diagnostics. CONCLUSIONS: It is possible to compile label-free signatures for diseases that allow for diagnosing the disease in situ, i.e., right at the mass spectrometer without complex data processing. This achievement makes all mass spectrometers potentially versatile diagnostic devices and accelerates the introduction of metabolomics into medicine.

Parkinson's Disease: Available Clinical and Promising Omics Tests for Diagnostics, Disease Risk Assessment, and Pharmacotherapy Personalization.

Parkinson's disease is the second most frequent neurodegenerative disease, representing a significant medical and socio-economic problem. Modern medicine still has no answer to the question of why Parkinson's disease develops and whether it is possible to develop an effective system of prevention. Therefore, active work is currently underway to find ways to assess the risks of the disease, as well as a means to extend the life of patients and improve its quality. Modern studies aim to create a method of assessing the risk of occurrence of Parkinson's disease (PD), to search for the specific ways of correction of biochemical disorders occurring in the prodromal stage of Parkinson's disease, and to personalize approaches to antiparkinsonian pharmacotherapy. In this review, we summarized all available clinically approved tests and techniques for PD diagnostics. Then, we reviewed major improvements and recent advancements in genomics, transcriptomics, and proteomics studies and application of metabolomics in PD research, and discussed the major metabolomics findings for diagnostics and therapy of the disease.

Diagnosis of Parkinson's Disease by A Metabolomics-Based Laboratory-Developed Test (LDT).

A laboratory-developed test (LDT) is a type of in vitro diagnostic test that is designed, manufactured and used in the same laboratory (i.e., an in-house test). In this study, a metabolomics-based LDT was developed. This test involves a blood plasma preparation, direct-infusion mass spectrometry analysis with a high-resolution mass spectrometer, alignment and normalization of mass peaks using original algorithms, metabolite annotation by a biochemical context-driven algorithm, detection of overrepresented metabolic pathways and results in a visualization in the form of a pathway names cloud. The LDT was applied to detect early stage Parkinson's disease (PD)-the diagnosis of which currently requires great effort due to the lack of available laboratory tests. In a case-control study (n = 56), the LDT revealed a statistically sound pattern in the PD-relevant pathways. Usage of the LDT for individuals confirmed its ability to reveal this pattern and thus diagnose PD at the early-stage (1-2.5 stages, according to Hoehn and Yahr scale). The detection of this pattern by LDT could diagnose PD with a specificity of 64%, sensitivity of 86% and an accuracy of 75%. Thus, this LDT can be used for further widespread testing.

Mass Spectrometry-Based Metabolomics Analysis of Obese Patients' Blood Plasma.

Scientists currently use only a small portion of the information contained in the blood metabolome. The identification of metabolites is a huge challenge because only highly abundant and well-separated compounds can be easily identified in complex samples. However, new approaches that enhance the identification of compounds have emerged; among them, the identification of compounds based on their involvement in a particular biological context is a recent development. In this work, this approach was first applied to identify metabolites in complex samples and, together with metabolite set enrichment analysis, was used for the evaluation of blood plasma from obese patients. The proposed approach was found to provide a statistically sound overview of the biochemical pathways, thus presenting additional information on obesity. Obesity progression was demonstrated to be accompanied by marked alterations in steroidogenesis, androstenedione metabolism, and androgen and estrogen metabolism. The findings of this study suggest that the workflow used for blood analysis is sufficient to demonstrate obesity at the biochemical pathway level as well as to monitor the response to treatment. This workflow is also expected to be suitable for studying other metabolic diseases.

Holistic Metabolomic Laboratory-Developed Test (LDT): Development and Use for the Diagnosis of Early-Stage Parkinson's Disease.

A laboratory-developed test (LDT) is a type of in vitro diagnostic test that is developed and used within a single laboratory. The holistic metabolomic LDT integrating the currently available data on human metabolic pathways, changes in the concentrations of low-molecular-weight compounds in the human blood during diseases and other conditions, and their prevalent location in the body was developed. That is, the LDT uses all of the accumulated metabolic data relevant for disease diagnosis and high-resolution mass spectrometry with data processing by in-house software. In this study, the LDT was applied to diagnose early-stage Parkinson's disease (PD), which currently lacks available laboratory tests. The use of the LDT for blood plasma samples confirmed its ability for such diagnostics with 73% accuracy. The diagnosis was based on relevant data, such as the detection of overrepresented metabolite sets associated with PD and other neurodegenerative diseases. Additionally, the ability of the LDT to detect normal composition of low-molecular-weight compounds in blood was demonstrated, thus providing a definition of healthy at the molecular level. This LDT approach as a screening tool can be used for the further widespread testing for other diseases, since 'omics' tests, to which the metabolomic LDT belongs, cover a variety of them.

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

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.