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Seo JP, Trippett JS, Huang Z, Lee S, Nouraein S, Wang RZ, Szablowski JO. Acoustically targeted measurement of transgene expression in the brain. SCIENCE ADVANCES 2024; 10:eadj7686. [PMID: 39110811 PMCID: PMC11305388 DOI: 10.1126/sciadv.adj7686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Accepted: 06/28/2024] [Indexed: 08/10/2024]
Abstract
Gene expression is a critical component of brain physiology, but monitoring this expression in the living brain represents a major challenge. Here, we introduce a new paradigm called recovery of markers through insonation (REMIS) for noninvasive measurement of gene expression in the brain with cell type, spatial, and temporal specificity. Our approach relies on engineered protein markers that are produced in neurons but exit into the brain's interstitium. When ultrasound is applied to targeted brain regions, it opens the blood-brain barrier and releases these markers into the bloodstream. Once in blood, the markers can be readily detected using biochemical techniques. REMIS can noninvasively confirm gene delivery and measure endogenous signaling in specific brain sites through a simple insonation and a subsequent blood test. REMIS is reliable and demonstrated consistent improvement in recovery of markers from the brain into the blood. Overall, this work establishes a noninvasive, spatially specific method of monitoring gene delivery and endogenous signaling in the brain.
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Affiliation(s)
- Joon Pyung Seo
- Applied Physics Program, Rice University, Houston, TX, USA
| | | | - Zhimin Huang
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Sangsin Lee
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Shirin Nouraein
- Systems, Synthetic, and Physical Biology Program, Rice University, Houston, TX, USA
| | - Ryan Z. Wang
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Jerzy O. Szablowski
- Applied Physics Program, Rice University, Houston, TX, USA
- Department of Bioengineering, Rice University, Houston, TX, USA
- Systems, Synthetic, and Physical Biology Program, Rice University, Houston, TX, USA
- Rice Neuroengineering Initiative, Rice University, Houston, TX, USA
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2
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Abdullah G, Akpan A, Phelan MM, Wright HL. New insights into healthy ageing, inflammageing and frailty using metabolomics. FRONTIERS IN AGING 2024; 5:1426436. [PMID: 39044748 PMCID: PMC11263002 DOI: 10.3389/fragi.2024.1426436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Accepted: 06/24/2024] [Indexed: 07/25/2024]
Abstract
Human ageing is a normal process and does not necessarily result in the development of frailty. A mix of genetic, environmental, dietary, and lifestyle factors can have an impact on ageing, and whether an individual develops frailty. Frailty is defined as the loss of physiological reserve both at the physical and cellular levels, where systemic processes such as oxidative stress and inflammation contribute to physical decline. The newest "omics" technology and systems biology discipline, metabolomics, enables thorough characterisation of small-molecule metabolites in biological systems at a particular time and condition. In a biological system, metabolites-cellular intermediate products of metabolic reactions-reflect the system's final response to genomic, transcriptomic, proteomic, epigenetic, or environmental alterations. As a relatively newer technique to characterise metabolites and biomarkers in ageing and illness, metabolomics has gained popularity and has a wide range of applications. We will give a comprehensive summary of what is currently known about metabolomics in studies of ageing, with a focus on biomarkers for frailty. Metabolites related to amino acids, lipids, carbohydrates, and redox metabolism may function as biomarkers of ageing and/or frailty development, based on data obtained from human studies. However, there is a complexity that underpins biological ageing, due to both genetic and environmental factors that play a role in orchestrating the ageing process. Therefore, there is a critical need to identify pathways that contribute to functional decline in people with frailty.
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Affiliation(s)
- Genna Abdullah
- Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Asangaedem Akpan
- Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, United Kingdom
- Division of Internal Medicine, University of Western Australia, Bunbury, WA, Australia
- Faculty of Health Sciences, Curtis University, Bunbury, WA, Australia
- Department of Geriatric Medicine, Bunbury Regional Hospital, Bunbury, WA, Australia
| | - Marie M. Phelan
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
- High Field NMR Facility, Liverpool Shared Research Facilities University of Liverpool, Liverpool, United Kingdom
| | - Helen L. Wright
- Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, United Kingdom
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3
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Li Q, Wei Z, Zhang Y, Zheng C. Causal role of metabolites in non-small cell lung cancer: Mendelian randomization (MR) study. PLoS One 2024; 19:e0300904. [PMID: 38517880 PMCID: PMC10959361 DOI: 10.1371/journal.pone.0300904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 03/06/2024] [Indexed: 03/24/2024] Open
Abstract
On a global scale, lung cancer(LC) is the most commonly occurring form of cancer. Nonetheless, the process of screening and detecting it in its early stages presents significant challenges. Earlier research endeavors have recognized metabolites as potentially reliable biomarkers for LC. However, the majority of these studies have been limited in scope, featuring inconsistencies in terms of the relationships and levels of association observed.Moreover, there has been a lack of consistency in the types of biological samples utilized in previous studies. Therefore, the main objective of our research was to explore the correlation between metabolites and Non-small cell lung cancer (NSCLC).Thorough two-sample Mendelian randomization (TSMR) analysis, we investigated potential cause-and-effect relationships between 1400 metabolites and the risk of NSCLC.The analysis of TSMR revealed a significant causal impact of 61 metabolites on NSCLC.To ensure the reliability and validity of our findings, we perform FDR correction for P-values by Benjaminiand Hochberg(BH) method, Our results indicate that Oleate/vaccenate (18:1) levels and Caffeine to paraxanthine ratio may be causally associated with an increased risk of NSCLC [Oleate/vaccenate(18:1)levels: OR = 1.171,95%CI: 1.085-1.265, FDR = 0.036; Caffeine to paraxanthine ratio: OR = 1.386, 95%CI:1.191-1.612,FDR = 0.032].
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Affiliation(s)
- Qian Li
- Department of Cardiac Surgery, The First Affiliated Hospital of Kunming Medical University, Kunming, 650000, China
| | - Zedong Wei
- Department of Thoracic Surgery, Qianjiang Central Hospital, Qianjiang, 433100, China
| | - Yonglun Zhang
- Department of Thoracic Surgery, Qianjiang Central Hospital, Qianjiang, 433100, China
| | - Chongqing Zheng
- Department of Thoracic Surgery, Qianjiang Central Hospital, Qianjiang, 433100, China
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4
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Seo JP, Trippett JS, Huang Z, Wang RZ, Lee S, Szablowski JO. Acoustically-Targeted Measurement of Transgene Expression in the Brain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.23.541868. [PMID: 37292585 PMCID: PMC10245922 DOI: 10.1101/2023.05.23.541868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Gene expression is a critical component of brain physiology and activity, but monitoring this expression in the living brain represents a significant challenge. Here, we introduce a new paradigm called Recovery of Markers through InSonation (REMIS) for noninvasive measurement of gene expression in the brain with cell-type, spatial, and temporal specificity. Our approach relies on engineered protein markers that are designed to be expressed in neurons and exit into the interstitium. By applying ultrasound to targeted brain regions, these markers are released into the bloodstream, where they can be readily detected using biochemical techniques. REMIS can noninvasively confirm gene delivery and measure endogenous signaling in specific brain sites through a simple insonation and a subsequent blood test. Using REMIS, we successfully measured chemogenetic induction of neuronal activity in ultrasound-tar-geted brain regions. REMIS recovery of markers is reliable and demonstrated improved recovery of markers from the brain into the blood in every tested animal. Overall, our work establishes a noninvasive, spatially-specific means of monitoring gene delivery outcomes and endogenous signaling in mammalian brains, opening up possibilities for brain research and noninvasive monitoring of gene therapies in the brain.
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5
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Balashova E, Trifonova O, Maslov D, Lichtenberg S, Lokhov P, Archakov A. Metabolome profiling in the study of aging processes. BIOMEDITSINSKAYA KHIMIYA 2022; 68:321-338. [DOI: 10.18097/pbmc20226805321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
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.
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Affiliation(s)
| | | | - D.L. Maslov
- Institute of Biomedical Chemistry, Moscow, Russia
| | | | - P.G. Lokhov
- Institute of Biomedical Chemistry, Moscow, Russia
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da Silva Barison GA, D’Amora P, Izidoro MA, Son MC, Martins LM, Bonduki CE, de Aquino Castro R, Girão MJBC, Gomes MTV. Metabolomic profiling of peripheral plasma by GC-MS and correlation with size of uterine leiomyomas. J Endocr Soc 2022; 6:bvac061. [PMID: 35611322 PMCID: PMC9123306 DOI: 10.1210/jendso/bvac061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Indexed: 12/04/2022] Open
Abstract
Background Uterine leiomyomas are benign monoclonal tumors originating from the myometrium. Little information exists concerning metabolomics and the presence of leiomyomas. Objective The present study evaluated circulating metabolites in the plasma and their correlation with the presence and size of leiomyomas. Study Design Cross-sectional observational study, including women divided into 3 groups: 37 with leiomyomas and uterus >500 cm3, 17 with leiomyomas and uterus ≤150 cm3, and 21 leiomyoma-free. Patients underwent peripheral blood collection using untargeted metabolic assessment by gas chromatography coupled to mass spectrometer. Results There was no statistical difference between patients’ anthropometric and demographic features and laboratory tests. Statistical differences in uterus volume (P < 0.0001) were found. Forty-six metabolites were identified (35% amino acids and derivatives, 22% fatty acids, and 18% carbohydrates). Statistically significant metabolic distinction (P < 0.05, false discovery rate< 0.05) was observed for 14 metabolites. Most amino acids (L-isoleucine, L-valine, and pyroglutamic acid) were significantly reduced in plasma levels of patients with large leiomyomas. The only exception was L-glutamine, with a significant increase. Fatty acids (arachidonic acid, alfa-tocopherol, palmitic acid, and stearic acid) were similarly reduced in large leiomyomas patients, except for alpha-linolenic acid, which increased. For carbohydrates (myo-inositol, D-threitol, and D-ribose), there was a decrease in the plasma of patients with leiomyomas. Conclusion There are different plasma metabolites levels of amino acids, fatty acids, and carbohydrates among patients with leiomyomas, most of them reduced, but some significantly increased in large leiomyomas, compared to leiomyoma-free patients.
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Affiliation(s)
| | - Paulo D’Amora
- Department of Gynecology, Federal University of Sao Paulo, Sao Paulo, Brazil
| | - Mário Augusto Izidoro
- Spectrometry Laboratory; Beneficent Association for Blood Collection (COLSAN), Sao Paulo, Brazil
| | - Mariana Corinti Son
- Department of Gynecology, Federal University of Sao Paulo, Sao Paulo, Brazil
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Trifonova OP, Maslov DL, Balashova EE, Lokhov PG. Mass spectrometry-based metabolomics diagnostics - myth or reality? Expert Rev Proteomics 2021; 18:7-12. [PMID: 33653222 DOI: 10.1080/14789450.2021.1893695] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
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.
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Affiliation(s)
- Oxana P Trifonova
- Analytical Branch, Laboratory of Mass Spectrometry-based Metabolomic Diagnostic, Institute of Biomedical Chemistry, Moscow, Russia
| | - Dmitri L Maslov
- Analytical Branch, Laboratory of Mass Spectrometry-based Metabolomic Diagnostic, Institute of Biomedical Chemistry, Moscow, Russia
| | - Elena E Balashova
- Analytical Branch, Laboratory of Mass Spectrometry-based Metabolomic Diagnostic, Institute of Biomedical Chemistry, Moscow, Russia
| | - Petr G Lokhov
- Analytical Branch, Laboratory of Mass Spectrometry-based Metabolomic Diagnostic, Institute of Biomedical Chemistry, Moscow, Russia
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Lokhov PG, Maslov DL, Lichtenberg S, Trifonova OP, Balashova EE. Holistic Metabolomic Laboratory-Developed Test (LDT): Development and Use for the Diagnosis of Early-Stage Parkinson's Disease. Metabolites 2020; 11:metabo11010014. [PMID: 33383698 PMCID: PMC7824177 DOI: 10.3390/metabo11010014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 12/24/2020] [Accepted: 12/24/2020] [Indexed: 02/04/2023] Open
Abstract
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.
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Affiliation(s)
- Petr G. Lokhov
- Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, 119121 Moscow, Russia; (D.L.M.); (O.P.T.); (E.E.B.)
- Correspondence:
| | - Dmitry L. Maslov
- Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, 119121 Moscow, Russia; (D.L.M.); (O.P.T.); (E.E.B.)
| | - Steven Lichtenberg
- Metabometrics, Inc, 651 N Broad St, Suite 205 #1370, Middletown, DE 19709, USA;
| | - Oxana P. Trifonova
- Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, 119121 Moscow, Russia; (D.L.M.); (O.P.T.); (E.E.B.)
| | - Elena E. Balashova
- Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, 119121 Moscow, Russia; (D.L.M.); (O.P.T.); (E.E.B.)
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Lokhov PG, Trifonova OP, Maslov DL, Balashova EE. In Situ Mass Spectrometry Diagnostics of Impaired Glucose Tolerance Using Label-Free Metabolomic Signature. Diagnostics (Basel) 2020; 10:E1052. [PMID: 33291514 PMCID: PMC7762113 DOI: 10.3390/diagnostics10121052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 11/30/2020] [Accepted: 12/04/2020] [Indexed: 11/17/2022] Open
Abstract
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.
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Affiliation(s)
- Petr G. Lokhov
- Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, 119121 Moscow, Russia; (O.P.T.); (D.L.M.); (E.E.B.)
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10
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Metabolomics Community in Russia: History of Development, Key Participants, and Results. BIOTECH 2020; 9:biotech9040020. [PMID: 35822823 PMCID: PMC9258313 DOI: 10.3390/biotech9040020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 10/18/2020] [Accepted: 10/21/2020] [Indexed: 12/05/2022] Open
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.
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11
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Lokhov PG, Balashova EE, Trifonova OP, Maslov DL, Archakov AI. [Ten years of the Russian metabolomics: history of development and achievements]. BIOMEDIT︠S︡INSKAI︠A︡ KHIMII︠A︡ 2020; 66:279-293. [PMID: 32893819 DOI: 10.18097/pbmc20206604279] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
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.
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Affiliation(s)
- P G Lokhov
- Institute of Biomedical Chemistry, Moscow, Russia
| | | | | | - D L Maslov
- Institute of Biomedical Chemistry, Moscow, Russia
| | - A I Archakov
- Institute of Biomedical Chemistry, Moscow, Russia
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12
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Trifonova OP, Balashova EE, Maslov DL, Grigoriev AI, Lisitsa AV, Ponomarenko EA, Archakov AI. [Blood metabolome analysis for creating a digital image of a healthy person]. BIOMEDITSINSKAIA KHIMIIA 2020; 66:216-223. [PMID: 32588827 DOI: 10.18097/pbmc20206603216] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
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.
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Affiliation(s)
| | | | - D L Maslov
- Institute of Biomedical Chemistry, Moscow, Russia
| | - A I Grigoriev
- Institute of Biomedical Problems of the Russian Academy of Sciences, Moscow, Russia
| | - A V Lisitsa
- Institute of Biomedical Chemistry, Moscow, Russia
| | | | - A I Archakov
- Institute of Biomedical Chemistry, Moscow, Russia
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13
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Trifonova OP, Maslov DL, Balashova EE, Urazgildeeva GR, Abaimov DA, Fedotova EY, Poleschuk VV, Illarioshkin SN, Lokhov PG. Parkinson's Disease: Available Clinical and Promising Omics Tests for Diagnostics, Disease Risk Assessment, and Pharmacotherapy Personalization. Diagnostics (Basel) 2020; 10:E339. [PMID: 32466249 PMCID: PMC7277996 DOI: 10.3390/diagnostics10050339] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/21/2020] [Accepted: 05/22/2020] [Indexed: 12/15/2022] Open
Abstract
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.
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Affiliation(s)
- Oxana P. Trifonova
- Laboratory of mass spectrometry-based metabolomics diagnostics, Institute of Biomedical Chemistry, 10 building 8, Pogodinskaya street, 119121 Moscow, Russia; (D.L.M.); (E.E.B.); (P.G.L.)
| | - Dmitri L. Maslov
- Laboratory of mass spectrometry-based metabolomics diagnostics, Institute of Biomedical Chemistry, 10 building 8, Pogodinskaya street, 119121 Moscow, Russia; (D.L.M.); (E.E.B.); (P.G.L.)
| | - Elena E. Balashova
- Laboratory of mass spectrometry-based metabolomics diagnostics, Institute of Biomedical Chemistry, 10 building 8, Pogodinskaya street, 119121 Moscow, Russia; (D.L.M.); (E.E.B.); (P.G.L.)
| | - Guzel R. Urazgildeeva
- 5th Neurological Department (Department of Neurogenetics), Research Centre of Neurology, Volokolamskoe shosse, 80, 125367 Moscow, Russia; (G.R.U.); (D.A.A.); (E.Y.F.); (V.V.P.); (S.N.I.)
| | - Denis A. Abaimov
- 5th Neurological Department (Department of Neurogenetics), Research Centre of Neurology, Volokolamskoe shosse, 80, 125367 Moscow, Russia; (G.R.U.); (D.A.A.); (E.Y.F.); (V.V.P.); (S.N.I.)
| | - Ekaterina Yu. Fedotova
- 5th Neurological Department (Department of Neurogenetics), Research Centre of Neurology, Volokolamskoe shosse, 80, 125367 Moscow, Russia; (G.R.U.); (D.A.A.); (E.Y.F.); (V.V.P.); (S.N.I.)
| | - Vsevolod V. Poleschuk
- 5th Neurological Department (Department of Neurogenetics), Research Centre of Neurology, Volokolamskoe shosse, 80, 125367 Moscow, Russia; (G.R.U.); (D.A.A.); (E.Y.F.); (V.V.P.); (S.N.I.)
| | - Sergey N. Illarioshkin
- 5th Neurological Department (Department of Neurogenetics), Research Centre of Neurology, Volokolamskoe shosse, 80, 125367 Moscow, Russia; (G.R.U.); (D.A.A.); (E.Y.F.); (V.V.P.); (S.N.I.)
| | - Petr G. Lokhov
- Laboratory of mass spectrometry-based metabolomics diagnostics, Institute of Biomedical Chemistry, 10 building 8, Pogodinskaya street, 119121 Moscow, Russia; (D.L.M.); (E.E.B.); (P.G.L.)
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14
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Lokhov PG, Trifonova OP, Maslov DL, Lichtenberg S, Balashova EE. Diagnosis of Parkinson's Disease by A Metabolomics-Based Laboratory-Developed Test (LDT). Diagnostics (Basel) 2020; 10:diagnostics10050332. [PMID: 32455603 PMCID: PMC7277951 DOI: 10.3390/diagnostics10050332] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/29/2020] [Accepted: 05/19/2020] [Indexed: 01/02/2023] Open
Abstract
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.
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Affiliation(s)
- Petr G. Lokhov
- Institute of Biomedical Chemistry, 10 building 8, Pogodinskaya Street, 119121 Moscow, Russia; (O.P.T.); (D.L.M.); (E.E.B.)
- Correspondence:
| | - Oxana P. Trifonova
- Institute of Biomedical Chemistry, 10 building 8, Pogodinskaya Street, 119121 Moscow, Russia; (O.P.T.); (D.L.M.); (E.E.B.)
| | - Dmitry L. Maslov
- Institute of Biomedical Chemistry, 10 building 8, Pogodinskaya Street, 119121 Moscow, Russia; (O.P.T.); (D.L.M.); (E.E.B.)
| | - Steven Lichtenberg
- Metabometrics, Inc., 651 N Broad St., Suite 205 #1370, Middletown, DE 19709, USA;
| | - Elena E. Balashova
- Institute of Biomedical Chemistry, 10 building 8, Pogodinskaya Street, 119121 Moscow, Russia; (O.P.T.); (D.L.M.); (E.E.B.)
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15
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Balashova EE, Lokhov PG, Ponomarenko EA, Markin SS, Lisitsa AV, Archakov AI. Metabolomic diagnostics and human digital image. Per Med 2019; 16:133-144. [PMID: 30767631 DOI: 10.2217/pme-2018-0066] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The existing clinical laboratory practice has limitations in terms of specificity and sensitivity of diagnosis, making the introduction of new methods in medicine more topical. Application of 'omics' technologies, especially metabolomics, allows overcoming these limitations. The composition of blood metabolites reflects the physical state of an organism at the molecular level. The analysis of blood metabolome can serve as effective means of diagnosis, implementation of which in healthcare is timely and relevant. This paper demonstrates the versatility of metabolomic diagnostics, its applicability to various diseases. We discussed the standard of human digital image, which includes the metabolomic data sufficient to make an accurate assessment of general health and carry out precision diagnostics of a wide range of diseases.
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Affiliation(s)
- Elena E Balashova
- Department of Proteomics & Mass Spectrometry, Institute of Biomedical Chemistry, Pogodinskaya st 10, 119121, Moscow, Russia
| | - Petr G Lokhov
- Department of Proteomics & Mass Spectrometry, Institute of Biomedical Chemistry, Pogodinskaya st 10, 119121, Moscow, Russia
| | - Elena A Ponomarenko
- Department of Proteomics & Mass Spectrometry, Institute of Biomedical Chemistry, Pogodinskaya st 10, 119121, Moscow, Russia.,PostGenTech LLC, Pogodinskaya st 10, 119121, Moscow, Russia
| | - Sergey S Markin
- Department of Proteomics & Mass Spectrometry, Institute of Biomedical Chemistry, Pogodinskaya st 10, 119121, Moscow, Russia
| | - Andrey V Lisitsa
- Department of Proteomics & Mass Spectrometry, Institute of Biomedical Chemistry, Pogodinskaya st 10, 119121, Moscow, Russia
| | - Alexander I Archakov
- Department of Proteomics & Mass Spectrometry, Institute of Biomedical Chemistry, Pogodinskaya st 10, 119121, Moscow, Russia
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16
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Balashova EE, Maslov DL, Lokhov PG. A Metabolomics Approach to Pharmacotherapy Personalization. J Pers Med 2018; 8:jpm8030028. [PMID: 30189667 PMCID: PMC6164342 DOI: 10.3390/jpm8030028] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 08/17/2018] [Accepted: 09/03/2018] [Indexed: 12/27/2022] Open
Abstract
The optimization of drug therapy according to the personal characteristics of patients is a perspective direction in modern medicine. One of the possible ways to achieve such personalization is through the application of "omics" technologies, including current, promising metabolomics methods. This review demonstrates that the analysis of pre-dose metabolite biofluid profiles allows clinicians to predict the effectiveness of a selected drug treatment for a given individual. In the review, it is also shown that the monitoring of post-dose metabolite profiles could allow clinicians to evaluate drug efficiency, the reaction of the host to the treatment, and the outcome of the therapy. A comparative description of pharmacotherapy personalization (pharmacogenomics, pharmacoproteomics, and therapeutic drug monitoring) and personalization based on the analysis of metabolite profiles for biofluids (pharmacometabolomics) is also provided.
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Affiliation(s)
- Elena E Balashova
- Institute of Biomedical Chemistry, Pogodinskaya St. 10, Moscow 119121, Russia.
| | - Dmitry L Maslov
- Institute of Biomedical Chemistry, Pogodinskaya St. 10, Moscow 119121, Russia.
| | - Petr G Lokhov
- Institute of Biomedical Chemistry, Pogodinskaya St. 10, Moscow 119121, Russia.
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17
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Filippova JA, Semenov DV, Juravlev ES, Komissarov AB, Richter VA, Stepanov GA. Modern Approaches for Identification of Modified Nucleotides in RNA. BIOCHEMISTRY (MOSCOW) 2018; 82:1217-1233. [PMID: 29223150 DOI: 10.1134/s0006297917110013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
This review considers approaches for detection of modified monomers in the RNA structure of living organisms. Recently, some data on dynamic alterations in the pool of modifications of the key RNA species that depend on external factors affecting the cells and physiological conditions of the whole organism have been accumulated. The recent studies have presented experimental data on relationship between the mechanisms of formation of modified/minor nucleotides of RNA in mammalian cells and the development of various pathologies. The development of novel methods for detection of chemical modifications of RNA nucleotides in the cells of living organisms and accumulation of knowledge on the contribution of modified monomers to metabolism and functioning of individual RNA species establish the basis for creation of novel diagnostic and therapeutic approaches. This review includes a short description of routine methods for determination of modified nucleotides in RNA and considers in detail modern approaches that enable not only detection but also quantitative assessment of the modification level of various nucleotides in individual RNA species.
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Affiliation(s)
- J A Filippova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.
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18
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Kurreck A, Vandergrift LA, Fuss TL, Habbel P, Agar NYR, Cheng LL. Prostate cancer diagnosis and characterization with mass spectrometry imaging. Prostate Cancer Prostatic Dis 2017; 21:297-305. [PMID: 29209003 PMCID: PMC5988647 DOI: 10.1038/s41391-017-0011-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 08/15/2017] [Indexed: 02/06/2023]
Abstract
Background Prostate cancer (PCa), the most common cancer and second leading cause of cancer death in American men, presents the clinical challenge of distinguishing between indolent and aggressive tumors for proper treatment. PCa presents significant alterations in metabolic pathways that can potentially be measured using techniques like mass spectrometry (MS) or mass spectrometry imaging (MSI) and used to characterize PCa aggressiveness. MS quantifies metabolomic, proteomic, and lipidomic profiles of biological systems that can be further visualized for their spatial distributions through MSI. Methods PubMed was queried for all publications relating to MS and MSI in human prostate cancer from April 2007 to April 2017. With the goal of reviewing the utility of MSI in diagnosis and prognostication of human PCa, MSI articles that reported investigations of PCa-specific metabolites or metabolites indicating PCa aggressiveness were selected for inclusion. Articles were included that covered MS and MSI principles, limitations, and applications in PCa. Results We identified nine key studies on MSI in intact human prostate tissue specimens that determined metabolites which could either differentiate between benign and malignant prostate tissue or indicate prostate cancer aggressiveness. These MSI-detected biomarkers show promise in reliably identifying PCa and determining disease aggressiveness. Conclusions MSI represents an innovative technique with the ability to interrogate cancer biomarkers in relation to tissue pathologies and investigate tumor aggressiveness. We propose MSI as a powerful adjuvant histopathology imaging tool for prostate tissue evaluations, where clinical translation of this ex vivo technique could make possible the use of MSI for personalized medicine in diagnosis and prognosis of prostate cancer. Moreover, the knowledge provided from this technique can majorly contribute to the understanding of molecular pathogenesis of PCa and other malignant diseases.
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Affiliation(s)
- Annika Kurreck
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.,Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.,Department of Hematology and Oncology, Charité Medical University of Berlin, Berlin, Germany
| | - Lindsey A Vandergrift
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.,Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Taylor L Fuss
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.,Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Piet Habbel
- Department of Hematology and Oncology, Charité Medical University of Berlin, Berlin, Germany
| | - Nathalie Y R Agar
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Leo L Cheng
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA. .,Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
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19
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Shen J, Ye Y, Chang DW, Huang M, Heymach JV, Roth JA, Wu X, Zhao H. Circulating metabolite profiles to predict overall survival in advanced non-small cell lung cancer patients receiving first-line chemotherapy. Lung Cancer 2017; 114:70-78. [PMID: 29173770 DOI: 10.1016/j.lungcan.2017.10.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 10/12/2017] [Accepted: 10/30/2017] [Indexed: 12/15/2022]
Abstract
OBJECTIVES The prognosis for advanced-stage non-small cell lung cancer (NSCLC) is usually poor. However, survival may be variable and difficult to predict. In the current study, we aimed to identify circulating metabolites as potential predictive biomarkers for overall survival of advanced-stage (III/IV) NSCLC patients treated with first-line platinum-based chemotherapy. MATERIALS AND METHODS Using two-stage study design, we performed global metabolomic profiling in blood of 220 advanced-stage NSCLC patients, including 110 with poor survival and 110 with good survival. Metabolomic profiling was conducted using Metabolon platform. The association of each metabolite with survival was assessed by Cox proportional hazard regression model with adjustment for covariates. RESULTS AND CONCLUSION We found levels of 4 metabolites, caffeine, paraxanthine, stachydrine, and methyl glucopyranoside (alpha+beta), differed significantly between NSCLC patients with poor and good survival in both discovery and validation phases (P<0.05). Interestingly, majority of the identified metabolites are involved in caffeine metabolism, and 2 metabolites are related to coffee intake. In fact, caffeine metabolism pathway was the only significant pathway identified which significantly differed between NSCLC patients with poor and good survival (P=1.48E-07) in the pathway analysis. We also found 4 metabolites whose levels were significantly associated with good survival in both discovery and validation phases. Strong cumulative effects on overall survival were observed for these 4 metabolites. In conclusion, we identified a panel of metabolites including metabolites in caffeine metabolism pathway that may predict survival outcome in advanced-stage NSCLC patients. The identified small metabolites may be useful biomarker candidates to help identify patients who may benefit from platinum-based chemotherapy.
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Affiliation(s)
- Jie Shen
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Yuanqing Ye
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - David W Chang
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Maosheng Huang
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - John V Heymach
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jack A Roth
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Xifeng Wu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
| | - Hua Zhao
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
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20
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Lokhov P, Lisitsa A, Archakov A. Metabolomic blood test: purpose, implementation and interpretation of data. ACTA ACUST UNITED AC 2017; 63:232-240. [DOI: 10.18097/pbmc20176303232] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
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.
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Affiliation(s)
- P.G. Lokhov
- Institute of Biomedical Chemistry, Moscow, Russia
| | - A.V. Lisitsa
- Institute of Biomedical Chemistry, Moscow, Russia
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