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Sillé F, Hartung T. Metabolomics in Preclinical Drug Safety Assessment: Current Status and Future Trends. Metabolites 2024; 14:98. [PMID: 38392990 PMCID: PMC10890122 DOI: 10.3390/metabo14020098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/17/2024] [Accepted: 01/27/2024] [Indexed: 02/25/2024] Open
Abstract
Metabolomics is emerging as a powerful systems biology approach for improving preclinical drug safety assessment. This review discusses current applications and future trends of metabolomics in toxicology and drug development. Metabolomics can elucidate adverse outcome pathways by detecting endogenous biochemical alterations underlying toxicity mechanisms. Furthermore, metabolomics enables better characterization of human environmental exposures and their influence on disease pathogenesis. Metabolomics approaches are being increasingly incorporated into toxicology studies and safety pharmacology evaluations to gain mechanistic insights and identify early biomarkers of toxicity. However, realizing the full potential of metabolomics in regulatory decision making requires a robust demonstration of reliability through quality assurance practices, reference materials, and interlaboratory studies. Overall, metabolomics shows great promise in strengthening the mechanistic understanding of toxicity, enhancing routine safety screening, and transforming exposure and risk assessment paradigms. Integration of metabolomics with computational, in vitro, and personalized medicine innovations will shape future applications in predictive toxicology.
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Affiliation(s)
- Fenna Sillé
- Center for Alternatives to Animal Testing (CAAT), Department of Environmental Health Sciences, Johns Hopkins Bloomberg School of Public Health and Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Thomas Hartung
- Center for Alternatives to Animal Testing (CAAT), Department of Environmental Health Sciences, Johns Hopkins Bloomberg School of Public Health and Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21205, USA
- CAAT-Europe, University of Konstanz, Universitätsstraße 10, 78464 Konstanz, Germany
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Kim HY, Lee JD, Lee YH, Seo SW, Lee HS, Kim S, Kim KB. Urinary Metabolomics in Young Soccer Players after Winter Training Season. Metabolites 2022; 12:metabo12121283. [PMID: 36557321 PMCID: PMC9784126 DOI: 10.3390/metabo12121283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/06/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022] Open
Abstract
During the off-season, soccer players in Korea attend the winter training season (WTS) to build running stamina for the next season. For young soccer players, proper recovery time is needed to prevent injury or muscle damage. In this study, urinary metabolites in young players after 1, 5, and 10 days of the WTS were analyzed using nuclear magnetic resonance spectroscopy (NMR) combined with multivariate analysis to suggest appropriate recovery times for improving their soccer skills. After NMR analysis of the urine samples obtained from young players, 79 metabolites were identified, and each group (1, 5, or 10 days after WTS) was separated from the before the WTS group in the target profiling analysis using partial least squares-discriminant analysis (PLS-DA). Of these, 15 metabolites, including 1-methylnicotinamide, 3-indoxylsulfate, galactarate, glutamate, glycerol, histamine, methylmalonate, maltose, N-phenylacetylglycine, trimethylamine, urea, 2-hydroxybutyrate, adenine, alanine, and lactate, were significantly different than those from before the WTS and were mainly involved in the urea, purine nucleotide, and glucose-alanine cycles. In this study, most selected metabolites increased 1 day after the WTS and then returned to normal levels. However, 4 metabolites, adenine, 2-hydroxybutyrate, alanine, and lactate, increased during the 5 days of recovery time following the WTS. Based on excess ammonia, adenine, and lactate levels in the urine, at least 5 days of recovery time can be considered appropriate.
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Affiliation(s)
- Hyang-Yeon Kim
- College of Pharmacy, Dankook University, 119 Dandae-ro, Cheonan 31116, Republic of Korea
- Center for Human Risk Assessment, Dankook University, 119 Dandae-ro, Cheonan 31116, Republic of Korea
| | - Jung-Dae Lee
- College of Pharmacy, Dankook University, 119 Dandae-ro, Cheonan 31116, Republic of Korea
- Center for Human Risk Assessment, Dankook University, 119 Dandae-ro, Cheonan 31116, Republic of Korea
| | - Yun-Hwan Lee
- Department of Exercise and Medical Science, Graduate School, Dankook University, 119 Dandae-ro, Cheonan 31116, Republic of Korea
| | - Sang-Won Seo
- Department of Sports Science, Gwangju University, Gwangju 61743, Republic of Korea
| | - Ho-Seong Lee
- Department of Exercise and Medical Science, Graduate School, Dankook University, 119 Dandae-ro, Cheonan 31116, Republic of Korea
- Correspondence: (H.-S.L.); (K.-B.K.)
| | - Suhkmann Kim
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan Daehak-ro 63 beon-gil 2, Busan 46241, Republic of Korea
| | - Kyu-Bong Kim
- Center for Human Risk Assessment, Dankook University, 119 Dandae-ro, Cheonan 31116, Republic of Korea
- Correspondence: (H.-S.L.); (K.-B.K.)
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Yu S, He Y, Ji W, Yang R, Zhao Y, Li Y, Liu Y, Ding L, Ma M, Wang H, Yang X. Metabolic and Proteomic Profiles Associated with Immune Responses Induced by Different Inactivated SARS-CoV-2 Vaccine Candidates. Int J Mol Sci 2022; 23:ijms231810644. [PMID: 36142558 PMCID: PMC9503298 DOI: 10.3390/ijms231810644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/02/2022] [Accepted: 09/09/2022] [Indexed: 12/04/2022] Open
Abstract
Since the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in late 2019, the virus has been mutating continuously, resulting in the continuous emergence of variants and creating challenges for epidemic prevention and control. Here, we immunized mice with different vaccine candidates, revealing the immune, protein, and metabolomic changes that take place in vaccines composed of different variants. We found that the prototype strain and Delta- and Omicron-variant inactivated vaccine candidates could all induce a high level of neutralizing antibodies and cellular immunity responses in mice. Next, we found that the metabolic and protein profiles were changed, showing a positive association with immune responses, and the level of the change was distinct in different inactivated vaccines, indicating that amino acid variations could affect metabolomics and proteomics. Our findings reveal differences between vaccines at the metabolomic and proteomic levels. These insights provide a novel direction for the immune evaluation of vaccines and could be used to guide novel strategies for vaccine design.
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Affiliation(s)
- Shouzhi Yu
- Beijing Institute of Biological Products Company Limited, Beijing 100176, China
| | - Yao He
- Beijing Institute of Biological Products Company Limited, Beijing 100176, China
| | - Wenheng Ji
- Beijing Institute of Biological Products Company Limited, Beijing 100176, China
| | - Rong Yang
- Beijing Institute of Biological Products Company Limited, Beijing 100176, China
| | - Yuxiu Zhao
- Beijing Institute of Biological Products Company Limited, Beijing 100176, China
| | - Yan Li
- Beijing Institute of Biological Products Company Limited, Beijing 100176, China
| | - Yingwei Liu
- Beijing Institute of Biological Products Company Limited, Beijing 100176, China
| | - Ling Ding
- Beijing Institute of Biological Products Company Limited, Beijing 100176, China
| | - Meng Ma
- Beijing Institute of Biological Products Company Limited, Beijing 100176, China
| | - Hui Wang
- Beijing Institute of Biological Products Company Limited, Beijing 100176, China
- Correspondence: (H.W.); (X.Y.)
| | - Xiaoming Yang
- China National Biotec Group Company Limited, Beijing 100024, China
- Correspondence: (H.W.); (X.Y.)
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A Metabolomics Approach to Sulforaphane Efficacy in Secondhand Smoking-Induced Pulmonary Damage in Mice. Metabolites 2022; 12:metabo12060518. [PMID: 35736451 PMCID: PMC9227370 DOI: 10.3390/metabo12060518] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/27/2022] [Accepted: 05/30/2022] [Indexed: 02/01/2023] Open
Abstract
Sulforaphane is an isocyanate abundantly present in cruciferous vegetables. In the present study, we aimed to investigate the effects of sulforaphane on secondhand smoking (SHS)-induced pulmonary damage in mice. Additionally, a metabolomic study was performed to identify biomarkers associated with pulmonary disease using proton nuclear magnetic resonance (1H-NMR) analysis. Male C57BL6J mice were divided into a control group, an SHS exposure group (positive control group, PC), and a sulforaphane treatment group exposed to secondhand smoke (SS) (n = 5 per group). The PC and SS groups were exposed to secondhand smoke in a chamber twice daily for four weeks. Mice in the SS group were orally administered sulforaphane (50 mg/kg) for four weeks during secondhand smoke exposure. Histopathological examination of the lungs revealed pulmonary damage in PC mice, including loss of bronchial epithelial cells, bronchial wall thickening, and infiltration of macrophages. In contrast, mice in the SS group showed little or no epithelial thickening, thereby exhibiting reduced lung damage. Mouse serum and lung tissues were collected and analyzed to determine changes in endogenous metabolites using 1H-NMR. After target profiling, we identified metabolites showing the same tendency in the serum and lung as biomarkers for SHS-induced pulmonary damage, including taurine, glycerol, creatine, arginine, and leucine. As a result of histopathological examination, sulforaphane might inhibit SHS-induced lung damage, and metabolite analysis results suggest potential biomarkers for SHS-induced pulmonary damage in mice.
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Kim HY, Lee YJ, Kim SJ, Lee JD, Kim S, Ko MJ, Kim JW, Shin CY, Kim KB. Metabolomics profiling of valproic acid-induced symptoms resembling autism spectrum disorders using 1H NMR spectral analysis in rat model. JOURNAL OF TOXICOLOGY AND ENVIRONMENTAL HEALTH. PART A 2022; 85:1-13. [PMID: 34445937 DOI: 10.1080/15287394.2021.1967821] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Prenatal exposure to valproic acid (VPA) has been implicated in the manifestation of autism spectrum disorder (ASD)-like behavioral and functional changes both in human and rodents including mice and rats. The objective of this study was to determine metabolomics profiling and biomarkers related to VPA-induced symptoms resembling ASD using proton nuclear magnetic resonance (1H-NMR) spectral data. VPA was administered to pregnant rats at gestation day 12.5 and effects measured subsequently in male 4-week-old offspring pups. The sociability of VPA-treated animals was significantly diminished and exhibited ASD-like behavior as evidenced by reduction of social adaptation disorder and lack of social interactions. To find biomarkers related to ASD, the following were collected prefrontal brain cortices, urine bladder and blood samples directly from heart puncture. In all samples, principal component analysis (PCA) and partial least-squares discriminant analysis (PLS-DA) displayed significant clustering pattern differences between control and treated groups. Valine, taurine, myo-inositol, 3-hydroxybutyrate and 1,3-dihydroxyacetone were significantly decreased in brain cortices in treated rats. Serum metabolites of glucose, creatine phosphate, lactate, glutamine and threonine were significantly increased in VPA-administered animals. Urinary metabolites of pimelate, 3-hydroxyisovalerate and valerate were significantly reduced in VPA-treated rat, whereas galactose and galactonate levels were elevated. Various metabolites were associated with mitochondrial dysfunction metabolism and central nervous system disorders. Data demonstrated that VPA-induced alterations in endogenous metabolites of serum, urine, and brain cortex which might prove useful as biomarkers for symptoms resembling ASD as a model of this disorder.
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Affiliation(s)
- Hyang Yeon Kim
- College of Pharmacy, Dankook University, Cheonan, Chungnam, Republic of Korea
- Center for Human Risk Assessment, Dankook University, Cheonan, Chungnam Republic of Korea
| | - Yong-Jae Lee
- College of Pharmacy, Dankook University, Cheonan, Chungnam, Republic of Korea
| | - Sun Jae Kim
- College of Pharmacy, Dankook University, Cheonan, Chungnam, Republic of Korea
| | - Jung Dae Lee
- College of Pharmacy, Dankook University, Cheonan, Chungnam, Republic of Korea
- Center for Human Risk Assessment, Dankook University, Cheonan, Chungnam Republic of Korea
| | - Suhkmann Kim
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan Republic of Korea
| | - Mee Jung Ko
- Department Of Neuroscience, School Of Medicine, Konkuk University, Seoul, Republic of Korea
| | - Ji-Woon Kim
- Department Of Neuroscience, School Of Medicine, Konkuk University, Seoul, Republic of Korea
| | - Chan Young Shin
- Department Of Neuroscience, School Of Medicine, Konkuk University, Seoul, Republic of Korea
| | - Kyu-Bong Kim
- College of Pharmacy, Dankook University, Cheonan, Chungnam, Republic of Korea
- Center for Human Risk Assessment, Dankook University, Cheonan, Chungnam Republic of Korea
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Unravelling the Anticancer Mechanisms of Traditional Herbal Medicines with Metabolomics. Molecules 2021; 26:molecules26216541. [PMID: 34770949 PMCID: PMC8587539 DOI: 10.3390/molecules26216541] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/13/2021] [Accepted: 10/18/2021] [Indexed: 12/26/2022] Open
Abstract
Metabolite profiling of cancer cells presents many opportunities for anticancer drug discovery. The Chinese, Indian, and African flora, in particular, offers a diverse source of anticancer therapeutics as documented in traditional folklores. In-depth scientific information relating to mechanisms of action, quality control, and safety profile will promote their extensive usage in cancer therapy. Metabolomics may be a more holistic strategy to gain valuable insights into the anticancer mechanisms of action of plants but this has remained largely unexplored. This review, therefore, presents the available metabolomics studies on the anticancer effects of herbal medicines commonly used in Africa and Asia. In addition, we present some scientifically understudied ‘candidate plants’ for cancer metabolomics studies and highlight the relevance of metabolomics in addressing other challenges facing the drug development of anticancer herbs. Finally, we discussed the challenges of using metabolomics to uncover the underlying mechanisms of potential anticancer herbs and the progress made in this regard.
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Lee JD, Kim HY, Park JJ, Oh SB, Goo H, Cho KJ, Kim S, Kim KB. Metabolomics approach to biomarkers of dry eye disease using 1H-NMR in rats. JOURNAL OF TOXICOLOGY AND ENVIRONMENTAL HEALTH. PART A 2021; 84:313-330. [PMID: 33393448 DOI: 10.1080/15287394.2020.1867274] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Dry eye disease (DED) is a chronic and progressive lesion on the ocular surface and induces symptoms, such as burning sensation, itchy eyes, heavy eyes, tired eyes, dry feeling, facial flushing, and blurred vision. The present study was performed to develop DED biomarkers using metabolomics in a rat model. DED was induced by injecting scopolamine and exposing rats to a dry condition. Scopolamine (12 mg/kg/day for 7 days) was subcutaneously injected to male Sprague-Dawley rats. The rats were placed in dry condition with air-flow and dehumidifier. Tear volume and tear breakup time (TBUT) were measured, and eyes were examined through fluorescein staining to assess DED. Mucosal damage and immune reactions were also determined. Plasma and urinary endogenous metabolites were determined using 1H-NMR analysis. Compared with control tear and TBUT levels were significantly decreased in the DED group whereas corneal damage was significantly increased. The levels of interleukins (IL-6) and IL-1β significantly elevated in the cornea and lacrimal glands in the DED group. TNF-α was numerically increased but not significantly different between groups. Pattern recognition using principal component analysis (PCA) and orthogonal projections to latent structure-discriminant analysis (OPLS-DA) of the NMR spectra in global profiling revealed different clusters between DED and control groups. Target profiling demonstrated that PCA and OPLS-DA score plots were separated between DED and controls in plasma and urine. Subsequently, 9 plasma metabolites were selected to examine different clustering between groups, and 26 urinary metabolites were also selected. Plasma metabolites showed a non-significant rising tendency in the DED group. Urinary phenylalanine, phenylacetate, pantothenate, glycine, succinate, methanol, valine, propylene glycol, histidine, threonine, lactate, and acetate were significantly different between control and DED rats. These results may contribute to understanding the metabolic regulation that is involved in DED and might be useful for potential biomarkers related to DED in rats.
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Affiliation(s)
- Jung Dae Lee
- College of Pharmacy, Dankook University, Cheonan, Republic of Korea
- Center for Human Risk Assessment, Dankook University, Chungnam, Republic of Korea
| | - Hyang Yeon Kim
- College of Pharmacy, Dankook University, Cheonan, Republic of Korea
- Center for Human Risk Assessment, Dankook University, Chungnam, Republic of Korea
| | - Jin Ju Park
- College of Pharmacy, Dankook University, Cheonan, Republic of Korea
- Center for Human Risk Assessment, Dankook University, Chungnam, Republic of Korea
| | - Soo Bean Oh
- Department of Ophthalmology, Dankook University, Cheonan, Republic of Korea
| | - Hyeyoon Goo
- Department of Ophthalmology, Dankook University, Cheonan, Republic of Korea
| | - Kyong Jin Cho
- Department of Ophthalmology, Dankook University, Cheonan, Republic of Korea
| | - Suhkmann Kim
- Department of Chemistry and Chemistry Institute of Functional Materials, Pusan National University, Busan, Republic of Korea
| | - Kyu-Bong Kim
- College of Pharmacy, Dankook University, Cheonan, Republic of Korea
- Center for Human Risk Assessment, Dankook University, Chungnam, Republic of Korea
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König S. Urine molecular profiling distinguishes health and disease: new methods in diagnostics? Focus on UPLC–MS. Expert Rev Mol Diagn 2014; 11:383-91. [DOI: 10.1586/erm.11.13] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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Kim KB, Yang JY, Kwack SJ, Kim HS, Ryu DH, Kim YJ, Bae JY, Lim DS, Choi SM, Kwon MJ, Bang DY, Lim SK, Kim YW, Hwang GS, Lee BM. Potential metabolomic biomarkers for evaluation of adriamycin efficacy using a urinary 1H-NMR spectroscopy. J Appl Toxicol 2012; 33:1251-9. [PMID: 22782856 DOI: 10.1002/jat.2778] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Revised: 04/19/2012] [Accepted: 04/19/2012] [Indexed: 12/16/2022]
Abstract
A metabolomics approach using proton nuclear magnetic resonance (NMR) was applied to investigate metabolic alterations following adriamycin (ADR) treatment for gastric adenocarcinoma. After BALB/c-nu/nu mice were implanted with human gastric adenocarcinoma, ADR (1 or 3 mg kg(-1) per day) was intraperitoneally administered for 5 days. Urine was collected on days 2 and 5 and analyzed by NMR. The levels of trimethylamine oxide (TMAO, ×0.3), hippurate (×0.3) and taurine (×0.6) decreased significantly (P < 0.05), whereas the levels of 3-indoxylsulfate (×12.6), trigonelline (×1.5), citrate (×2.5), trimethylamine (TMA, ×2.0) and 2-oxoglutarate (×2.3) increased significantly (P < 0.05) in the tumor model. After ADR treatment, TMAO, hippuarte and taurine were increased significantly on day 5 compared with those of the tumor model. The levels of 2-oxoglutarate, 3-indoxylsulfate, trigonelline, TMA and citrate, which increased in the tumor model, significantly decreased to those of normal control by ADR treatment. Furthermore, the ratio between TMA and TMAO was dramatically altered in both tumor and ADR-treated groups. Overall, metabolites such as TMAO, TMA, 3-indoxylsulfate, hippurate, trigonelline, citrate and 2-oxoglutarate related to the tricarboxylic acid (TCA) cycle might be considered as therapeutic targets to potentiate the efficacy of ADR. Thus, these results suggest that the metabolomics analysis of tumor response to ADR treatment may be applicable for demonstrating the efficacy of anticancer agent, ADR and treatment adaptation.
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Affiliation(s)
- Kyu-Bong Kim
- College of Pharmacy, Dankook University, Dandae-ro, Cheonan, Chungnam, 330-714, Korea
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Kim MJ, Kim BK, Kim SM, Park JS, Hong JK. Profiling analysis of catecholamines and polyamines in biological samples. ANALYTICAL SCIENCE AND TECHNOLOGY 2011. [DOI: 10.5806/ast.2011.24.5.319] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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