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Wang X, Ding Q, Groleau RR, Wu L, Mao Y, Che F, Kotova O, Scanlan EM, Lewis SE, Li P, Tang B, James TD, Gunnlaugsson T. Fluorescent Probes for Disease Diagnosis. Chem Rev 2024; 124:7106-7164. [PMID: 38760012 PMCID: PMC11177268 DOI: 10.1021/acs.chemrev.3c00776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 04/09/2024] [Accepted: 04/10/2024] [Indexed: 05/19/2024]
Abstract
The identification and detection of disease-related biomarkers is essential for early clinical diagnosis, evaluating disease progression, and for the development of therapeutics. Possessing the advantages of high sensitivity and selectivity, fluorescent probes have become effective tools for monitoring disease-related active molecules at the cellular level and in vivo. In this review, we describe current fluorescent probes designed for the detection and quantification of key bioactive molecules associated with common diseases, such as organ damage, inflammation, cancers, cardiovascular diseases, and brain disorders. We emphasize the strategies behind the design of fluorescent probes capable of disease biomarker detection and diagnosis and cover some aspects of combined diagnostic/therapeutic strategies based on regulating disease-related molecules. This review concludes with a discussion of the challenges and outlook for fluorescent probes, highlighting future avenues of research that should enable these probes to achieve accurate detection and identification of disease-related biomarkers for biomedical research and clinical applications.
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Affiliation(s)
- Xin Wang
- College
of Chemistry, Chemical Engineering and Materials Science, Key Laboratory
of Molecular and Nano Probes, Ministry of Education, Collaborative
Innovation Center of Functionalized Probes for Chemical Imaging in
Universities of Shandong, Institutes of Biomedical Sciences, Shandong Normal University, Jinan 250014, People’s Republic of China
| | - Qi Ding
- College
of Chemistry, Chemical Engineering and Materials Science, Key Laboratory
of Molecular and Nano Probes, Ministry of Education, Collaborative
Innovation Center of Functionalized Probes for Chemical Imaging in
Universities of Shandong, Institutes of Biomedical Sciences, Shandong Normal University, Jinan 250014, People’s Republic of China
| | | | - Luling Wu
- Department
of Chemistry, University of Bath, Bath BA2 7AY, U.K.
| | - Yuantao Mao
- College
of Chemistry, Chemical Engineering and Materials Science, Key Laboratory
of Molecular and Nano Probes, Ministry of Education, Collaborative
Innovation Center of Functionalized Probes for Chemical Imaging in
Universities of Shandong, Institutes of Biomedical Sciences, Shandong Normal University, Jinan 250014, People’s Republic of China
| | - Feida Che
- College
of Chemistry, Chemical Engineering and Materials Science, Key Laboratory
of Molecular and Nano Probes, Ministry of Education, Collaborative
Innovation Center of Functionalized Probes for Chemical Imaging in
Universities of Shandong, Institutes of Biomedical Sciences, Shandong Normal University, Jinan 250014, People’s Republic of China
| | - Oxana Kotova
- School
of Chemistry and Trinity Biomedical Sciences Institute (TBSI), Trinity College Dublin, The University of Dublin, Dublin 2 D02 R590, Ireland
- Advanced
Materials and BioEngineering Research (AMBER) Centre, Trinity College
Dublin, The University of Dublin, Dublin 2 D02 W9K7, Ireland
| | - Eoin M. Scanlan
- School
of Chemistry and Trinity Biomedical Sciences Institute (TBSI), Trinity College Dublin, The University of Dublin, Dublin 2 D02 R590, Ireland
- Synthesis
and Solid-State Pharmaceutical Centre (SSPC), School of Chemistry, Trinity College Dublin, The University of Dublin, Dublin 2 , Ireland
| | - Simon E. Lewis
- Department
of Chemistry, University of Bath, Bath BA2 7AY, U.K.
| | - Ping Li
- College
of Chemistry, Chemical Engineering and Materials Science, Key Laboratory
of Molecular and Nano Probes, Ministry of Education, Collaborative
Innovation Center of Functionalized Probes for Chemical Imaging in
Universities of Shandong, Institutes of Biomedical Sciences, Shandong Normal University, Jinan 250014, People’s Republic of China
| | - Bo Tang
- College
of Chemistry, Chemical Engineering and Materials Science, Key Laboratory
of Molecular and Nano Probes, Ministry of Education, Collaborative
Innovation Center of Functionalized Probes for Chemical Imaging in
Universities of Shandong, Institutes of Biomedical Sciences, Shandong Normal University, Jinan 250014, People’s Republic of China
- Laoshan
Laboratory, 168 Wenhai
Middle Road, Aoshanwei Jimo, Qingdao 266237, Shandong, People’s Republic of China
| | - Tony D. James
- Department
of Chemistry, University of Bath, Bath BA2 7AY, U.K.
- School
of Chemistry and Chemical Engineering, Henan
Normal University, Xinxiang 453007, People’s
Republic of China
| | - Thorfinnur Gunnlaugsson
- School
of Chemistry and Trinity Biomedical Sciences Institute (TBSI), Trinity College Dublin, The University of Dublin, Dublin 2 D02 R590, Ireland
- Advanced
Materials and BioEngineering Research (AMBER) Centre, Trinity College
Dublin, The University of Dublin, Dublin 2 D02 W9K7, Ireland
- Synthesis
and Solid-State Pharmaceutical Centre (SSPC), School of Chemistry, Trinity College Dublin, The University of Dublin, Dublin 2 , Ireland
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2
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Yu SM, Zheng HC, Wang SC, Rong WY, Li P, Jing J, He TT, Li JH, Ding X, Wang RL. Salivary metabolites are promising noninvasive biomarkers of drug-induced liver injury. World J Gastroenterol 2024; 30:2454-2466. [PMID: 38764769 PMCID: PMC11099387 DOI: 10.3748/wjg.v30.i18.2454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 04/05/2024] [Accepted: 04/18/2024] [Indexed: 05/11/2024] Open
Abstract
BACKGROUND Drug-induced liver injury (DILI) is one of the most common adverse events of medication use, and its incidence is increasing. However, early detection of DILI is a crucial challenge due to a lack of biomarkers and noninvasive tests. AIM To identify salivary metabolic biomarkers of DILI for the future development of noninvasive diagnostic tools. METHODS Saliva samples from 31 DILI patients and 35 healthy controls (HCs) were subjected to untargeted metabolomics using ultrahigh-pressure liquid chromatography coupled with tandem mass spectrometry. Subsequent analyses, including partial least squares-discriminant analysis modeling, t tests and weighted metabolite coexpression network analysis (WMCNA), were conducted to identify key differentially expressed metabolites (DEMs) and metabolite sets. Furthermore, we utilized least absolute shrinkage and selection operato and random fores analyses for biomarker prediction. The use of each metabolite and metabolite set to detect DILI was evaluated with area under the receiver operating characteristic curves. RESULTS We found 247 differentially expressed salivary metabolites between the DILI group and the HC group. Using WMCNA, we identified a set of 8 DEMs closely related to liver injury for further prediction testing. Interestingly, the distinct separation of DILI patients and HCs was achieved with five metabolites, namely, 12-hydroxydodecanoic acid, 3-hydroxydecanoic acid, tetradecanedioic acid, hypoxanthine, and inosine (area under the curve: 0.733-1). CONCLUSION Salivary metabolomics revealed previously unreported metabolic alterations and diagnostic biomarkers in the saliva of DILI patients. Our study may provide a potentially feasible and noninvasive diagnostic method for DILI, but further validation is needed.
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Affiliation(s)
- Si-Miao Yu
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Hao-Cheng Zheng
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Si-Ci Wang
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Wen-Ya Rong
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510515, Guangdong Province, China
| | - Ping Li
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Jing Jing
- Department of Hepatology of Traditional Chinese Medicine, The Fifth Medical Center of PLA General Hospital, Beijing 100039, China
| | - Ting-Ting He
- Department of Hepatology of Traditional Chinese Medicine, The Fifth Medical Center of PLA General Hospital, Beijing 100039, China
| | - Jia-Hui Li
- The First Clinical Medical College, Henan University of Traditional Chinese Medicine, Zhengzhou 450000, Henan Province, China
| | - Xia Ding
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Rui-Lin Wang
- Department of Hepatology of Traditional Chinese Medicine, The Fifth Medical Center of PLA General Hospital, Beijing 100039, China
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3
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Dong X, Qu Y, Sheng T, Fan Y, Chen S, Yuan Q, Ma G, Ge Y. HCMMD: systematic evaluation of metabolites in body fluids as liquid biopsy biomarker for human cancers. Aging (Albany NY) 2024; 16:7487-7504. [PMID: 38683118 PMCID: PMC11087094 DOI: 10.18632/aging.205779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 01/03/2024] [Indexed: 05/01/2024]
Abstract
Metabolomics is a rapidly expanding field in systems biology used to measure alterations of metabolites and identify metabolic biomarkers in response to disease processes. The discovery of metabolic biomarkers can improve early diagnosis, prognostic prediction, and therapeutic intervention for cancers. However, there are currently no databases that provide a comprehensive evaluation of the relationship between metabolites and cancer processes. In this review, we summarize reported metabolites in body fluids across pan-cancers and characterize their clinical applications in liquid biopsy. We conducted a search for metabolic biomarkers using the keywords ("metabolomics" OR "metabolite") AND "cancer" in PubMed. Of the 22,254 articles retrieved, 792 were deemed potentially relevant for further review. Ultimately, we included data from 573,300 samples and 17,083 metabolic biomarkers. We collected information on cancer types, sample size, the human metabolome database (HMDB) ID, metabolic pathway, area under the curve (AUC), sensitivity and specificity of metabolites, sample source, detection method, and clinical features were collected. Finally, we developed a user-friendly online database, the Human Cancer Metabolic Markers Database (HCMMD), which allows users to query, browse, and download metabolite information. In conclusion, HCMMD provides an important resource to assist researchers in reviewing metabolic biomarkers for diagnosis and progression of cancers.
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Affiliation(s)
- Xun Dong
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Yaoyao Qu
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Tongtong Sheng
- School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yuanming Fan
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Silu Chen
- School of Public Health, Nanjing Medical University, Nanjing, China
| | - Qinbo Yuan
- Department of Urology, Wuxi Fifth People’s Hospital, Wuxi, China
| | - Gaoxiang Ma
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
- The Clinical Metabolomics Center, China Pharmaceutical University, Nanjing, China
- Deparment of Oncology, Pukou Hospital of Chinese Medicine affiliated to China Pharmaceutical University, Nanjing, China
| | - Yuqiu Ge
- Department of Public Health and Preventive Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, China
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4
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Ikeda Y, Fujii J. The Emerging Roles of γ-Glutamyl Peptides Produced by γ-Glutamyltransferase and the Glutathione Synthesis System. Cells 2023; 12:2831. [PMID: 38132151 PMCID: PMC10741565 DOI: 10.3390/cells12242831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 12/03/2023] [Accepted: 12/06/2023] [Indexed: 12/23/2023] Open
Abstract
L-γ-Glutamyl-L-cysteinyl-glycine is commonly referred to as glutathione (GSH); this ubiquitous thiol plays essential roles in animal life. Conjugation and electron donation to enzymes such as glutathione peroxidase (GPX) are prominent functions of GSH. Cellular glutathione balance is robustly maintained via regulated synthesis, which is catalyzed via the coordination of γ-glutamyl-cysteine synthetase (γ-GCS) and glutathione synthetase, as well as by reductive recycling by glutathione reductase. A prevailing short supply of L-cysteine (Cys) tends to limit glutathione synthesis, which leads to the production of various other γ-glutamyl peptides due to the unique enzymatic properties of γ-GCS. Extracellular degradation of glutathione by γ-glutamyltransferase (GGT) is a dominant source of Cys for some cells. GGT catalyzes the hydrolytic removal of the γ-glutamyl group of glutathione or transfers it to amino acids or to dipeptides outside cells. Such processes depend on an abundance of acceptor substrates. However, the physiological roles of extracellularly preserved γ-glutamyl peptides have long been unclear. The identification of γ-glutamyl peptides, such as glutathione, as allosteric modulators of calcium-sensing receptors (CaSRs) could provide insights into the significance of the preservation of γ-glutamyl peptides. It is conceivable that GGT could generate a new class of intercellular messaging molecules in response to extracellular microenvironments.
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Affiliation(s)
- Yoshitaka Ikeda
- Division of Molecular Cell Biology, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, 5-1-1 Nabeshima, Saga 849-8501, Japan
| | - Junichi Fujii
- Department of Biochemistry and Molecular Biology, Graduate School of Medical Science, Yamagata University, 2-2-2 Iidanishi, Yamagata City 990-9585, Japan
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5
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Liu X, Wu Y, Guo L, Wang X, Shan C, Liu Y, An H, Kang X, Ding R, Cai Z, Dong J, Zhao Y, Gao X. Comprehensive Profiling of Amine-Containing Metabolite Isomers with Chiral Phosphorus Reagents. Anal Chem 2023; 95:16830-16839. [PMID: 37943818 DOI: 10.1021/acs.analchem.3c02325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
Metabolite isomers play diverse and crucial roles in various metabolic processes. However, in untargeted metabolomics analysis, it remains a great challenge to distinguish between the constitutional isomers and enantiomers of amine-containing metabolites due to their similar chemical structures and physicochemical properties. In this work, the triplex stable isotope N-phosphoryl amino acids labeling (SIPAL) is developed to identify and relatively quantify the amine-containing metabolites and their isomers by using chiral phosphorus reagents coupled with high-resolution tandem mass spectroscopy. The constitutional isomers could be effectively distinguished with stereo isomers by using the diagnosis ions in MS/MS spectra. The in-house software MS-Isomerism has been parallelly developed for high-throughput screening and quantification. The proposed strategy enables the unbiased detection and relative quantification of isomers of amine-containing metabolites. Based on the characteristic triplet peaks with SIPAL tags, a total of 854 feature peaks with 154 isomer groups are successfully recognized as amine-containing metabolites in liver cells, in which 37 amine-containing metabolites, including amino acids, polyamines, and small peptides, are found to be significantly different between liver cancer cells and normal cells. Notably, it is the first time to identify S-acetyl-glutathione as an endogenous metabolite in liver cells. The SIPAL strategy could provide spectacular insight into the chemical structures and biological functions of the fascinating amine-containing metabolite isomers. The feasibility of SIPAL in isomeric metabolomics analysis may reach a deeper understanding of the mirror-chemistry in life and further advance the discovery of novel biomarkers for disease diagnosis.
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Affiliation(s)
- Xingxing Liu
- Department of Electronic Science, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen 361005, China
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China
| | - Yifan Wu
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China
| | - Lei Guo
- Department of Electronic Science, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen 361005, China
| | - Xiaoyu Wang
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China
- Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Changkai Shan
- Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Yaru Liu
- Department of Electronic Science, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen 361005, China
| | - Hanxiang An
- Xiang'an Hospital of Xiamen University, Xiamen University, Xiamen 361102, China
| | - Xinmei Kang
- Xiang'an Hospital of Xiamen University, Xiamen University, Xiamen 361102, China
| | - Rong Ding
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China
| | - Zongwei Cai
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong, SAR 999077, China
| | - Jiyang Dong
- Department of Electronic Science, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen 361005, China
| | - Yufen Zhao
- Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315221, China
| | - Xiang Gao
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China
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6
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Anh NH, Long NP, Min YJ, Ki Y, Kim SJ, Jung CW, Park S, Kwon SW, Lee SJ. Molecular and Metabolic Phenotyping of Hepatocellular Carcinoma for Biomarker Discovery: A Meta-Analysis. Metabolites 2023; 13:1112. [PMID: 37999208 PMCID: PMC10672761 DOI: 10.3390/metabo13111112] [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: 09/25/2023] [Revised: 10/20/2023] [Accepted: 10/24/2023] [Indexed: 11/25/2023] Open
Abstract
Identifying and translating hepatocellular carcinoma (HCC) biomarkers from bench to bedside using mass spectrometry-based metabolomics and lipidomics is hampered by inconsistent findings. Here, we investigated HCC at systemic and metabolism-centric multiomics levels by conducting a meta-analysis of quantitative evidence from 68 cohorts. Blood transcript biomarkers linked to the HCC metabolic phenotype were externally validated and prioritized. In the studies under investigation, about 600 metabolites were reported as putative HCC-associated biomarkers; 39, 20, and 10 metabolites and 52, 12, and 12 lipids were reported in three or more studies in HCC vs. Control, HCC vs. liver cirrhosis (LC), and LC vs. Control groups, respectively. Amino acids, fatty acids (increased 18:1), bile acids, and lysophosphatidylcholine were the most frequently reported biomarkers in HCC. BAX and RAC1 showed a good correlation and were associated with poor prognosis. Our study proposes robust HCC biomarkers across diverse cohorts using a data-driven knowledge-based approach that is versatile and affordable for studying other diseases.
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Affiliation(s)
- Nguyen Hoang Anh
- College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea; (N.H.A.); (Y.J.M.); (S.J.K.); (C.W.J.); (S.W.K.)
| | - Nguyen Phuoc Long
- Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan 47392, Republic of Korea
| | - Young Jin Min
- College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea; (N.H.A.); (Y.J.M.); (S.J.K.); (C.W.J.); (S.W.K.)
| | - Yujin Ki
- School of Mathematics, Statistics and Data Science, Sungshin Women’s University, Seoul 08826, Republic of Korea; (Y.K.); (S.P.)
| | - Sun Jo Kim
- College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea; (N.H.A.); (Y.J.M.); (S.J.K.); (C.W.J.); (S.W.K.)
| | - Cheol Woon Jung
- College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea; (N.H.A.); (Y.J.M.); (S.J.K.); (C.W.J.); (S.W.K.)
| | - Seongoh Park
- School of Mathematics, Statistics and Data Science, Sungshin Women’s University, Seoul 08826, Republic of Korea; (Y.K.); (S.P.)
| | - Sung Won Kwon
- College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea; (N.H.A.); (Y.J.M.); (S.J.K.); (C.W.J.); (S.W.K.)
| | - Seul Ji Lee
- College of Pharmacy, Kangwon National University, Chuncheon 24341, Republic of Korea
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7
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Lu X, Dou P, Li C, Zheng F, Zhou L, Xie X, Wang Z, Xu G. Annotation of Dipeptides and Tripeptides Derivatized via Dansylation Based on Liquid Chromatography-Mass Spectrometry and Iterative Quantitative Structure Retention Relationship. J Proteome Res 2023. [PMID: 37163573 DOI: 10.1021/acs.jproteome.3c00002] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Small peptides such as dipeptides and tripeptides show various biological activities in organisms. However, methods for identifying dipeptides/tripeptides from complex biological samples are lacking. Here, an annotation strategy involving the derivatization of dipeptides and tripeptides via dansylation was suggested based on liquid chromatography-mass spectrometry (LC-MS) and iterative quantitative structure retention relationship (QSRR) to choose dipeptides/tripeptides by using a small number of standards. First, the LC-autoMS/MS method and initial QSRR model were built based on 25 selected grid-dipeptides and 18 test-dipeptides. To achieve high-coverage detection, dipeptide/tripeptide pools containing abundant dipeptides/tripeptides were then obtained from four dansylated biological samples including serum, tissue, feces, and soybean paste by using the parameter-optimized LC-autoMS/MS method. The QSRR model was further optimized through an iterative train-by-pick strategy. Based on the specific fragments and tR tolerances, 198 dipeptides and 149 tripeptides were annotated. The dipeptides at lower annotation levels were verified by using authentic standards and grid-correlation analysis. Finally, variation in serum dipeptides/tripeptides of three different liver diseases including hepatitis B infection, liver cirrhosis, and hepatocellular carcinoma was characterized. Dipeptides with N-prolinyl, C-proline, N-glutamyl, and N-valinyl generally increased with disease severity. In conclusion, this study provides an efficient strategy for annotating dipeptides/tripeptides from complex samples.
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Affiliation(s)
- Xin Lu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- Liaoning Province Key Laboratory of Metabolomics, Dalian 116031, China
| | - Peng Dou
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- Liaoning Province Key Laboratory of Metabolomics, Dalian 116031, China
| | - Chao Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Fujian Zheng
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lina Zhou
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- Liaoning Province Key Laboratory of Metabolomics, Dalian 116031, China
| | - Xiaoyu Xie
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), Key Laboratory of Phytochemical R&D of Hunan Province, Hunan Normal University, Changsha 410081, China
| | - Zixuan Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guowang Xu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- Liaoning Province Key Laboratory of Metabolomics, Dalian 116031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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8
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Fujii J, Osaki T, Soma Y, Matsuda Y. Critical Roles of the Cysteine-Glutathione Axis in the Production of γ-Glutamyl Peptides in the Nervous System. Int J Mol Sci 2023; 24:ijms24098044. [PMID: 37175751 PMCID: PMC10179188 DOI: 10.3390/ijms24098044] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 04/24/2023] [Accepted: 04/26/2023] [Indexed: 05/15/2023] Open
Abstract
γ-Glutamyl moiety that is attached to the cysteine (Cys) residue in glutathione (GSH) protects it from peptidase-mediated degradation. The sulfhydryl group of the Cys residue represents most of the functions of GSH, which include electron donation to peroxidases, protection of reactive sulfhydryl in proteins via glutaredoxin, and glutathione conjugation of xenobiotics, whereas Cys-derived sulfur is also a pivotal component of some redox-responsive molecules. The amount of Cys that is available tends to restrict the capacity of GSH synthesis. In in vitro systems, cystine is the major form in the extracellular milieu, and a specific cystine transporter, xCT, is essential for survival in most lines of cells and in many primary cultivated cells as well. A reduction in the supply of Cys causes GPX4 to be inhibited due to insufficient GSH synthesis, which leads to iron-dependent necrotic cell death, ferroptosis. Cells generally cannot take up GSH without the removal of γ-glutamyl moiety by γ-glutamyl transferase (GGT) on the cell surface. Meanwhile, the Cys-GSH axis is essentially common to certain types of cells; primarily, neuronal cells that contain a unique metabolic system for intercellular communication concerning γ-glutamyl peptides. After a general description of metabolic processes concerning the Cys-GSH axis, we provide an overview and discuss the significance of GSH-related compounds in the nervous system.
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Affiliation(s)
- Junichi Fujii
- Department of Biochemistry and Molecular Biology, Graduate School of Medical Science, Yamagata University, Yamagata 990-9585, Japan
| | - Tsukasa Osaki
- Department of Biochemistry and Molecular Biology, Graduate School of Medical Science, Yamagata University, Yamagata 990-9585, Japan
| | - Yuya Soma
- Graduate School of Nursing, Yamagata University Faculty of Medicine, Yamagata 990-9585, Japan
| | - Yumi Matsuda
- Graduate School of Nursing, Yamagata University Faculty of Medicine, Yamagata 990-9585, Japan
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9
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Tandem mass tag-based quantitative proteomic profiling identifies candidate serum biomarkers of drug-induced liver injury in humans. Nat Commun 2023; 14:1215. [PMID: 36869085 PMCID: PMC9984368 DOI: 10.1038/s41467-023-36858-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 02/16/2023] [Indexed: 03/05/2023] Open
Abstract
Diagnosis of drug-induced liver injury (DILI) and its distinction from other liver diseases are significant challenges in drug development and clinical practice. Here, we identify, confirm, and replicate the biomarker performance characteristics of candidate proteins in patients with DILI at onset (DO; n = 133) and follow-up (n = 120), acute non-DILI at onset (NDO; n = 63) and follow-up (n = 42), and healthy volunteers (HV; n = 104). Area under the receiver operating characteristic curve (AUC) for cytoplasmic aconitate hydratase, argininosuccinate synthase, carbamoylphosphate synthase, fumarylacetoacetase, fructose-1,6-bisphosphatase 1 (FBP1) across cohorts achieved near complete separation (range: 0.94-0.99) of DO and HV. In addition, we show that FBP1, alone or in combination with glutathione S-transferase A1 and leukocyte cell-derived chemotaxin 2, could potentially assist in clinical diagnosis by distinguishing NDO from DO (AUC range: 0.65-0.78), but further technical and clinical validation of these candidate biomarkers is needed.
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10
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Iannone V, Lok J, Babu AF, Gómez-Gallego C, Willman RM, Koistinen VM, Klåvus A, Kettunen MI, Kårlund A, Schwab U, Hanhineva K, Kolehmainen M, El-Nezami H. Associations of altered hepatic gene expression in American lifestyle-induced obesity syndrome diet-fed mice with metabolic changes during NAFLD development and progression. J Nutr Biochem 2023; 115:109307. [PMID: 36868506 DOI: 10.1016/j.jnutbio.2023.109307] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 01/20/2023] [Accepted: 02/24/2023] [Indexed: 03/05/2023]
Abstract
Non-alcoholic fatty liver disease (NAFLD) pathogenesis remains poorly understood due to the complex metabolic and inflammatory changes in the liver. This study aimed to elucidate hepatic events related to inflammation and lipid metabolism and their linkage with metabolic alterations during NAFLD in American lifestyle-induced obesity syndrome (ALIOS) diet-fed mice. Forty-eight C57BL/6J male mice were fed with ALIOS diet (n=24) or control chow diet (n=24) for 8, 12, and 16 weeks. At the end of each timepoint, eight mice were sacrificed where plasma and liver were collected. Hepatic fat accumulation was followed using magnetic resonance imaging and confirmed with histology. Further, targeted gene expression and non-targeted metabolomics analysis were conducted. Our results showed higher hepatic steatosis, body weight, energy consumption, and liver mass in ALIOS diet-fed mice compared to control mice. ALIOS diet altered expression of genes related to inflammation (Tnfa and IL-6) and lipid metabolism (Cd36, Fasn, Scd1, Cpt1a, and Ppara). Metabolomics analysis indicated decrease of lipids containing polyunsaturated fatty acids such as LPE(20:5) and LPC(20:5) with increase of other lipid species such as LPI(16:0) and LPC(16:2) and peptides such as alanyl-phenylalanine and glutamyl-arginine. We further observed novel correlations between different metabolites including sphingolipid, lysophospholipids, peptides, and bile acid with inflammation, lipid uptake and synthesis. Together with the reduction of antioxidant metabolites and gut microbiota-derived metabolites contribute to NAFLD development and progression. The combination of non-targeted metabolomics with gene expression in future studies can further identify key metabolic routes during NAFLD which could be the targets of potential novel therapeutics.
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Affiliation(s)
- Valeria Iannone
- School of Medicine, Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
| | - Johnson Lok
- School of Medicine, Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
| | - Ambrin Farizah Babu
- School of Medicine, Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland; Afekta Technologies Ltd., Kuopio, Finland
| | - Carlos Gómez-Gallego
- School of Medicine, Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
| | - Roosa Maria Willman
- School of Medicine, Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland; Department of Medicine, Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Ville Mikael Koistinen
- School of Medicine, Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland; Afekta Technologies Ltd., Kuopio, Finland; Department of Life technologies, Food Sciences Unit, University of Turku, Turku, Finland
| | | | - Mikko I Kettunen
- Kuopio Biomedical Imaging Unit, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Anna Kårlund
- School of Medicine, Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
| | - Ursula Schwab
- School of Medicine, Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland; Department of Medicine, Endocrinology and Clinical Nutrition, Kuopio University Hospital, Kuopio, Finland
| | - Kati Hanhineva
- School of Medicine, Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland; Afekta Technologies Ltd., Kuopio, Finland; Department of Life technologies, Food Sciences Unit, University of Turku, Turku, Finland.
| | - Marjukka Kolehmainen
- School of Medicine, Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland.
| | - Hani El-Nezami
- School of Medicine, Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland; Molecular and Cell Biology Division, School of Biological Sciences, University of Hong Kong, Hong Kong China
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11
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Lagies S, Pan D, Mohl DA, Plattner DA, Gentle IE, Kammerer B. Mitochondrial Metabolomics of Sym1-Depleted Yeast Cells Revealed Them to Be Lysine Auxotroph. Cells 2023; 12:692. [PMID: 36899826 PMCID: PMC10000845 DOI: 10.3390/cells12050692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/10/2023] [Accepted: 02/17/2023] [Indexed: 02/24/2023] Open
Abstract
Metabolomics has expanded from cellular to subcellular level to elucidate subcellular compartmentalization. By applying isolated mitochondria to metabolome analysis, the hallmark of mitochondrial metabolites has been unraveled, showing compartment-specific distribution and regulation of metabolites. This method was employed in this work to study a mitochondrial inner membrane protein Sym1, whose human ortholog MPV17 is related to mitochondria DNA depletion syndrome. Gas chromatography-mass spectrometry-based metabolic profiling was combined with targeted liquid chromatography-mass spectrometry analysis to cover more metabolites. Furthermore, we applied a workflow employing ultra-high performance liquid chromatography-quadrupole time of flight mass spectrometry with a powerful chemometrics platform, focusing on only significantly changed metabolites. This workflow highly reduced the complexity of acquired data without losing metabolites of interest. Consequently, forty-one novel metabolites were identified in addition to the combined method, of which two metabolites, 4-guanidinobutanal and 4-guanidinobutanoate, were identified for the first time in Saccharomyces cerevisiae. With compartment-specific metabolomics, we identified sym1Δ cells as lysine auxotroph. The highly reduced carbamoyl-aspartate and orotic acid indicate a potential role of the mitochondrial inner membrane protein Sym1 in pyrimidine metabolism.
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Affiliation(s)
- Simon Lagies
- Core Competence Metabolomics, Hilde-Mangold-Haus, University of Freiburg, 79104 Freiburg, Germany
- Institute of Organic Chemistry, University of Freiburg, 79104 Freiburg, Germany
| | - Daqiang Pan
- Core Competence Metabolomics, Hilde-Mangold-Haus, University of Freiburg, 79104 Freiburg, Germany
- Institute of Pharmaceutical Science, University of Freiburg, 79104 Freiburg, Germany
| | - Daniel A. Mohl
- Core Competence Metabolomics, Hilde-Mangold-Haus, University of Freiburg, 79104 Freiburg, Germany
- Institute of Organic Chemistry, University of Freiburg, 79104 Freiburg, Germany
| | - Dietmar A. Plattner
- Institute of Organic Chemistry, University of Freiburg, 79104 Freiburg, Germany
| | - Ian E. Gentle
- Institute of Medical Microbiology and Hygiene, Medical Center–University of Freiburg, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Bernd Kammerer
- Core Competence Metabolomics, Hilde-Mangold-Haus, University of Freiburg, 79104 Freiburg, Germany
- Institute of Organic Chemistry, University of Freiburg, 79104 Freiburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, 79104 Freiburg, Germany
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12
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Qiu Y, Zhang M, Lai Z, Zhang R, Tian H, Liu S, Li D, Zhou J, Li Z. Profiling of amines in biological samples using polythioester-functionalized magnetic nanoprobe. Front Bioeng Biotechnol 2023; 10:1103995. [PMID: 36686230 PMCID: PMC9846243 DOI: 10.3389/fbioe.2022.1103995] [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: 11/21/2022] [Accepted: 12/19/2022] [Indexed: 01/05/2023] Open
Abstract
Introduction: The metabolic balance of amines is closely related to human health. It remains a great challenge to analyze amines with high-throughput and high-coverage. Methods: Polythioester-functionalized magnetic nanoprobes (PMPs) have been prepared under mild conditions and applied in chemoselective capture of amides. With the introduction of polythioester, PMPs demonstrate remarkably increased capture efficiency, leading to the dramatically improved sensitivity of mass spectrometry detection. Results: The analysis method with PMPs treatment has been applied in rapid detection of more than 100 amines in lung adenocarcinoma cell lines, mouse organ tissues, and 103 human serum samples with high-throughput and high-coverage. Statistical analysis shows that arginine biosynthesis differed between lung adenocarcinoma cell lines. Discussion: Phenylalanine, tyrosine and tryptophan biosynthesis differed between tissues. The combination indicators demonstrate a great diagnostic accuracy for distinguishing between health and lung disease subjects as well as differentiating the patients with benign lung disease and lung cancer. With powerful capture ability, low-cost preparation, and convenient separation, the PMPs demonstrate promising application in the intensive study of metabolic pathways and early diagnosis of disease.high-throughput and high-coverage. Here, polythioester-functionalized magnetic nanoprobes (PMPs) have been prepared under mild conditions and applied in chemoselective capture of amides. With the introduction of polythioester, PMPs demonstrate remarkably increased capture efficiency, leading to the dramatically improved sensitivity of mass spectrometry detection. The analysis method with PMPs treatment has been applied in rapid detection of more than 100 amines in lung adenocarcinoma cell lines, mouse organ tissues, and 103 human serum samples with high-throughput and high-coverage. Statistical analysis shows that arginine biosynthesis differed between lung adenocarcinoma cell lines. Phenylalanine, tyrosine and tryptophan biosynthesis differed between tissues. The combination indicators demonstrate a great diagnostic accuracy for distinguishing between health and lung disease subjects as well as differentiating the patients with benign lung disease and lung cancer. With powerful capture ability, low-cost preparation, and convenient separation, the PMPs demonstrate promising application in the intensive study of metabolic pathways and early diagnosis of disease.
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Affiliation(s)
- Yuming Qiu
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Mo Zhang
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhizhen Lai
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Renjun Zhang
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hongtao Tian
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shuai Liu
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Dan Li
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jiang Zhou
- Analytical Instrumentation Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, China,*Correspondence: Zhili Li, ; Jiang Zhou,
| | - Zhili Li
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China,*Correspondence: Zhili Li, ; Jiang Zhou,
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13
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Morine Y, Utsunomiya T, Yamanaka-Okumura H, Saito Y, Yamada S, Ikemoto T, Imura S, Kinoshita S, Hirayama A, Tanaka Y, Shimada M. Essential amino acids as diagnostic biomarkers of hepatocellular carcinoma based on metabolic analysis. Oncotarget 2022; 13:1286-1298. [PMID: 36441784 DOI: 10.18632/oncotarget.28306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Metabolomics, defined as the comprehensive identification of all small metabolites in a biological sample, has the power to shed light on phenotypic changes associated with various diseases, including cancer. To discover potential metabolomic biomarkers of hepatocellular carcinoma (HCC), we investigated the metabolomes of tumor and non-tumor tissue in 20 patients with primary HCC using capillary electrophoresis-time-of-flight mass spectrometry. We also analyzed blood samples taken immediately before and 14 days after hepatectomy to identify associated changes in the serum metabolome. Marked changes were detected in the different quantity of 61 metabolites that could discriminate between HCC tumor and paired non-tumor tissue and additionally between HCC primary tumors and colorectal liver metastases. Among the 30 metabolites significantly upregulated in HCC tumors compared with non-tumor tissues, 10 were amino acids, and 7 were essential amino acids (leucine, valine, tryptophan, isoleucine, methionine, lysine, and phenylalanine). Similarly, the serum metabolomes of HCC patients before hepatectomy revealed a significant increase in 16 metabolites, including leucine, valine, and tryptophan. Our results reveal striking differences in the metabolomes of HCC tumor tissue compared with non-tumor tissue, and identify the essential amino acids leucine, valine, and tryptophan as potential metabolic biomarkers for HCC.
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Affiliation(s)
- Yuji Morine
- Department of Surgery, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima 770-8503, Japan
| | - Tohru Utsunomiya
- Department of Surgery, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima 770-8503, Japan
| | - Hisami Yamanaka-Okumura
- Department of Clinical Nutrition and Food Management, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima 770-8503, Japan
| | - Yu Saito
- Department of Surgery, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima 770-8503, Japan
| | - Shinichiro Yamada
- Department of Surgery, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima 770-8503, Japan
| | - Tetsuya Ikemoto
- Department of Surgery, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima 770-8503, Japan
| | - Satoru Imura
- Department of Surgery, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima 770-8503, Japan
| | - Shohei Kinoshita
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0052, Japan.,Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Kanagawa 252-0882, Japan
| | - Akiyoshi Hirayama
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0052, Japan.,Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Kanagawa 252-0882, Japan
| | - Yasuhito Tanaka
- Department of Gastroenterology and Hepatology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Mitsuo Shimada
- Department of Surgery, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima 770-8503, Japan
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14
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Jiang HY, Gao HY, Li J, Zhou TY, Wang ST, Yang JB, Hao RR, Pang F, Wei F, Liu ZG, Kuang L, Ma SC, He JM, Jin HT. Integrated spatially resolved metabolomics and network toxicology to investigate the hepatotoxicity mechanisms of component D of Polygonum multiflorum Thunb. JOURNAL OF ETHNOPHARMACOLOGY 2022; 298:115630. [PMID: 35987407 DOI: 10.1016/j.jep.2022.115630] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 07/25/2022] [Accepted: 08/06/2022] [Indexed: 06/15/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE The liver toxicity of Reynoutria multiflora (Thunb.) Moldenke. (Polygonaceae) (Polygonum multiflorum Thunb, PM) has always attracted much attention, but the related toxicity materials and mechanisms have not been elucidated due to multi-component and multi-target characteristics. In previous hepatotoxicity screening, different components of PM were first evaluated and the hepatotoxicity of component D [95% ethanol (EtOH) elution] in a 70% EtOH extract of PM (PM-D) showed the highest hepatotoxicity. Furthermore, the main components of PM-D were identified and their hepatotoxicity was evaluated based on a zebrafish embryo model. However, the hepatotoxicity mechanism of PM-D is unknown. AIM OF THE STUDY This work is to explore the hepatotoxicity mechanisms of PM-D by integrating network toxicology and spatially resolved metabolomics strategy. MATERIALS AND METHODS A hepatotoxicity interaction network of PM-D was constructed based on toxicity target prediction for eight key toxic ingredients and a hepatotoxicity target collection. Then the key signaling pathways were enriched, and molecular docking verification was implemented to evaluate the ability of toxic ingredients to bind to the core targets. The pathological changes of liver tissues and serum biochemical assays of mice were used to evaluate the liver injury effect of mice with oral administration of PM-D. Furthermore, spatially resolved metabolomics was used to visualize significant differences in metabolic profiles in mice after drug administration, to screen hepatotoxicity-related biomarkers and analyze metabolic pathways. RESULTS The contents of four key toxic compounds in PM-D were detected. Network toxicology identified 30 potential targets of liver toxicity of PM-D. GO and KEGG enrichment analyses indicated that the hepatotoxicity of PM-D involved multiple biological activities, including cellular response to endogenous stimulus, organonitrogen compound metabolic process, regulation of the apoptotic process, regulation of kinase, regulation of reactive oxygen species metabolic process and signaling pathways including PI3K-Akt, AMPK, MAPK, mTOR, Ras and HIF-1. The molecular docking confirmed the high binding activity of 8 key toxic ingredients with 10 core targets, including mTOR, PIK3CA, AKT1, and EGFR. The high distribution of metabolites of PM-D in the liver of administrated mice was recognized by mass spectrometry imaging. Spatially resolved metabolomics results revealed significant changes in metabolic profiles after PM-D administration, and metabolites such as taurine, taurocholic acid, adenosine, and acyl-carnitines were associated with PM-D-induced liver injury. Enrichment analyses of metabolic pathways revealed tht linolenic acid and linoleic acid metabolism, carnitine synthesis, oxidation of branched-chain fatty acids, and six other metabolic pathways were significantly changed. Comprehensive analysis revealed that the hepatotoxicity caused by PM-D was closely related to cholestasis, mitochondrial damage, oxidative stress and energy metabolism, and lipid metabolism disorders. CONCLUSIONS In this study, the hepatotoxicity mechanisms of PM-D were comprehensively identified through an integrated spatially resolved metabolomics and network toxicology strategy, providing a theoretical foundation for the toxicity mechanisms of PM and its safe clinical application.
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Affiliation(s)
- Hai-Yan Jiang
- New Drug Safety Evaluation Center, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Hui-Yu Gao
- Institute for Control of Chinese Traditional Medicine and Ethnic Medicine, National Institutes for Food and Drug Control, Beijing, China
| | - Jie Li
- New Drug Safety Evaluation Center, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Tian-Yu Zhou
- College of Pharmacy, Shaanxi University of Traditional Chinese Medicine, Xianyang, China
| | - Shu-Ting Wang
- New Drug Safety Evaluation Center, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Jian-Bo Yang
- Institute for Control of Chinese Traditional Medicine and Ethnic Medicine, National Institutes for Food and Drug Control, Beijing, China
| | - Rui-Rui Hao
- New Drug Safety Evaluation Center, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Fei Pang
- New Drug Safety Evaluation Center, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Feng Wei
- Institute for Control of Chinese Traditional Medicine and Ethnic Medicine, National Institutes for Food and Drug Control, Beijing, China
| | - Zhi-Gang Liu
- School of Biological Science and Engineering, South China University of Technology, Guangzhou, China
| | - Lian Kuang
- New Drug Safety Evaluation Center, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Shuang-Cheng Ma
- Institute for Control of Chinese Traditional Medicine and Ethnic Medicine, National Institutes for Food and Drug Control, Beijing, China.
| | - Jiu-Ming He
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China; NMPA Key Laboratory for Safety Research and Evaluation of Innovative Drug, Beijing, China.
| | - Hong-Tao Jin
- New Drug Safety Evaluation Center, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China; Beijing Union-Genius Pharmaceutical Technology Development Co., Ltd., Beijing, China; NMPA Key Laboratory for Safety Research and Evaluation of Innovative Drug, Beijing, China.
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15
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Guha S, Majumder K. Comprehensive Review of γ-Glutamyl Peptides (γ-GPs) and Their Effect on Inflammation Concerning Cardiovascular Health. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:7851-7870. [PMID: 35727887 DOI: 10.1021/acs.jafc.2c01712] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
γ-Glutamyl peptides (γ-GPs) are a group of peptides naturally found in various food sources. The unique γ-bond potentially enables them to resist gastrointestinal digestion and offers high stability in vivo with a longer half-life. In recent years, these peptides have caught researchers' attention due to their ability to impart kokumi taste and elicit various physiological functions via the allosteric activation of the calcium-sensing receptor (CaSR). This review discusses the various food sources of γ-glutamyl peptides, different synthesis modes, allosteric activation of CaSR for taste perception, and associated multiple biological functions they can exhibit, with a special emphasis on their role in modulating chronic inflammation concerning cardiovascular health.
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Affiliation(s)
- Snigdha Guha
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Kaustav Majumder
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
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16
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Ozawa H, Miyazawa T, Burdeos GC, Miyazawa T. Biological Functions of Antioxidant Dipeptides. J Nutr Sci Vitaminol (Tokyo) 2022; 68:162-171. [PMID: 35768247 DOI: 10.3177/jnsv.68.162] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In the history of modern nutritional science, understanding antioxidants is one of the major topics. In many cases, food-derived antioxidants have π conjugate or thiol group in their molecular structures because π conjugate stabilizes radical by its delocalization and two thiol groups form a disulfide bond in its antioxidative process. In recent years, antioxidant peptides have received much attention because for their ability to scavenge free radicals, inhibition of lipid peroxidation, chelation of transition metal ions, as well as their additional nutritional value. Among them, dipeptides are attracting much interest as post-amino acids, which have residues in common with amino acids, but also have different physiological properties and functions from those of amino acids. Especially, dipeptides containing moieties of several amino acid (tryptophan, tyrosine, histidine, cysteine, and methionine) possess potent antioxidant activity. This review summarizes previous details of structural property, radical scavenging activity, and biological activity of antioxidant dipeptide. Hopefully, this review will help provide a new insight into the study of the biological functions of antioxidant dipeptides.
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Affiliation(s)
- Hitoshi Ozawa
- New Industry Creation Hatchery Center (NICHe), Tohoku University
| | - Taiki Miyazawa
- New Industry Creation Hatchery Center (NICHe), Tohoku University
| | | | - Teruo Miyazawa
- New Industry Creation Hatchery Center (NICHe), Tohoku University
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17
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U MRA, Shen EYL, Cartlidge C, Alkhatib A, Thursz MR, Waked I, Gomaa AI, Holmes E, Sharma R, Taylor-Robinson SD. Optimized Systematic Review Tool: Application to Candidate Biomarkers for the Diagnosis of Hepatocellular Carcinoma. Cancer Epidemiol Biomarkers Prev 2022; 31:1261-1274. [PMID: 35545293 DOI: 10.1158/1055-9965.epi-21-0687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 09/17/2021] [Accepted: 05/09/2022] [Indexed: 12/24/2022] Open
Abstract
This review aims to develop an appropriate review tool for systematically collating metabolites that are dysregulated in disease and applies the method to identify novel diagnostic biomarkers for hepatocellular carcinoma (HCC). Studies that analyzed metabolites in blood or urine samples where HCC was compared with comparison groups (healthy, precirrhotic liver disease, cirrhosis) were eligible. Tumor tissue was included to help differentiate primary and secondary biomarkers. Searches were conducted on Medline and EMBASE. A bespoke "risk of bias" tool for metabolomic studies was developed adjusting for analytic quality. Discriminant metabolites for each sample type were ranked using a weighted score accounting for the direction and extent of change and the risk of bias of the reporting publication. A total of 84 eligible studies were included in the review (54 blood, 9 urine, and 15 tissue), with six studying multiple sample types. High-ranking metabolites, based on their weighted score, comprised energy metabolites, bile acids, acylcarnitines, and lysophosphocholines. This new review tool addresses an unmet need for incorporating quality of study design and analysis to overcome the gaps in standardization of reporting of metabolomic data. Validation studies, standardized study designs, and publications meeting minimal reporting standards are crucial for advancing the field beyond exploratory studies.
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Affiliation(s)
- Mei Ran Abellona U
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, United Kingdom
| | - Eric Yi-Liang Shen
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, United Kingdom
- Department of Radiation Oncology, Chang Gung Memorial Hospital and Chang Gung University, Taoyuan, Taiwan
| | | | - Alzhraa Alkhatib
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, United Kingdom
- National Liver Unit, Menoufiya University, Shbeen El Kom, Egypt
| | - Mark R Thursz
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, United Kingdom
| | - Imam Waked
- National Liver Unit, Menoufiya University, Shbeen El Kom, Egypt
| | - Asmaa I Gomaa
- National Liver Unit, Menoufiya University, Shbeen El Kom, Egypt
| | - Elaine Holmes
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, United Kingdom
- Health Futures Institute, Murdoch University, Perth WA, Australia
| | - Rohini Sharma
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Simon D Taylor-Robinson
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, United Kingdom
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18
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Moreno-Torres M, Quintás G, Castell JV. The Potential Role of Metabolomics in Drug-Induced Liver Injury (DILI) Assessment. Metabolites 2022; 12:metabo12060564. [PMID: 35736496 PMCID: PMC9227129 DOI: 10.3390/metabo12060564] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/31/2022] [Accepted: 06/13/2022] [Indexed: 12/19/2022] Open
Abstract
Drug-induced liver injury (DILI) is one of the most frequent adverse clinical reactions and a relevant cause of morbidity and mortality. Hepatotoxicity is among the major reasons for drug withdrawal during post-market and late development stages, representing a major concern to the pharmaceutical industry. The current biochemical parameters for the detection of DILI are based on enzymes (alanine aminotransferase (ALT), aspartate aminotransferase (AST), gamma-glutamyl transpeptidase (GGT), alkaline phosphatase (ALP)) and bilirubin serum levels that are not specific of DILI and therefore there is an increasing interest on novel, specific, DILI biomarkers discovery. Metabolomics has emerged as a tool with a great potential for biomarker discovery, especially in disease diagnosis, and assessment of drug toxicity or efficacy. This review summarizes the multistep approaches in DILI biomarker research and discovery based on metabolomics and the principal outcomes from the research performed in this field. For that purpose, we have reviewed the recent scientific literature from PubMed, Web of Science, EMBASE, and PubTator using the terms “metabolomics”, “DILI”, and “humans”. Despite the undoubted contribution of metabolomics to our understanding of the underlying mechanisms of DILI and the identification of promising novel metabolite biomarkers, there are still some inconsistencies and limitations that hinder the translation of these research findings into general clinical practice, probably due to the variability of the methods used as well to the different mechanisms elicited by the DILI causing agent.
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Affiliation(s)
- Marta Moreno-Torres
- Unidad de Hepatología Experimental, Instituto de Investigación Sanitaria Hospital La Fe, 46026 Valencia, Spain
- CIBEREHD, Instituto de Salud Carlos III, 28029 Madrid, Spain
- Correspondence: (M.M.-T.); (J.V.C.)
| | - Guillermo Quintás
- Unidad Analítica, Instituto de Investigación Sanitaria Hospital La Fe, 46026 Valencia, Spain;
- Health and Biomedicine, LEITAT Technological Center, 46026 Valencia, Spain
| | - José V. Castell
- Unidad de Hepatología Experimental, Instituto de Investigación Sanitaria Hospital La Fe, 46026 Valencia, Spain
- CIBEREHD, Instituto de Salud Carlos III, 28029 Madrid, Spain
- Departamento de Bioquímica y Biología Molecular, Facultad de Medicina, Universidad de Valencia, 46010 Valencia, Spain
- Correspondence: (M.M.-T.); (J.V.C.)
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19
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The concerted elevation of conjugation reactions is associated with the aggravation of acetaminophen toxicity in Akr1a-knockout mice with an ascorbate insufficiency. Life Sci 2022; 304:120694. [DOI: 10.1016/j.lfs.2022.120694] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 05/24/2022] [Accepted: 06/03/2022] [Indexed: 11/23/2022]
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20
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Weber S, Gerbes AL. Challenges and Future of Drug-Induced Liver Injury Research-Laboratory Tests. Int J Mol Sci 2022; 23:ijms23116049. [PMID: 35682731 PMCID: PMC9181520 DOI: 10.3390/ijms23116049] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 05/22/2022] [Accepted: 05/24/2022] [Indexed: 02/04/2023] Open
Abstract
Drug-induced liver injury (DILI) is a rare but potentially severe adverse drug event, which is also a major cause of study cessation and market withdrawal during drug development. Since no acknowledged diagnostic tests are available, DILI diagnosis poses a major challenge both in clinical practice as well as in pharmacovigilance. Differentiation from other liver diseases and the identification of the causative agent in the case of polymedication are the main issues that clinicians and drug developers face in this regard. Thus, efforts have been made to establish diagnostic testing methods and biomarkers in order to safely diagnose DILI and ensure a distinguishment from alternative liver pathologies. This review provides an overview of the diagnostic methods used in differential diagnosis, especially with regards to autoimmune hepatitis (AIH) and drug-induced autoimmune hepatitis (DI-AIH), in vitro causality methods using individual blood samples, biomarkers for diagnosis and severity prediction, as well as experimental predictive models utilized in pre-clinical settings during drug development regimes.
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21
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Pang Y, Kartsonaki C, Lv J, Millwood IY, Fairhurst-Hunter Z, Turnbull I, Bragg F, Hill MR, Yu C, Guo Y, Chen Y, Yang L, Clarke R, Walters RG, Wu M, Chen J, Li L, Chen Z, Holmes MV. Adiposity, metabolomic biomarkers, and risk of nonalcoholic fatty liver disease: a case-cohort study. Am J Clin Nutr 2022; 115:799-810. [PMID: 34902008 PMCID: PMC8895224 DOI: 10.1093/ajcn/nqab392] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 11/06/2021] [Accepted: 11/18/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Globally, the burden of obesity and associated nonalcoholic fatty liver disease (NAFLD) are rising, but little is known about the role that circulating metabolomic biomarkers play in mediating their association. OBJECTIVES We aimed to examine the observational and genetic associations of adiposity with metabolomic biomarkers and the observational associations of metabolomic biomarkers with incident NAFLD. METHODS A case-subcohort study within the prospective China Kadoorie Biobank included 176 NAFLD cases and 180 subcohort individuals and measured 1208 metabolites in stored baseline plasma using a Metabolon assay. In the subcohort the observational and genetic associations of BMI with biomarkers were assessed using linear regression, with adjustment for multiple testing. Cox regression was used to estimate adjusted HRs for NAFLD associated with biomarkers. RESULTS In observational analyses, BMI (kg/m2; mean: 23.9 in the subcohort) was associated with 199 metabolites at a 5% false discovery rate. The effects of genetically elevated BMI with specific metabolites were directionally consistent with the observational associations. Overall, 35 metabolites were associated with NAFLD risk, of which 15 were also associated with BMI, including glutamate (HR per 1-SD higher metabolite: 1.95; 95% CI: 1.48, 2.56), cysteine-glutathione disulfide (0.44; 0.31, 0.62), diaclyglycerol (C32:1) (1.71; 1.24, 2.35), behenoyl dihydrosphingomyelin (C40:0) (1.92; 1.42, 2.59), butyrylcarnitine (C4) (1.91; 1.38, 2.35), 2-hydroxybehenate (1.81; 1.34, 2.45), and 4-cholesten-3-one (1.79; 1.27, 2.54). The discriminatory performance of known risk factors was increased when 28 metabolites were also considered simultaneously in the model (weighted C-statistic: 0.84 to 0.90; P < 0.001). CONCLUSIONS Among relatively lean Chinese adults, a range of metabolomic biomarkers are associated with NAFLD risk and these biomarkers may lie on the pathway between adiposity and NAFLD.
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Affiliation(s)
- Yuanjie Pang
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Christiana Kartsonaki
- Clinical Trial Service Unit and Epidemiological Studies Unit (CTSU), Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
- Medical Research Council Population Health Research Unit (MRC PHRU) at the University of Oxford, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
| | - Jun Lv
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
- Peking University Center for Public Health and Epidemic Preparedness and Response (PKU-PHEPR), Peking University, Beijing, China
| | - Iona Y Millwood
- Clinical Trial Service Unit and Epidemiological Studies Unit (CTSU), Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
- Medical Research Council Population Health Research Unit (MRC PHRU) at the University of Oxford, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
| | - Zammy Fairhurst-Hunter
- Clinical Trial Service Unit and Epidemiological Studies Unit (CTSU), Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
| | - Iain Turnbull
- Clinical Trial Service Unit and Epidemiological Studies Unit (CTSU), Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
| | - Fiona Bragg
- Clinical Trial Service Unit and Epidemiological Studies Unit (CTSU), Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
- Medical Research Council Population Health Research Unit (MRC PHRU) at the University of Oxford, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
| | - Michael R Hill
- Clinical Trial Service Unit and Epidemiological Studies Unit (CTSU), Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
| | - Canqing Yu
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
- Peking University Center for Public Health and Epidemic Preparedness and Response (PKU-PHEPR), Peking University, Beijing, China
| | - Yu Guo
- Chinese Academy of Medical Sciences, Beijing, China
| | - Yiping Chen
- Clinical Trial Service Unit and Epidemiological Studies Unit (CTSU), Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
- Medical Research Council Population Health Research Unit (MRC PHRU) at the University of Oxford, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
| | - Ling Yang
- Clinical Trial Service Unit and Epidemiological Studies Unit (CTSU), Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
- Medical Research Council Population Health Research Unit (MRC PHRU) at the University of Oxford, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
| | - Robert Clarke
- Clinical Trial Service Unit and Epidemiological Studies Unit (CTSU), Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
| | - Robin G Walters
- Clinical Trial Service Unit and Epidemiological Studies Unit (CTSU), Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
- Medical Research Council Population Health Research Unit (MRC PHRU) at the University of Oxford, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
| | - Ming Wu
- Jiangsu Center for Disease Control and Prevention, Nanjing, China
| | - Junshi Chen
- National Center for Food Safety Risk Assessment, Beijing, China
| | - Liming Li
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
- Peking University Center for Public Health and Epidemic Preparedness and Response (PKU-PHEPR), Peking University, Beijing, China
| | - Zhengming Chen
- Clinical Trial Service Unit and Epidemiological Studies Unit (CTSU), Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
- Medical Research Council Population Health Research Unit (MRC PHRU) at the University of Oxford, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
| | - Michael V Holmes
- Clinical Trial Service Unit and Epidemiological Studies Unit (CTSU), Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
- Medical Research Council Population Health Research Unit (MRC PHRU) at the University of Oxford, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
- National Institute for Health Research Oxford Biomedical Research Centre, Oxford University Hospital, Oxford, United Kingdom
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22
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Jaiswal D, Nenwani M, Mishra V, Wangikar PP. Probing the metabolism of γ-glutamyl peptides in cyanobacteria via metabolite profiling and 13 C labeling. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:708-726. [PMID: 34727398 DOI: 10.1111/tpj.15564] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 10/20/2021] [Accepted: 10/25/2021] [Indexed: 06/13/2023]
Abstract
Cyanobacteria are attractive model organisms for the study of photosynthesis and diurnal metabolism and as hosts for photoautotrophic production of chemicals. Exposure to bright light or environmental pollutants and a diurnal lifestyle of these prokaryotes may result in significant oxidative stress. Glutathione is a widely studied γ-glutamyl peptide that plays a key role in managing oxidative stress and detoxification of xenobiotics in cyanobacteria. The functional role and biosynthesis pathways of this tripeptide have been studied in detail in various phyla, including cyanobacteria. However, other γ-glutamyl peptides remain largely unexplored. We use an integrated approach to identify a number of γ-glutamyl peptides based on signature mass fragments and mass shifts in them in 13 C and 15 N enriched metabolite extracts. The newly identified compounds include γ-glutamyl dipeptides and derivatives of glutathione. Carbon backbones of the former turn over much faster than that of glutathione, suggesting that they follow a distinct biosynthesis pathway. Further, transients of isotopic 13 C enrichment show positional labeling in these peptides, which allows us to delineate the alternative biosynthesis pathways. Importantly, the amino acid of γ-glutamyl dipeptides shows much faster turnover compared to the glutamate moiety. The significant accumulation of γ-glutamyl dipeptides under slow-growth conditions combined with the results from dynamic 13 C labeling suggests that these compounds may act as reservoirs of amino acids in cyanobacteria.
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Affiliation(s)
- Damini Jaiswal
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Minal Nenwani
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Vivek Mishra
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Pramod P Wangikar
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
- DBT-PAN IIT Centre for Bioenergy, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
- Wadhwani Research Centre for Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
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23
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Xie Z, Zhang L, Chen E, Lu J, Xiao L, Liu Q, Zhu D, Zhang F, Xu X, Li L. Targeted Metabolomics Analysis of Bile Acids in Patients with Idiosyncratic Drug-Induced Liver Injury. Metabolites 2021; 11:852. [PMID: 34940610 PMCID: PMC8706581 DOI: 10.3390/metabo11120852] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/26/2021] [Accepted: 12/04/2021] [Indexed: 12/12/2022] Open
Abstract
Drug-induced liver injury (DILI) is rare but clinically important due to a high rate of mortality. However, specific biomarkers for diagnosing and predicting the severity and prognosis of DILI are lacking. Here, we used targeted metabolomics to identify and quantify specific types of bile acids that can predict the severity of DILI. A total of 161 DILI patients were enrolled in this prospective cohort study, as well as 31 health controls. A targeted metabolomics method was used to identify 24 types of bile acids. DILI patients were divided into mild, moderate, and severe groups according to disease severity. A multivariate analysis was performed to identify characteristic bile acids. Then the patients were divided into severe and non-severe groups, and logistic regression was used to identify bile acids that could predict DILI severity. Among the enrolled DILI patients, 32 were in the mild group, 90 were in the moderate group, and 39 were in the severe group. Orthogonal partial least squares-discriminant analysis (OPLS-DA) modeling clearly discriminated among the different groups. Among the four groups, glycochenodeoxycholate (GCDCA), taurochenodeoxycholate (TCDCA), deoxycholic acid (DCA), Nor Cholic acid (NorCA), glycocholic acid (GCA), and taurocholic acid (TCA) showed significant differences in concentration between at least two groups. NorCA, GCDCA, and TCDCA were all independent risk factors that differentiated severe DILI patients from the other groups. The area under the receiver operating characteristic curve (AUROC) of GCDCA, TCDCA, and NorCA was 0.856, 0.792, and 0.753, respectively. Together, these three bile acids had an AUROC of 0.895 for predicting severe DILI patients. DILI patients with different disease severities have specific bile acid metabolomics. NorCA, GCDTA, and TCDCA were independent risk factors for differentiating severe DILI patients from less-severe patients and have the potential to predict DILI severity.
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Affiliation(s)
- Zhongyang Xie
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310009, China; (Z.X.); (L.Z.); (J.L.); (L.X.); (Q.L.); (D.Z.); (F.Z.)
| | - Lingjian Zhang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310009, China; (Z.X.); (L.Z.); (J.L.); (L.X.); (Q.L.); (D.Z.); (F.Z.)
| | - Ermei Chen
- Department of Gastroenterology, Zhongshan Hospital Affiliated to Xiamen University, Xiamen 361004, China;
| | - Juan Lu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310009, China; (Z.X.); (L.Z.); (J.L.); (L.X.); (Q.L.); (D.Z.); (F.Z.)
| | - Lanlan Xiao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310009, China; (Z.X.); (L.Z.); (J.L.); (L.X.); (Q.L.); (D.Z.); (F.Z.)
| | - Qiuhong Liu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310009, China; (Z.X.); (L.Z.); (J.L.); (L.X.); (Q.L.); (D.Z.); (F.Z.)
| | - Danhua Zhu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310009, China; (Z.X.); (L.Z.); (J.L.); (L.X.); (Q.L.); (D.Z.); (F.Z.)
| | - Fen Zhang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310009, China; (Z.X.); (L.Z.); (J.L.); (L.X.); (Q.L.); (D.Z.); (F.Z.)
| | - Xiaowei Xu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310009, China; (Z.X.); (L.Z.); (J.L.); (L.X.); (Q.L.); (D.Z.); (F.Z.)
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310009, China; (Z.X.); (L.Z.); (J.L.); (L.X.); (Q.L.); (D.Z.); (F.Z.)
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24
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Masoodi M, Gastaldelli A, Hyötyläinen T, Arretxe E, Alonso C, Gaggini M, Brosnan J, Anstee QM, Millet O, Ortiz P, Mato JM, Dufour JF, Orešič M. Metabolomics and lipidomics in NAFLD: biomarkers and non-invasive diagnostic tests. Nat Rev Gastroenterol Hepatol 2021; 18:835-856. [PMID: 34508238 DOI: 10.1038/s41575-021-00502-9] [Citation(s) in RCA: 175] [Impact Index Per Article: 58.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/15/2021] [Indexed: 02/07/2023]
Abstract
Nonalcoholic fatty liver disease (NAFLD) is one of the most common liver diseases worldwide and is often associated with aspects of metabolic syndrome. Despite its prevalence and the importance of early diagnosis, there is a lack of robustly validated biomarkers for diagnosis, prognosis and monitoring of disease progression in response to a given treatment. In this Review, we provide an overview of the contribution of metabolomics and lipidomics in clinical studies to identify biomarkers associated with NAFLD and nonalcoholic steatohepatitis (NASH). In addition, we highlight the key metabolic pathways in NAFLD and NASH that have been identified by metabolomics and lipidomics approaches and could potentially be used as biomarkers for non-invasive diagnostic tests. Overall, the studies demonstrated alterations in amino acid metabolism and several aspects of lipid metabolism including circulating fatty acids, triglycerides, phospholipids and bile acids. Although we report several studies that identified potential biomarkers, few have been validated.
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Affiliation(s)
- Mojgan Masoodi
- Institute of Clinical Chemistry, Bern University Hospital, Bern, Switzerland.
| | | | - Tuulia Hyötyläinen
- School of Natural Sciences and Technology, Örebro University, Örebro, Sweden
| | - Enara Arretxe
- OWL Metabolomics, Bizkaia Technology Park, Derio, Spain
| | | | | | | | - Quentin M Anstee
- Clinical & Translational Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Oscar Millet
- Precision Medicine & Metabolism, CIC bioGUNE, CIBERehd, BRTA, Bizkaia Technology Park, Derio, Spain
| | - Pablo Ortiz
- OWL Metabolomics, Bizkaia Technology Park, Derio, Spain
| | - Jose M Mato
- Precision Medicine & Metabolism, CIC bioGUNE, CIBERehd, BRTA, Bizkaia Technology Park, Derio, Spain
| | - Jean-Francois Dufour
- University Clinic of Visceral Surgery and Medicine, Inselspital Bern, Bern, Switzerland.,Hepatology, Department of BioMedical Research, University of Bern, Bern, Switzerland
| | - Matej Orešič
- School of Medical Sciences, Örebro University, Örebro, Sweden. .,Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland.
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25
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Atallah E, Freixo C, Alvarez-Alvarez I, Cubero FJ, Gerbes AL, Kullak-Ublick GA, Aithal GP. Biomarkers of idiosyncratic drug-induced liver injury (DILI) - a systematic review. Expert Opin Drug Metab Toxicol 2021; 17:1327-1343. [PMID: 34727797 DOI: 10.1080/17425255.2021.1999410] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
INTRODUCTION Idiosyncratic drug-induced liver injury (DILI) is an unpredictable event, and there are no specific biomarkers that can distinguish DILI from alternative explanations or predict its clinical outcomes. AREAS COVERED This systematic review summarizes the available evidence for all biomarkers proposed to have a role in the diagnosis or prognosis of DILI. Following a comprehensive search, we included all types of studies in humans. We included DILI cases based on any threshold criteria but excluded intrinsic DILI, commonly caused by paracetamol overdose. We classified studies into diagnostic and prognostic categories and assessed their methodological quality. After reviewing the literature, 14 studies were eligible. EXPERT OPINION Diagnostic studies were heterogeneous with regard to the study population and outcomes measured. Prognostic models were developed by integrating novel biomarkers, risk scores, and traditional biomarkers, which increased their prognostic ability to predict death or transplantation by 6 months. This systematic review highlights the case of need for non-genetic biomarkers that distinguish DILI from acute liver injury related to alternative etiology. Biomarkers with the potential to identify serious adverse outcomes from acute DILI should be validated in independent prospective cohorts with a substantial number of cases.
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Affiliation(s)
- Edmond Atallah
- School of Medicine, Nottingham Digestive Diseases Centre, University of Nottingham, Nottingham, UK.,National Institute for Health Research (NIHR) Nottingham Biomedical Research Centre, Nottingham University Hospitals Nhs Trust and the University of Nottingham, Nottingham, UK
| | - Cristiana Freixo
- Cintesis, Center for Health Technology and Services Research, Faculdade De Medicina Da Universidade Do Porto, Porto, Portugal
| | - Ismael Alvarez-Alvarez
- Servicio De Farmacología Clínica and Ugc Aparato Digestivo, Hospital Universitario Virgen De La Victoria, Instituto De Investigación Biomédica De Málaga-IBIMA, Universidad De Málaga, Málaga, Spain.,Centro De Investigación Biomédica En Red De Enfermedades Hepáticas Y Digestivas (Ciberehd), Madrid, Spain
| | - F J Cubero
- Centro De Investigación Biomédica En Red De Enfermedades Hepáticas Y Digestivas (Ciberehd), Madrid, Spain.,Department of Immunology, Ophthalmology, and ENT, Complutense University School of Medicine, Madrid, Spain
| | - Alexander L Gerbes
- Department of Medicine, Liver Centre Munich, University Hospital Munich, Munich, Germany
| | - Gerd A Kullak-Ublick
- Department of Clinical Pharmacology and Toxicology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Mechanistic Safety, CMO & Patient Safety, Global Drug Development, Novartis Pharma, Basel, Switzerland
| | - Guruprasad P Aithal
- School of Medicine, Nottingham Digestive Diseases Centre, University of Nottingham, Nottingham, UK.,National Institute for Health Research (NIHR) Nottingham Biomedical Research Centre, Nottingham University Hospitals Nhs Trust and the University of Nottingham, Nottingham, UK
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26
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Buck A, Prade VM, Kunzke T, Feuchtinger A, Kröll D, Feith M, Dislich B, Balluff B, Langer R, Walch A. Metabolic tumor constitution is superior to tumor regression grading for evaluating response to neoadjuvant therapy of esophageal adenocarcinoma patients. J Pathol 2021; 256:202-213. [PMID: 34719782 DOI: 10.1002/path.5828] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 10/04/2021] [Accepted: 10/28/2021] [Indexed: 11/11/2022]
Abstract
The response to neoadjuvant therapy can vary widely between individual patients. Histopathological tumor regression grading (TRG) is a strong factor for treatment response and survival prognosis of esophageal adenocarcinoma (EAC) patients following neoadjuvant treatment and surgery. However, TRG systems are usually based on the estimation of residual tumor but do not consider stromal or metabolic changes after treatment. Spatial metabolomics analysis is a powerful tool for molecular tissue phenotyping but has not been used so far in the context of neoadjuvant treatment of esophageal cancer. We used imaging mass spectrometry to assess the potential of spatial metabolomics on tumor and stroma tissue for evaluating therapy response of neoadjuvant-treated EAC patients. With an accuracy of 89.7%, the binary classifier trained on spatial tumor metabolite data proved to be superior for stratifying patients when compared to histopathological response assessment which had an accuracy of 70.5%. Sensitivities and specificities for the poor and favorable survival patient groups ranged from 84.9 to 93.3% using the metabolic classifier and from 62.2 to 78.1% using TRG. The tumor classifier was the only significant prognostic factor (HR 3.38, 95% CI = 1.40-8.12, P = 0.007) when adjusted for clinicopathological parameters such as TRG (HR 1.01, 95% CI = 0.67-1.53, P = 0.968) or stromal classifier (HR 1.856, 95% CI = 0.81-4.25, P = 0.143). The classifier even allowed to further stratify patients within the TRG1-3 categories. The underlying mechanisms of response to treatment has been figured out through network analysis. In summary, metabolic response evaluation outperformed histopathological response evaluation in our study with regard to prognostic stratification. This finding indicates that the metabolic constitution of tumor may have a greater impact on patient survival than the quantity of residual tumor cells or the stroma. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Achim Buck
- Research Unit Analytical Pathology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Verena M Prade
- Research Unit Analytical Pathology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Thomas Kunzke
- Research Unit Analytical Pathology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Annette Feuchtinger
- Research Unit Analytical Pathology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Dino Kröll
- Department of Visceral Surgery and Medicine, Inselspital, Bern University Hospital, University of Bern, 3008, Bern, Switzerland.,Department of Surgery, Campus Charité Mitte
- Campus Virchow-Klinikum, Charité-Universitätsmedizin Berlin, 10117, Berlin, Germany
| | - Marcus Feith
- Department of Surgery, Klinikum rechts der Isar, TUM School of Medicine, 81675, Munich, Germany
| | - Bastian Dislich
- Institute of Pathology, University of Bern, Bern, Switzerland
| | - Benjamin Balluff
- Maastricht Multimodal Molecular Imaging Institute (M4i), Maastricht University, Maastricht, The Netherlands
| | - Rupert Langer
- Institute of Pathology, University of Bern, Bern, Switzerland.,Institute of Clinical Pathology and Molecular Pathology, Kepler University Hospital and Johannes Kepler University, Linz, Austria
| | - Axel Walch
- Research Unit Analytical Pathology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
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27
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Mapping of population disparities in the cholangiocarcinoma urinary metabolome. Sci Rep 2021; 11:21286. [PMID: 34711878 PMCID: PMC8553759 DOI: 10.1038/s41598-021-00530-0] [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: 07/18/2021] [Accepted: 10/11/2021] [Indexed: 11/21/2022] Open
Abstract
Phenotypic diversity in urinary metabolomes of different geographical populations has been recognized recently. In this study, urinary metabolic signatures from Western (United Kingdom) and South-East Asian (Thai) cholangiocarcinoma patients were characterized to understand spectral variability due to host carcinogenic processes and/or exogenous differences (nutritional, environmental and pharmaceutical). Urinary liquid chromatography mass spectroscopy (LC–MS) spectral profiles from Thai (healthy = 20 and cholangiocarcinoma = 14) and UK cohorts (healthy = 22 and cholangiocarcinoma = 10) were obtained and modelled using chemometric data analysis. Healthy metabolome disparities between the two distinct populations were primarily related to differences in dietary practices and body composition. Metabolites excreted due to drug treatment were dominant in urine specimens from cholangiocarcinoma patients, particularly in Western individuals. Urine from participants with sporadic (UK) cholangiocarcinoma contained greater levels of a nucleotide metabolite (uridine/pseudouridine). Higher relative concentrations of 7-methylguanine were observed in urine specimens from Thai cholangiocarcinoma patients. The urinary excretion of hippurate and methyladenine (gut microbial-host co-metabolites) showed a similar pattern of lower levels in patients with malignant biliary tumours from both countries. Intrinsic (body weight and body composition) and extrinsic (xenobiotic metabolism) factors were the main causes of disparities between the two populations. Regardless of the underlying aetiology, biological perturbations associated with cholangiocarcinoma urine metabolome signatures appeared to be influenced by gut microbial community metabolism. Dysregulation in nucleotide metabolism was associated with sporadic cholangiocarcinoma, possibly indicating differences in mitochondrial energy production pathways between cholangiocarcinoma tumour subtypes. Mapping population-specific metabolic disparities may aid in interpretation of disease processes and identification of candidate biomarkers.
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Yang H, Mayneris-Perxachs J, Boqué N, del Bas JM, Arola L, Yuan M, Türkez H, Uhlén M, Borén J, Zhang C, Mardinoglu A, Caimari A. Combined Metabolic Activators Decrease Liver Steatosis by Activating Mitochondrial Metabolism in Hamsters Fed with a High-Fat Diet. Biomedicines 2021; 9:1440. [PMID: 34680557 PMCID: PMC8533474 DOI: 10.3390/biomedicines9101440] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 10/04/2021] [Accepted: 10/06/2021] [Indexed: 01/13/2023] Open
Abstract
Although the prevalence of non-alcoholic fatty liver disease (NAFLD) continues to increase, there is no effective treatment approved for this condition. We previously showed, in high-fat diet (HFD)-fed mice, that the supplementation of combined metabolic activators (CMA), including nicotinamide riboside (NAD+ precursor) and the potent glutathione precursors serine and N-acetyl-l-cysteine (NAC), significantly decreased fatty liver by promoting fat oxidation in mitochondria. Afterwards, in a one-day proof-of-concept human supplementation study, we observed that this CMA, including also L-carnitine tartrate (LCT), resulted in increased fatty acid oxidation and de novo glutathione synthesis. However, the underlying molecular mechanisms associated with supplementation of CMA have not been fully elucidated. Here, we demonstrated in hamsters that the chronic supplementation of this CMA (changing serine for betaine) at two doses significantly decreased hepatic steatosis. We further generated liver transcriptomics data and integrated these data using a liver-specific genome-scale metabolic model of liver tissue. We systemically determined the molecular changes after the supplementation of CMA and found that it activates mitochondria in the liver tissue by modulating global lipid, amino acid, antioxidant and folate metabolism. Our findings provide extra evidence about the beneficial effects of a treatment based on this CMA against NAFLD.
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Affiliation(s)
- Hong Yang
- Science for Life Laboratory, KTH Royal Institute of Technology, SE-17165 Stockholm, Sweden; (H.Y.); (M.Y.); (M.U.); (C.Z.)
| | - Jordi Mayneris-Perxachs
- Department of Diabetes, Endocrinology and Nutrition, Girona Biomedical Research Institute (IDIBGI), Hospital Universitari de Girona Doctor Josep Trueta, 17190 Girona, Spain;
- Center for Pathophysiology of Obesity and Nutrition (CIBEROBN), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Noemí Boqué
- Eurecat, Centre Tecnològic de Catalunya, Technological Unit of Nutrition and Health, 43204 Reus, Spain; (N.B.); (J.M.d.B.); (L.A.)
| | - Josep M. del Bas
- Eurecat, Centre Tecnològic de Catalunya, Technological Unit of Nutrition and Health, 43204 Reus, Spain; (N.B.); (J.M.d.B.); (L.A.)
| | - Lluís Arola
- Eurecat, Centre Tecnològic de Catalunya, Technological Unit of Nutrition and Health, 43204 Reus, Spain; (N.B.); (J.M.d.B.); (L.A.)
- Nutrigenomics Research Group, Department of Biochemistry and Biotechnology, Campus Sescelades, Universitat Rovira i Virgili, 43007 Tarragona, Spain
| | - Meng Yuan
- Science for Life Laboratory, KTH Royal Institute of Technology, SE-17165 Stockholm, Sweden; (H.Y.); (M.Y.); (M.U.); (C.Z.)
| | - Hasan Türkez
- Department of Medical Biology, Faculty of Medicine, Atatürk University, Erzurum 25030, Turkey;
| | - Mathias Uhlén
- Science for Life Laboratory, KTH Royal Institute of Technology, SE-17165 Stockholm, Sweden; (H.Y.); (M.Y.); (M.U.); (C.Z.)
| | - Jan Borén
- Department of Molecular and Clinical Medicine, University of Gothenburg and Sahlgrenska University Hospital, SE-40233 Gothenburg, Sweden;
| | - Cheng Zhang
- Science for Life Laboratory, KTH Royal Institute of Technology, SE-17165 Stockholm, Sweden; (H.Y.); (M.Y.); (M.U.); (C.Z.)
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Adil Mardinoglu
- Science for Life Laboratory, KTH Royal Institute of Technology, SE-17165 Stockholm, Sweden; (H.Y.); (M.Y.); (M.U.); (C.Z.)
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King’s College London, London WC2R 2LS, UK
| | - Antoni Caimari
- Eurecat, Centre Tecnològic de Catalunya, Technological Unit of Nutrition and Health, 43204 Reus, Spain; (N.B.); (J.M.d.B.); (L.A.)
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Shanmuganathan M, Sarfaraz MO, Kroezen Z, Philbrick H, Poon R, Don-Wauchope A, Puglia M, Wishart D, Britz-McKibbin P. A Cross-Platform Metabolomics Comparison Identifies Serum Metabolite Signatures of Liver Fibrosis Progression in Chronic Hepatitis C Patients. Front Mol Biosci 2021; 8:676349. [PMID: 34414211 PMCID: PMC8370474 DOI: 10.3389/fmolb.2021.676349] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 07/19/2021] [Indexed: 12/15/2022] Open
Abstract
Metabolomics offers new insights into disease mechanisms that is enhanced when adopting orthogonal instrumental platforms to expand metabolome coverage, while also reducing false discoveries by independent replication. Herein, we report the first inter-method comparison when using multisegment injection-capillary electrophoresis-mass spectrometry (MSI-CE-MS) and nuclear magnetic resonance (NMR) spectroscopy for characterizing the serum metabolome of patients with liver fibrosis in chronic hepatitis C virus (HCV) infection (n = 20) and non-HCV controls (n = 14). In this study, 60 and 30 serum metabolites were detected frequently (>75%) with good technical precision (median CV < 10%) from serum filtrate samples (n = 34) when using standardized protocols for MSI-CE-MS and NMR, respectively. Also, 20 serum metabolite concentrations were consistently measured by both methods over a 500-fold concentration range with an overall mean bias of 9.5% (n = 660). Multivariate and univariate statistical analyses independently confirmed that serum choline and histidine were consistently elevated (p < 0.05) in HCV patients with late-stage (F2-F4) as compared to early-stage (F0-F1) liver fibrosis. Overall, the ratio of serum choline to uric acid provided optimal differentiation of liver disease severity (AUC = 0.848, p = 0.00766) using a receiver operating characteristic curve, which was positively correlated with liver stiffness measurements by ultrasound imaging (r = 0.606, p = 0.0047). Moreover, serum 5-oxo-proline concentrations were higher in HCV patients as compared to non-HCV controls (F = 4.29, p = 0.0240) after adjustment for covariates (age, sex, BMI), indicative of elevated oxidative stress from glutathione depletion with the onset and progression of liver fibrosis. Both instrumental techniques enable rapid yet reliable quantification of serum metabolites in large-scale metabolomic studies with good overlap for biomarker replication. Advantages of MSI-CE-MS include greater metabolome coverage, lower operating costs, and smaller sample volume requirements, whereas NMR offers a robust platform supported by automated spectral and data processing software.
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Affiliation(s)
- Meera Shanmuganathan
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON, Canada
| | | | - Zachary Kroezen
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON, Canada
| | - Holly Philbrick
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON, Canada
| | - Richel Poon
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON, Canada
| | - Andrew Don-Wauchope
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
| | - Marco Puglia
- Department of Medicine, Division of Gastroenterology, McMaster University, Hamilton, ON, Canada
| | - David Wishart
- Departments of Biological Sciences and Computing Science, University of Alberta, Edmonton, AB, Canada
| | - Philip Britz-McKibbin
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON, Canada
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Sato H, Shimizu A, Okawa T, Uzu M, Goto M, Hisaka A. Metabolome Shift in Both Metastatic Breast Cancer Cells and Astrocytes Which May Contribute to the Tumor Microenvironment. Int J Mol Sci 2021; 22:ijms22147430. [PMID: 34299050 PMCID: PMC8308096 DOI: 10.3390/ijms22147430] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 06/26/2021] [Accepted: 07/09/2021] [Indexed: 12/17/2022] Open
Abstract
The role of astrocytes in the periphery of metastatic brain tumors is unclear. Since astrocytes regulate central nervous metabolism, we hypothesized that changes in astrocytes induced by contact with cancer cells would appear in the metabolome of both cells and contribute to malignant transformation. Coculture of astrocytes with breast cancer cell supernatants altered glutamate (Glu)-centered arginine–proline metabolism. Similarly, the metabolome of cancer cells was also altered by astrocyte culture supernatants, and the changes were further amplified in astrocytes exposed to Glu. Inhibition of Glu uptake in astrocytes reduces the variability in cancer cells. Principal component analysis of the cancer cells revealed that all these changes were in the first principal component (PC1) axis, where the responsible metabolites were involved in the metabolism of the arginine–proline, pyrimidine, and pentose phosphate pathways. The contribution of these changes to the tumor microenvironment needs to be further pursued.
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Affiliation(s)
- Hiromi Sato
- Laboratory of Clinical Pharmacology and Pharmacometrics, Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba-shi, Chiba 260-8675, Japan; (A.S.); (T.O.); (M.U.); (M.G.); (A.H.)
- Correspondence:
| | - Ayaka Shimizu
- Laboratory of Clinical Pharmacology and Pharmacometrics, Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba-shi, Chiba 260-8675, Japan; (A.S.); (T.O.); (M.U.); (M.G.); (A.H.)
| | - Toya Okawa
- Laboratory of Clinical Pharmacology and Pharmacometrics, Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba-shi, Chiba 260-8675, Japan; (A.S.); (T.O.); (M.U.); (M.G.); (A.H.)
| | - Miaki Uzu
- Laboratory of Clinical Pharmacology and Pharmacometrics, Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba-shi, Chiba 260-8675, Japan; (A.S.); (T.O.); (M.U.); (M.G.); (A.H.)
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 1-2 Owashi, Tsukuba, Ibaraki 305-8634, Japan
| | - Momoko Goto
- Laboratory of Clinical Pharmacology and Pharmacometrics, Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba-shi, Chiba 260-8675, Japan; (A.S.); (T.O.); (M.U.); (M.G.); (A.H.)
| | - Akihiro Hisaka
- Laboratory of Clinical Pharmacology and Pharmacometrics, Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba-shi, Chiba 260-8675, Japan; (A.S.); (T.O.); (M.U.); (M.G.); (A.H.)
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Lu Y, Wang J, Soladoye OP, Aluko RE, Fu Y, Zhang Y. Preparation, receptors, bioactivity and bioavailability of γ-glutamyl peptides: A comprehensive review. Trends Food Sci Technol 2021. [DOI: 10.1016/j.tifs.2021.04.051] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Igarashi K, Ota S, Kaneko M, Hirayama A, Enomoto M, Katumata K, Sugimoto M, Soga T. High-throughput screening of salivary polyamine markers for discrimination of colorectal cancer by multisegment injection capillary electrophoresis tandem mass spectrometry. J Chromatogr A 2021; 1652:462355. [PMID: 34233246 DOI: 10.1016/j.chroma.2021.462355] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 06/03/2021] [Accepted: 06/15/2021] [Indexed: 01/05/2023]
Abstract
Polyamine metabolites provide pathophysiological information on disease or therapeutic efficacy, yet rapid screening methods for these biomarkers are lacking. Here, we developed high-throughput polyamine metabolite profiling based on multisegment injection capillary electrophoresis triple quadrupole tandem mass spectrometry (MSI-CE-MS/MS), which allows sequential 40-sample injection followed by electrophoretic separation and specific mass detection. To achieve consecutive analysis of polyamine samples, 1 M formic acid was used as the background electrolyte (BGE). The BGE spacer volume had an apparent effect on peak resolution among samples, and 20 nL was selected as the optimal volume. The use of polyamine isotopomers as the internal standard enabled the correction of matrix effects in MS detection. This method is sensitive, selective and quantitative, and its utility was demonstrated by screening polyamines in 359 salivary samples within 360 min, resulting in discrimination of colorectal cancer patients from noncancer controls.
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Affiliation(s)
- Kaori Igarashi
- Institute for Advanced Biosciences, Keio University, 246-2 Mizukami, Kakuganji, Tsuruoka 997-0052, Japan.
| | - Sana Ota
- Institute for Advanced Biosciences, Keio University, 246-2 Mizukami, Kakuganji, Tsuruoka 997-0052, Japan.
| | - Miku Kaneko
- Institute for Advanced Biosciences, Keio University, 246-2 Mizukami, Kakuganji, Tsuruoka 997-0052, Japan.
| | - Akiyoshi Hirayama
- Institute for Advanced Biosciences, Keio University, 246-2 Mizukami, Kakuganji, Tsuruoka 997-0052, Japan.
| | - Masanobu Enomoto
- Department of Gastrointestinal and Pediatric Surgery, Tokyo Medical University, 6-7-1, Nishijinjuku, Shinjuku, Tokyo 160-0023, Japan.
| | - Kenji Katumata
- Department of Gastrointestinal and Pediatric Surgery, Tokyo Medical University, 6-7-1, Nishijinjuku, Shinjuku, Tokyo 160-0023, Japan.
| | - Masahiro Sugimoto
- Institute for Advanced Biosciences, Keio University, 246-2 Mizukami, Kakuganji, Tsuruoka 997-0052, Japan; Research and Development Center for Minimally Invasive Therapies, Medical Research Institute, Tokyo Medical University, 6-1-1, Sinjuku, Tokyo 160-0022, Japan.
| | - Tomoyoshi Soga
- Institute for Advanced Biosciences, Keio University, 246-2 Mizukami, Kakuganji, Tsuruoka 997-0052, Japan; Faculty of Environmental Information Studies, Keio University, 5322 Endo, Fujisawa 252-0882, Japan.
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Thacker JB, He C, Pennathur S. Quantitative analysis of γ-glutamylisoleucine, γ-glutamylthreonine, and γ-glutamylvaline in HeLa cells using UHPLC-MS/MS. J Sep Sci 2021; 44:2898-2907. [PMID: 34042281 DOI: 10.1002/jssc.202001266] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 05/20/2021] [Accepted: 05/25/2021] [Indexed: 12/30/2022]
Abstract
γ-Glutamylpeptides have been identified as potential biomarkers for a number of diseases including cancer, diabetes, and liver disease. In this study, we developed and validated a novel quantitative analytical strategy for measuring γ-glutamylisoleucine, γ-glutamylthreonine, and γ-glutamylvaline, all of which have been previously reported as potential biomarkers for prostate cancer in HeLa cells using ultra-high-performance liquid chromatography-tandem mass spectrometry. A BEH C18 column was used as the stationary phase. Mobile phase A was 99:1 water:formic acid and mobile phase B was acetonitrile. Chemical isotope labeling using benzoyl chloride was used as the internal standardization strategy. Sample preparation consisted of the addition of water to a frozen cell pellet, sonication, derivatization, centrifugation, and subsequent addition of an internal standard solution. The method was validated for selectivity, accuracy, precision, linearity, and stability. The determined concentrations of γ-glutamylisoleucine, γ-glutamylthreonine, and γ-glutamylvaline in HeLa cells were 1.92 ± 0.06, 10.8 ± 0.4, and 1.96 ± 0.04 pmol/mg protein, respectively. In addition, the qualitative analysis of these analytes in human serum was achieved using a modified sample preparation strategy. To the best of our knowledge, this is the first report of the use of benzoyl chloride for chemical isotope labeling for metabolite quantitation in cells.
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Affiliation(s)
- Jonathan B Thacker
- Division of Nephrology, Department of Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Chenchen He
- Division of Nephrology, Department of Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Subramaniam Pennathur
- Division of Nephrology, Department of Medicine, University of Michigan, Ann Arbor, Michigan, USA.,Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, Michigan, USA
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Khalil A, Elfert A, Ghanem S, Helal M, Abdelsattar S, Elgedawy G, Obada M, Abdel-Samiee M, El-Said H. The role of metabolomics in hepatocellular carcinoma. EGYPTIAN LIVER JOURNAL 2021. [DOI: 10.1186/s43066-021-00085-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Abstract
Background
Hepatocellular carcinoma is the most common primary liver malignancy, with the highest incidence in the developing world, including Egypt. Hepatocellular carcinoma is usually diagnosed in the terminal stage of the disease because of the low sensitivity of the available screening tests. During the process of carcinogenesis, the cellular metabolism is altered to allow cancer cells to adapt to the hypoxic environment and therefore increase anabolic synthesis and survival and avoid the apoptotic death signals. These changes in metabolic status can be tracked by metabolomics analysis.
Main body
Metabolomics is a comprehensive approach for identifying metabolic signatures towards the screening, prediction, and earlier diagnosis of hepatocellular carcinoma with greater efficiency than the conventional diagnostic biomarker. The identification of metabolic changes associated with hepatocellular carcinoma is essential to the understanding of disease pathophysiology and enables better monitoring of high-risk individuals. However, due to the complexity of the metabolic pathways associated with hepatocellular carcinoma, the details of these perturbations are still not adequately characterized. The current status of biomarkers for hepatocellular carcinoma and their insufficiencies and metabolic pathways linked to hepatocellular carcinogenesis are briefly addressed in this mini-review. The review focused on the significantly changed metabolites and pathways associated with hepatocellular carcinoma such as phospholipids, bile acids, amino acids, reactive oxygen species metabolism, and the metabolic changes related to energy production in a cancer cell. The review briefly discusses the sensitivity of metabolomics in the prediction and prognosis of hepatocellular carcinoma and the effect of coexisting multiple etiologies of the disease.
Conclusions
Metabolomics profiling is a potentially promising tool for better predicting, diagnosis, and prognosis of hepatocellular carcinoma.
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Guardiola JJ, Hardesty JE, Beier JI, Prough RA, McClain CJ, Cave MC. Plasma Metabolomics Analysis of Polyvinyl Chloride Workers Identifies Altered Processes and Candidate Biomarkers for Hepatic Hemangiosarcoma and Its Development. Int J Mol Sci 2021; 22:5093. [PMID: 34065028 PMCID: PMC8150673 DOI: 10.3390/ijms22105093] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 04/28/2021] [Accepted: 05/10/2021] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND High-level occupational vinyl chloride (VC) exposures have been associated with hepatic hemangiosarcoma, which typically develops following a long latency period. Although VC is genotoxic, a more comprehensive mode of action has not been determined and diagnostic biomarkers have not been established. The purpose of this study is to address these knowledge gaps through plasma metabolomics. METHODS Plasma samples from polyvinyl chloride polymerization workers who developed hemangiosarcoma (cases, n = 15) and VC exposure-matched controls (n = 17) underwent metabolomic analysis. Random forest and bioinformatic analyses were performed. RESULTS Cases and controls had similar demographics and routine liver biochemistries. Mass spectroscopy identified 606 known metabolites. Random forest analysis had an 82% predictive accuracy for group classification. 60 metabolites were significantly increased and 44 were decreased vs. controls. Taurocholate, bradykinin and fibrin degradation product 2 were up-regulated by greater than 80-fold. The naturally occurring anti-angiogenic phenol, 4-hydroxybenzyl alcohol, was down-regulated 5-fold. Top affected ontologies involved: (i) metabolism of bile acids, taurine, cholesterol, fatty acids and amino acids; (ii) inflammation and oxidative stress; and (iii) nicotinic cholinergic signaling. CONCLUSIONS The plasma metabolome was differentially regulated in polyvinyl chloride workers who developed hepatic hemangiosarcoma. Ontologies potentially involved in hemangiosarcoma pathogenesis and candidate biomarkers were identified.
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Affiliation(s)
- John J. Guardiola
- Department of Medicine, University of Louisville, Louisville, KY 40202, USA; (J.J.G.); (J.E.H.); (C.J.M.)
| | - Josiah E. Hardesty
- Department of Medicine, University of Louisville, Louisville, KY 40202, USA; (J.J.G.); (J.E.H.); (C.J.M.)
- Hepatology and Nutrition, University of Louisville Division of Gastroenterology, Louisville, KY 40202, USA
| | - Juliane I. Beier
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA;
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA 15213, USA
- University of Pittsburgh Liver Research Center (PLRC), Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Russell A. Prough
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY 40202, USA;
| | - Craig J. McClain
- Department of Medicine, University of Louisville, Louisville, KY 40202, USA; (J.J.G.); (J.E.H.); (C.J.M.)
- Hepatology and Nutrition, University of Louisville Division of Gastroenterology, Louisville, KY 40202, USA
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY 40202, USA
- The Robley Rex Veterans Affairs Medical Center, Louisville, KY 40206, USA
- The UofL Health—Jewish Hospital Trager Transplant Center, Louisville, KY 40202, USA
- The University of Louisville Superfund Research Center, Department of Medicine, University of Louisville, Louisville, KY 40202, USA
| | - Matthew C. Cave
- Department of Medicine, University of Louisville, Louisville, KY 40202, USA; (J.J.G.); (J.E.H.); (C.J.M.)
- Hepatology and Nutrition, University of Louisville Division of Gastroenterology, Louisville, KY 40202, USA
- University of Pittsburgh Liver Research Center (PLRC), Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY 40202, USA;
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY 40202, USA
- The Robley Rex Veterans Affairs Medical Center, Louisville, KY 40206, USA
- The UofL Health—Jewish Hospital Trager Transplant Center, Louisville, KY 40202, USA
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Yang Y, Huang Z, Yang Z, Qi Y, Shi H, Zhou Y, Wang F, Yang M. Serum metabolomic profiling reveals an increase in homocitrulline in Chinese patients with nonalcoholic fatty liver disease: a retrospective study. PeerJ 2021; 9:e11346. [PMID: 33987020 PMCID: PMC8101472 DOI: 10.7717/peerj.11346] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 04/03/2021] [Indexed: 12/28/2022] Open
Abstract
Backgrounds Nonalcoholic fatty liver disease (NAFLD) has multiple causes, is triggered by individual genetic susceptibility, environmental factors, and metabolic disturbances, and may be triggered by acquired metabolic stress. The metabolic profiles of NAFLD show significant ethnic differences, and the metabolic characteristics of NAFLD in Chinese individuals are unclear. Our study aimed to identify the metabolites and pathways associated with NAFLD in a Chinese cohort. Methods One hundred participants, including 50 NAFLD patients and 50 healthy controls, were enrolled in this retrospective observational study at Jinling Hospital in Nanjing; serum samples were collected from the patients and healthy subjects. The metabolome was determined in all samples by liquid chromatography-hybrid quadrupole time-of-flight mass spectrometry (LC-Q/TOF-MS). Univariate and multivariate statistical analyses were used to compare the metabolic profiles between the two groups. Results The comparison indicated that the levels of 89 metabolites were different between the two groups. The glycerophospholipid family of metabolites was the most abundant family of metabolites that demonstrated significant differences. L-acetylcarnitine, L-homocitrulline, and glutamic acid were the top three metabolites ranked by VIP score and had favorable effective functions for diagnosis. Moreover, pathway enrichment analysis suggested 14 potentially different metabolic pathways between NAFLD patients and healthy controls based on their impact value. Biological modules involved in the lipid and carbohydrate metabolism had the highest relevance to the conditions of NAFLD. Glycerophospholipid metabolism had the strongest associations with the conditions of NAFLD. Conclusions Our data suggest that the serum metabolic profiles of NAFLD patients and healthy controls are different. L-Homocitrulline was remarkably increased in NAFLD patients.
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Affiliation(s)
- Yarong Yang
- Department of Gastroenterology and Hepatology, Jinling Hospital, the First School of Clinical Medicine, Southern Medical University, Nanjing, Jiangsu, China
| | - Zexin Huang
- Department of Gastroenterology and Hepatology, Jinling Hospital, the First School of Clinical Medicine, Southern Medical University, Nanjing, Jiangsu, China
| | - Zhao Yang
- Department of Gastroenterology and Hepatology, Jinling Hospital, the First School of Clinical Medicine, Southern Medical University, Nanjing, Jiangsu, China
| | - Ying Qi
- Department of Gastroenterology and Hepatology, Jinling Hospital, Medical School of Nanjing University, Nanjing, Jiangsu, China
| | - Hui Shi
- Department of Gastroenterology and Hepatology, Jinling Hospital, the First School of Clinical Medicine, Southern Medical University, Nanjing, Jiangsu, China
| | - Yifei Zhou
- Department of Gastroenterology and Hepatology, Jinling Hospital, Medical School of Nanjing University, Nanjing, Jiangsu, China
| | - Fangyu Wang
- Department of Gastroenterology and Hepatology, Jinling Hospital, the First School of Clinical Medicine, Southern Medical University, Nanjing, Jiangsu, China
| | - Miaofang Yang
- Department of Gastroenterology and Hepatology, Jinling Hospital, the First School of Clinical Medicine, Southern Medical University, Nanjing, Jiangsu, China
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Bai C, Wang H, Dong D, Li T, Yu Z, Guo J, Zhou W, Li D, Yan R, Wang L, Wang Z, Li Y, Ren L. Urea as a By-Product of Ammonia Metabolism Can Be a Potential Serum Biomarker of Hepatocellular Carcinoma. Front Cell Dev Biol 2021; 9:650748. [PMID: 33869206 PMCID: PMC8047217 DOI: 10.3389/fcell.2021.650748] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 03/05/2021] [Indexed: 01/15/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is highly malignant; nearly half of the new cases and deaths are in China. The poor prognosis of HCC is mainly due to late diagnosis; many new biomarkers have been developed for HCC diagnosis. However, few markers are quickly translated into clinical practice; early and differential diagnosis of HCC from cirrhosis and/or hepatitis is still a clinical challenge. Metabolomics and biochemical methods were used to reveal specific serum biomarkers of HCC. Most of the elevated metabolites in HCC and HBV patients were overlapped compared with controls. Urea was the specifically elevated serum biomarker of HCC patients. Moreover, urea combined with AFP and CEA can improve the sensitivity of HCC diagnosis. The plasma ammonia of HCC patients was significantly higher than healthy controls. Co-culture cell model revealed normal liver cells cooperated with cancer cells to metabolize ammonia into urea. The urea metabolism in cancer cells marginally depended on the expression of CPS1. However, the expression of CPS1 did not change with ammonium chloride, which might regulate the urea cycle through enzyme activity. The urea cycle could detoxify high concentrations of ammonia to promote cancer cell proliferation. Therefore, urea was a by-product of ammonia metabolism and could be a potential serum biomarker for HCC. The combined application of metabolomics and biochemical methods can discover new biomarkers for the early diagnosis of HCC and be quickly applied to clinical diagnosis.
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Affiliation(s)
- Changsen Bai
- Department of Laboratory, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Hailong Wang
- Department of Cancer Cell Biology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Dong Dong
- Department of Laboratory, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Tong Li
- Department of Laboratory, Second Affiliated Hospital of Tianjin University of TCM, Tianjin, China
| | - Zhi Yu
- Department of Laboratory, First Affiliated Hospital of Shaoyang University, Shaoyang, China
| | - Junfei Guo
- Department of Laboratory, Guangdong Women and Children Hospital, Guangzhou, China
| | - Wei Zhou
- Department of Laboratory, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Ding Li
- Department of Laboratory, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Ruochen Yan
- School of Medical Laboratory, Tianjin Medical University, Tianjin, China
| | - Liyan Wang
- School of Medical Laboratory, Tianjin Medical University, Tianjin, China
| | - Zhaosong Wang
- Department of Public Laboratory, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer, Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Yueguo Li
- Department of Laboratory, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Li Ren
- Department of Laboratory, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, China
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Zhan Y, Wang J, He X, Huang M, Yang X, He L, Qiu Y, Lou Y. Plasma metabolites, especially lipid metabolites, are altered in pregnant women with gestational diabetes mellitus. Clin Chim Acta 2021; 517:139-148. [PMID: 33711327 DOI: 10.1016/j.cca.2021.02.023] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 02/23/2021] [Accepted: 02/24/2021] [Indexed: 10/22/2022]
Abstract
BACKGROUND AND AIMS Gestational diabetes mellitus (GDM) is a pathological condition of glucose intolerance associated with adverse pregnancy outcomes and increased risk of developing maternal type 2 diabetes later in life. Metabolomics is finding increasing use in the study of GDM. To date, GDM-specific metabolomic changes have not been completely elucidated. MATERIALS AND METHODS In this pilot study, metabolomics fingerprinting data, obtained by ultra-performance liquid chromatography quadrupole time-of-flight mass spectrometry (UHPLC/Q-TOF-MS), of 54 healthy pregnant women and 49 patients with GDM at the second and third gestational trimesters were analyzed. Multilevel statistical methods were used to process complex metabolomic data from the retrospective cohorts. RESULTS Using univariate analysis (p < 0.05), 41 metabolites were identified as having the most significant differences between these two groups. Lipid metabolites, particularly glycerophospholipids, were the most prevalent class of altered compounds. In addition, metabolites with previously unknown connection to GDM - such as monoacylglycerol, dihydrobiopterin, and 13S-hydroxyoctadecadienoic acid - were identified with strong discriminative power. The main metabolic pathways affected by GDM included glycerophospholipid metabolism, linoleic acid metabolism, and D-arginine and D-ornithine metabolism. CONCLUSION Our data provide a comprehensive overview of metabolite changes at different stages of pregnancy, which offers further insights into the pathogenesis of GDM.
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Affiliation(s)
- Yaqiong Zhan
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang Provincial Key Laboratory for Drug Clinical Research and Evaluation, The First Affiliated Hospital, College of Medicine, Zhejiang University, 79 QingChun Road, Hangzhou, Zhejiang 310000, People's Republic of China
| | - Jiali Wang
- Zhejiang Provincial Key Laboratory for Drug Clinical Research and Evaluation, The First Affiliated Hospital, College of Medicine, Zhejiang University, 79 QingChun Road, Hangzhou, Zhejiang 310000, People's Republic of China
| | - Xiaoying He
- Zhejiang Provincial Key Laboratory for Drug Clinical Research and Evaluation, The First Affiliated Hospital, College of Medicine, Zhejiang University, 79 QingChun Road, Hangzhou, Zhejiang 310000, People's Republic of China
| | - Mingzhu Huang
- Zhejiang Provincial Key Laboratory for Drug Clinical Research and Evaluation, The First Affiliated Hospital, College of Medicine, Zhejiang University, 79 QingChun Road, Hangzhou, Zhejiang 310000, People's Republic of China
| | - Xi Yang
- Zhejiang Provincial Key Laboratory for Drug Clinical Research and Evaluation, The First Affiliated Hospital, College of Medicine, Zhejiang University, 79 QingChun Road, Hangzhou, Zhejiang 310000, People's Republic of China
| | - Lingjuan He
- Zhejiang Provincial Key Laboratory for Drug Clinical Research and Evaluation, The First Affiliated Hospital, College of Medicine, Zhejiang University, 79 QingChun Road, Hangzhou, Zhejiang 310000, People's Republic of China
| | - Yunqing Qiu
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang Provincial Key Laboratory for Drug Clinical Research and Evaluation, The First Affiliated Hospital, College of Medicine, Zhejiang University, 79 QingChun Road, Hangzhou, Zhejiang 310000, People's Republic of China.
| | - Yan Lou
- Zhejiang Provincial Key Laboratory for Drug Clinical Research and Evaluation, The First Affiliated Hospital, College of Medicine, Zhejiang University, 79 QingChun Road, Hangzhou, Zhejiang 310000, People's Republic of China.
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Plasma metabolites to profile pathways in noncommunicable disease multimorbidity. Nat Med 2021; 27:471-479. [PMID: 33707775 PMCID: PMC8127079 DOI: 10.1038/s41591-021-01266-0] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 01/27/2021] [Indexed: 02/07/2023]
Abstract
Multimorbidity, the simultaneous presence of multiple chronic conditions, is an increasing global health problem and research into its determinants is of high priority. We used baseline untargeted plasma metabolomics profiling covering >1,000 metabolites as a comprehensive readout of human physiology to characterize pathways associated with and across 27 incident noncommunicable diseases (NCDs) assessed using electronic health record hospitalization and cancer registry data from over 11,000 participants (219,415 person years). We identified 420 metabolites shared between at least 2 NCDs, representing 65.5% of all 640 significant metabolite-disease associations. We integrated baseline data on over 50 diverse clinical risk factors and characteristics to identify actionable shared pathways represented by those metabolites. Our study highlights liver and kidney function, lipid and glucose metabolism, low-grade inflammation, surrogates of gut microbial diversity and specific health-related behaviors as antecedents of common NCD multimorbidity with potential for early prevention. We integrated results into an open-access webserver ( https://omicscience.org/apps/mwasdisease/ ) to facilitate future research and meta-analyses.
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40
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Recent Advances of Microbiome-Associated Metabolomics Profiling in Liver Disease: Principles, Mechanisms, and Applications. Int J Mol Sci 2021; 22:ijms22031160. [PMID: 33503844 PMCID: PMC7865944 DOI: 10.3390/ijms22031160] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/17/2021] [Accepted: 01/22/2021] [Indexed: 02/06/2023] Open
Abstract
Advances in high-throughput screening of metabolic stability in liver and gut microbiota are able to identify and quantify small-molecule metabolites (metabolome) in different cellular microenvironments that are closest to their phenotypes. Metagenomics and metabolomics are largely recognized to be the “-omics” disciplines for clinical therapeutic screening. Here, metabolomics activity screening in liver disease (LD) and gut microbiomes has significantly delivered the integration of metabolomics data (i.e., a set of endogenous metabolites) with metabolic pathways in cellular environments that can be tested for biological functions (i.e., phenotypes). A growing literature in LD and gut microbiomes reports the use of metabolites as therapeutic targets or biomarkers. Although growing evidence connects liver fibrosis, cirrhosis, and hepatocellular carcinoma, the genetic and metabolic factors are still mainly unknown. Herein, we reviewed proof-of-concept mechanisms for metabolomics-based LD and gut microbiotas’ role from several studies (nuclear magnetic resonance, gas/lipid chromatography, spectroscopy coupled with mass spectrometry, and capillary electrophoresis). A deeper understanding of these axes is a prerequisite for optimizing therapeutic strategies to improve liver health.
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41
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Kang YP, Mockabee-Macias A, Jiang C, Falzone A, Prieto-Farigua N, Stone E, Harris IS, DeNicola GM. Non-canonical Glutamate-Cysteine Ligase Activity Protects against Ferroptosis. Cell Metab 2021; 33:174-189.e7. [PMID: 33357455 PMCID: PMC7839835 DOI: 10.1016/j.cmet.2020.12.007] [Citation(s) in RCA: 156] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 10/09/2020] [Accepted: 12/08/2020] [Indexed: 02/06/2023]
Abstract
Cysteine is required for maintaining cellular redox homeostasis in both normal and transformed cells. Deprivation of cysteine induces the iron-dependent form of cell death known as ferroptosis; however, the metabolic consequences of cysteine starvation beyond impairment of glutathione synthesis are poorly characterized. Here, we find that cystine starvation of non-small-cell lung cancer cell lines induces an unexpected accumulation of γ-glutamyl-peptides, which are produced due to a non-canonical activity of glutamate-cysteine ligase catalytic subunit (GCLC). This activity is enriched in cell lines with high levels of NRF2, a key transcriptional regulator of GCLC, but is also inducible in healthy murine tissues following cysteine limitation. γ-glutamyl-peptide synthesis limits the accumulation of glutamate, thereby protecting against ferroptosis. These results indicate that GCLC has a glutathione-independent, non-canonical role in the protection against ferroptosis by maintaining glutamate homeostasis under cystine starvation.
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Affiliation(s)
- Yun Pyo Kang
- Department of Cancer Physiology, H. Lee. Moffitt Cancer Center, Tampa, FL 33612, USA
| | | | - Chang Jiang
- Department of Cancer Physiology, H. Lee. Moffitt Cancer Center, Tampa, FL 33612, USA
| | - Aimee Falzone
- Department of Cancer Physiology, H. Lee. Moffitt Cancer Center, Tampa, FL 33612, USA
| | | | - Everett Stone
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Isaac S Harris
- University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Gina M DeNicola
- Department of Cancer Physiology, H. Lee. Moffitt Cancer Center, Tampa, FL 33612, USA.
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42
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Gong Y, Lyu W, Shi X, Zou X, Lu L, Yang H, Xiao Y. A Serum Metabolic Profiling Analysis During the Formation of Fatty Liver in Landes Geese via GC-TOF/MS. Front Physiol 2020; 11:581699. [PMID: 33381050 PMCID: PMC7767842 DOI: 10.3389/fphys.2020.581699] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 11/19/2020] [Indexed: 11/25/2022] Open
Abstract
During the process of fatty liver production by overfeeding, the levels of endogenous metabolites in the serum of geese would change dramatically. This study investigated the effects of overfeeding on serum metabolism of Landes geese and the underlying mechanisms using a metabolomics approach. Sixty Landes geese of the same age were randomly divided into the following three groups with 20 replicates in each group: D0 group (free from gavage); D7 group (overfeeding for 7 days); D25 group (overfeeding for 25 days). At the end of the experiment, 10 geese of similar weight from each group were selected for slaughter and sampling. The results showed that overfeeding significantly increased the body weight and the liver weight of geese. Serum enzymatic activities and serum lipid levels were significantly enhanced following overfeeding. Gas chromatography time-of-flight/mass spectrometry (GC-TOF/MS) was employed to explore the serum metabolic patterns, and to identify potential contributors to the formation of fatty liver and the correlated metabolic pathways. Relative to overfeeding for 7 days, a large number of endogenous molecules in serum of geese overfed for 25 days were altered. Continuous elevated levels of pyruvic acid, alanine, proline and beta-glycerophosphoric acid and reduced lactic acid level were observed in the serum of overfed geese. Pathway exploration found that the most of significantly different metabolites were involved in amino acids, carbohydrate and lipid metabolism. The present study exhibited the efficient capability of Landes geese to produce fatty liver, identified potential biomarkers and disturbed metabolic pathways in liver steatosis. These findings might reveal the underlying mechanisms of fatty liver formation and provide some theoretical basis for the diagnosis and treatment of liver diseases.
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Affiliation(s)
- Yujie Gong
- Key Laboratory of Molecular Animal Nutrition of Ministry of Education, Key Laboratory of Animal Feed and Nutrition of Zhejiang Province, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Wentao Lyu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xingfen Shi
- Zhejiang Institute of Veterinary Drug and Feed Control, Hangzhou, China
| | - Xiaoting Zou
- Key Laboratory of Molecular Animal Nutrition of Ministry of Education, Key Laboratory of Animal Feed and Nutrition of Zhejiang Province, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Lizhi Lu
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Hua Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Yingping Xiao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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Huang Y, Zhao X, Zhang ZT, Chen SS, Li SS, Shi Z, Jing J, Huang A, Guo YM, Bai ZF, Zou ZS, Xiao XH, Wang JB, Niu M. Metabolomics Profiling and Diagnosis Biomarkers Searching for Drug-Induced Liver Injury Implicated to Polygonum multiflorum: A Cross-Sectional Cohort Study. Front Med (Lausanne) 2020; 7:592434. [PMID: 33330552 PMCID: PMC7734208 DOI: 10.3389/fmed.2020.592434] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 10/30/2020] [Indexed: 12/17/2022] Open
Abstract
Aim: The diagnosis of drug-induced liver injury (DILI) remains a challenge and the cases of Polygonum multiflorum Thunb. (PM) induced DILI (PM-DILI) have received much attention This study aimed to identify a simple and high-efficiency approach to PM-DILI diagnosis via metabolomics analysis. Methods: Plasma metabolites in 13 PM-DILI patients were profiled by liquid chromatography along with high-resolution mass spectrometry. Meanwhile, the metabolic characteristics of the PM-DILI were compared with that of autoimmune hepatitis (AIH), hepatitis B (HBV), and healthy volunteers. Results: Twenty-four metabolites were identified to present significantly different levels in PM-DILI patients compared with HBV and AIH groups. These metabolites were enriched into glucose, amino acids, and sphingolipids metabolisms. Among these essential metabolites, the ratios of P-cresol sulfate vs. phenylalanine and inosine vs. bilirubin were further selected using a stepwise decision tree to construct a classification model in order to differentiate PM-DILI from HBV and AIH. The model was highly effective with sensitivity of 92.3% and specificity of 88.9%. Conclusions: This study presents an integrated view of the metabolic features of PM-DILI induced by herbal medicine, and the four-metabolite decision tree technique imparts a potent tool in clinical diagnosis.
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Affiliation(s)
- Ying Huang
- College of Pharmacy, Hunan University of Chinese Medicine, Changsha, China.,China Military Institute of Chinese Medicine, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Xu Zhao
- China Military Institute of Chinese Medicine, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Zi-Teng Zhang
- China Military Institute of Chinese Medicine, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Shuai-Shuai Chen
- China Military Institute of Chinese Medicine, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Shan-Shan Li
- China Military Institute of Chinese Medicine, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Zhuo Shi
- China Military Institute of Chinese Medicine, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Jing Jing
- China Military Institute of Chinese Medicine, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Ang Huang
- Center for Non-Infectious Liver Disease, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Yu-Ming Guo
- China Military Institute of Chinese Medicine, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Zhao-Fang Bai
- China Military Institute of Chinese Medicine, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Zheng-Sheng Zou
- Center for Non-Infectious Liver Disease, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Xiao-He Xiao
- China Military Institute of Chinese Medicine, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Jia-Bo Wang
- China Military Institute of Chinese Medicine, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Ming Niu
- China Military Institute of Chinese Medicine, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China.,Department of Poisoning Treatment, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
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Tang J, Xiong K, Zhang T, Han Han. Application of Metabolomics in Diagnosis and Treatment of Chronic Liver Diseases. Crit Rev Anal Chem 2020; 52:906-916. [PMID: 33146026 DOI: 10.1080/10408347.2020.1842172] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Chronic liver disease represents stepwise destruction of the liver parenchyma after chronic liver injury, which is often difficult to be diagnosed accurately. Thus, the development of specific biomarkers of chronic liver disease is important. Metabolomics is a powerful tool for biomarker exploration, which enables the exploration of disease pathogenesis or drug action mechanisms at the global metabolic level. The metabolomics workflow generally includes collection, preparation, and analysis of samples, and data processing and bioinformatics. A metabolomics study can simultaneously detect the dysfunctions in the glucose, lipid, amino-acid, and nucleotide metabolisms. Hence, it facilitates the obtaining of a better understanding of the pathogenesis of chronic liver disease and its diagnosis. Many effective drugs could reverse the change of comprehensive biochemical phenotypes induced by chronic liver disease. They can even potentially restore the normal metabolic signatures of patients. Increasingly more researchers have begun to apply metabolomics technologies to diagnose chronic liver disease and investigate the mechanism of action of effective drugs or the variations in drug responses. We are convinced that deepening the understanding of the metabolic alterations could extend their use as powerful biomarkers, promoting the more effective clinical diagnosis and treatment of chronic liver disease in the future.
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Affiliation(s)
- Jie Tang
- Experiment Center for Teaching and Learning, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Kai Xiong
- Experiment Center for Teaching and Learning, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Tong Zhang
- Experiment Center for Teaching and Learning, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Han Han
- Experiment Center for Teaching and Learning, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, China
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Comprehensive Dipeptide Analysis Revealed Cancer-Specific Profile in the Liver of Patients with Hepatocellular Carcinoma and Hepatitis. Metabolites 2020; 10:metabo10110442. [PMID: 33139606 PMCID: PMC7692321 DOI: 10.3390/metabo10110442] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/28/2020] [Accepted: 10/28/2020] [Indexed: 02/06/2023] Open
Abstract
As the physical properties and functionality of dipeptides differ from those of amino acids, they have attracted attention in metabolomics; however, their functions in vivo have not been clarified in detail. Hepatocellular carcinoma (HCC) is the most common type of primary liver cancer, and its major cause is chronic hepatitis. This study was conducted to explore tumor-specific dipeptide characteristics by performing comprehensive dipeptide analysis in the tumor and surrounding nontumor tissue of patients with HCC. Dipeptides were analyzed by liquid chromatography tandem mass spectrometry and capillary electrophoresis tandem mass spectrometry. Principal component analysis using 236 detected dipeptides showed differences in the dipeptide profiles between nontumor and tumor tissues; however, no clear difference was observed in etiological comparison. In addition, the N- and C-terminal amino acid compositions of the detected dipeptides significantly differed, suggesting the substrate specificity of enzyme proteins, such as peptidase. Furthermore, hepatitis-derived HCC may show a characteristic dipeptide profile even before tumor formation. These results provide insight into HCC pathogenesis and may help identify novel biomarkers for diagnosis.
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46
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Parker ET, Karki M, Glavin DP, Dworkin JP, Krishnamurthy R. A sensitive quantitative analysis of abiotically synthesized short homopeptides using ultraperformance liquid chromatography and time-of-flight mass spectrometry. J Chromatogr A 2020; 1630:461509. [PMID: 32927393 DOI: 10.1016/j.chroma.2020.461509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 08/04/2020] [Accepted: 08/22/2020] [Indexed: 10/23/2022]
Abstract
In the origins of life field understanding the abiotic polymerization of simple organic monomers (e.g., amino acids) into larger biomolecules (e.g., oligopeptides), remains a seminal challenge. Recently, preliminary observations showed a limited set of peptides formed in the presence of the plausible prebiotic phosphorylating agent, diamidophosphate (DAP), highlighting the need for an analytical tool to critically evaluate the ability of DAP to induce oligomerization of simple organics under aqueous conditions. However, performing accurate and precise, targeted analyses of short oligopeptides remains a distinct challenge in the analytical chemistry field. Here, we developed a new technique to detect and quantitate amino acids and their homopeptides in a single run using ultraperformance liquid chromatography-fluorescence detection/time of flight mass spectrometry. Over an 8-minute retention time window, 18 target analytes were identified and quantitated, 16 of which were chromatographically separated at, or near baseline resolution. Compound identity was confirmed by accurate mass analysis using a 10 ppm mass tolerance window. This method featured limits of detection < 5 nM (< 1 fmol on column) and limits of quantitation (LOQs) <15 nM (< 3 fmol on column). The LODs and LOQs were upwards of ∼28x and ∼788x lower, respectively, than previous methods for the same analytes, highlighting the quantifiable advantages of this new method. Both detectors provided good quantitative linearity (R2 > 0.985) for all analytes spanning concentration ranges ∼3 - 4 orders of magnitude. We performed a series of laboratory experiments to investigate DAP-mediated oligomerization of amino acids and peptides and analyzed experimental products with the new method. DAP readily polymerized amino acids and peptides under a range of simulated environmental conditions. This research underscores the potential of DAP to have generated oligopeptides on the primordial Earth, enhancing prebiotic chemical diversity and complexity at or near the origin of life.
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Affiliation(s)
- Eric T Parker
- NASA Goddard Space Flight Center, Solar System Exploration Division, 8800 Greenbelt Road, Greenbelt, MD 20771, United States
| | - Megha Karki
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, CA 92037, United States
| | - Daniel P Glavin
- NASA Goddard Space Flight Center, Solar System Exploration Division, 8800 Greenbelt Road, Greenbelt, MD 20771, United States
| | - Jason P Dworkin
- NASA Goddard Space Flight Center, Solar System Exploration Division, 8800 Greenbelt Road, Greenbelt, MD 20771, United States.
| | - Ramanarayanan Krishnamurthy
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, CA 92037, United States.
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Low-Density Lipoprotein (LDL)-Triglyceride and Its Ratio to LDL-Cholesterol as Diagnostic Biomarkers for Nonalcoholic Steatohepatitis. J Appl Lab Med 2020; 5:1206-1215. [DOI: 10.1093/jalm/jfaa044] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 02/14/2020] [Indexed: 12/20/2022]
Abstract
Abstract
Background
Nonalcoholic fatty liver disease (NAFLD) is the most common type of liver disease, but it is difficult to distinguish its pathogenic phenotype, nonalcoholic steatohepatitis (NASH), from nonalcoholic fatty liver (NAFL) without a liver biopsy. We analyzed serum lipids, including low-density lipoprotein triglyceride (LDL-TG), to elucidate their usefulness for diagnosing NASH.
Patients and Methods
Serum samples obtained from 35 NASH and 9 NAFL biopsy-confirmed patients and 6 healthy volunteers (HLT) were studied for 13 lipid-related markers and compared between HLT, NAFL, and NASH groups. The relationship between histological findings and the lipid markers was also analyzed.
Results
There were significant differences in triglyceride, LDL-TG, the ratio of LDL-TG to the LDL-cholesterol (LDL-TG/LDL-C), small dense LDL-C, and apolipoprotein E between the three groups. Among the 5 lipid components, serum LDL-TG level and the ratio of LDL-TG to the LDL-cholesterol (LDL-TG/LDL-C) were significantly elevated in NASH. The median concentrations of LDL-TG in HLT, NAFL, and NASH were 9, 15, and 20 mg/dL (P < 0.001), and those of LDL-TG/LDL-C were 0.097, 0.102, and 0.173 (P < 0.001), respectively. Although the degree of steatosis was not correlated with the LDL-TG/LDL-C, the ratio was significantly higher in patients with lobular inflammation (P = 0.071), ballooning (P = 0.031), and fibrosis (P < 0.001). The area under the receiver operating characteristic curve of the ratio for distinguishing NASH from NAFL was 0.857. The rest of studied markers showed no significant utility.
Conclusion
Serum LDL-TG levels and the LDL-TG/LDL-C ratio might serve as simple and noninvasive diagnostic biomarkers for NASH.
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Miller-Atkins G, Acevedo-Moreno LA, Grove D, Dweik RA, Tonelli AR, Brown JM, Allende DS, Aucejo F, Rotroff DM. Breath Metabolomics Provides an Accurate and Noninvasive Approach for Screening Cirrhosis, Primary, and Secondary Liver Tumors. Hepatol Commun 2020; 4:1041-1055. [PMID: 32626836 PMCID: PMC7327218 DOI: 10.1002/hep4.1499] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 12/30/2019] [Accepted: 02/07/2020] [Indexed: 12/20/2022] Open
Abstract
Hepatocellular carcinoma (HCC) and secondary liver tumors, such as colorectal cancer liver metastases are significant contributors to the overall burden of cancer‐related morality. Current biomarkers, such as alpha‐fetoprotein (AFP) for HCC, result in too many false negatives, necessitating noninvasive approaches with improved sensitivity. Volatile organic compounds (VOCs) detected in the breath of patients can provide valuable insight into disease processes and can differentiate patients by disease status. Here, we investigate whether 22 VOCs from the breath of 296 patients can distinguish those with no liver disease (n = 54), cirrhosis (n = 30), HCC (n = 112), pulmonary hypertension (n = 49), or colorectal cancer liver metastases (n = 51). This work extends previous studies by evaluating the ability for VOC signatures to differentiate multiple diseases in a large cohort of patients. Pairwise disease comparisons demonstrated that most of the VOCs tested are present in significantly different relative abundances (false discovery rate P < 0.1), indicating broad impacts on the breath metabolome across diseases. A predictive model developed using random forest machine learning and cross validation classified patients with 85% classification accuracy and 75% balanced accuracy. Importantly, the model detected HCC with 73% sensitivity compared with 53% for AFP in the same cohort. An added value of this approach is that influential VOCs in the predictive model may provide insight into disease etiology. Acetaldehyde and acetone, both of which have roles in tumor promotion, were considered important VOCs for differentiating disease groups in the predictive model and were increased in patients with cirrhosis and HCC compared to patients with no liver disease (false discovery rate P < 0.1). Conclusion: The use of machine learning and breath VOCs shows promise as an approach to develop improved, noninvasive screening tools for chronic liver disease and primary and secondary liver tumors.
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Affiliation(s)
- Galen Miller-Atkins
- Department of Quantitative Health Sciences Lerner Research Institute Cleveland Clinic Cleveland OH
| | | | - David Grove
- Department of Inflammation and Immunity Lerner Research Institute Cleveland Clinic Cleveland OH
| | - Raed A Dweik
- Respiratory Institute Cleveland Clinic Cleveland OH
| | | | - J Mark Brown
- Department of Cardiovascular and Metabolic Sciences Cleveland Clinic Cleveland OH.,Center for Microbiome in Human Health Cleveland Clinic Cleveland OH
| | | | | | - Daniel M Rotroff
- Department of Quantitative Health Sciences Lerner Research Institute Cleveland Clinic Cleveland OH
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Takahashi S, Saegusa J, Onishi A, Morinobu A. Biomarkers identified by serum metabolomic analysis to predict biologic treatment response in rheumatoid arthritis patients. Rheumatology (Oxford) 2020; 58:2153-2161. [PMID: 31143951 DOI: 10.1093/rheumatology/kez199] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 04/23/2019] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES Biologic treatment has recently revolutionized the management of RA. Despite this success, ∼30-40% of the patients undergoing biologic treatment respond insufficiently. The aim of this study was to identify several specific reliable metabolites for predicting the response of RA patients to TNF-α inhibitors (TNFi) and abatacept (ABT), using capillary electrophoresis-time-of-flight mass spectrometry (CE-TOFMS). METHODS We collected serum from RA patients with moderate or high disease activity prior to biologic treatment, and obtained the serum metabolomic profiles of these samples using CE-TOFMS. The patients' response was determined 12 weeks after starting biologic treatment, according to the EULAR response criteria. We compared the metabolites between the response and non-response patient groups and analysed their discriminative ability. RESULTS Among 43 total patients, 14 of 26 patients in the TNFi group and 6 of 17 patients in the ABT group responded to the biologic treatment. Of the metabolites separated by CE-TOFMS, 196 were identified as known substances. Using an orthogonal partial least-squares discriminant analysis, we identified five metabolites as potential predictors of TNFi responders and three as predictors of ABT responders. Receiver operating characteristic analyses for multiple biomarkers revealed an area under the curve (AUC) of 0.941, with a sensitivity of 85.7% and specificity of 100% for TNFi, and an AUC of 0.985, with a sensitivity of 100% and specificity of 90.9% for ABT. CONCLUSION By metabolomic analysis, we identified serum biomarkers that have a high ability to predict the response of RA patients to TNFi or ABT treatment.
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Affiliation(s)
- Soshi Takahashi
- Department of Rheumatology and Clinical Immunology, Kobe University Graduate School of Medicine, Kobe,Japan.,Centre for Rheumatic Disease, Shinko Hospital, Kobe,Japan
| | - Jun Saegusa
- Department of Rheumatology and Clinical Immunology, Kobe University Graduate School of Medicine, Kobe,Japan
| | - Akira Onishi
- Department of Rheumatology and Clinical Immunology, Kobe University Graduate School of Medicine, Kobe,Japan
| | - Akio Morinobu
- Department of Rheumatology and Clinical Immunology, Kobe University Graduate School of Medicine, Kobe,Japan
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Hagenbeek FA, Roetman PJ, Pool R, Kluft C, Harms AC, van Dongen J, Colins OF, Talens S, van Beijsterveldt CEM, Vandenbosch MMLJZ, de Zeeuw EL, Déjean S, Fanos V, Ehli EA, Davies GE, Hottenga JJ, Hankemeier T, Bartels M, Vermeiren RRJM, Boomsma DI. Urinary Amine and Organic Acid Metabolites Evaluated as Markers for Childhood Aggression: The ACTION Biomarker Study. Front Psychiatry 2020; 11:165. [PMID: 32296350 PMCID: PMC7138132 DOI: 10.3389/fpsyt.2020.00165] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 02/21/2020] [Indexed: 01/05/2023] Open
Abstract
Biomarkers are of interest as potential diagnostic and predictive instruments in personalized medicine. We present the first urinary metabolomics biomarker study of childhood aggression. We aim to examine the association of urinary metabolites and neurotransmitter ratios involved in key metabolic and neurotransmitter pathways in a large cohort of twins (N = 1,347) and clinic-referred children (N = 183) with an average age of 9.7 years. This study is part of ACTION (Aggression in Children: Unraveling gene-environment interplay to inform Treatment and InterventiON strategies), in which we developed a standardized protocol for large-scale collection of urine samples in children. Our analytical design consisted of three phases: a discovery phase in twins scoring low or high on aggression (N = 783); a replication phase in twin pairs discordant for aggression (N = 378); and a validation phase in clinical cases and matched twin controls (N = 367). In the discovery phase, 6 biomarkers were significantly associated with childhood aggression, of which the association of O-phosphoserine (β = 0.36; SE = 0.09; p = 0.004), and gamma-L-glutamyl-L-alanine (β = 0.32; SE = 0.09; p = 0.01) remained significant after multiple testing. Although non-significant, the directions of effect were congruent between the discovery and replication analyses for six biomarkers and two neurotransmitter ratios and the concentrations of 6 amines differed between low and high aggressive twins. In the validation analyses, the top biomarkers and neurotransmitter ratios, with congruent directions of effect, showed no significant associations with childhood aggression. We find suggestive evidence for associations of childhood aggression with metabolic dysregulation of neurotransmission, oxidative stress, and energy metabolism. Although replication is required, our findings provide starting points to investigate causal and pleiotropic effects of these dysregulations on childhood aggression.
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Affiliation(s)
- Fiona A. Hagenbeek
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, Netherlands
| | - Peter J. Roetman
- Curium-LUMC, Department of Child and Adolescent Psychiatry, Leiden University Medical Center, Leiden, Netherlands
| | - René Pool
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, Netherlands
| | | | - Amy C. Harms
- Division of Analytical Biosciences, Leiden Academic Center for Drug Research, Leiden University, Leiden, Netherlands
- The Netherlands Metabolomics Centre, Leiden, Netherlands
| | - Jenny van Dongen
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, Netherlands
| | - Olivier F. Colins
- Curium-LUMC, Department of Child and Adolescent Psychiatry, Leiden University Medical Center, Leiden, Netherlands
- Department Special Needs Education, Ghent University, Ghent, Belgium
| | | | | | | | - Eveline L. de Zeeuw
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, Netherlands
| | - Sébastien Déjean
- Toulouse Mathematics Institute, University of Toulouse, CNRS, Toulouse, France
| | - Vassilios Fanos
- Department of Surgical Sciences, University of Cagliari and Neonatal Intensive Care Unit, Cagliari, Italy
| | - Erik A. Ehli
- Avera Institute for Human Genetics, Sioux Falls, SD, United States
| | - Gareth E. Davies
- Avera Institute for Human Genetics, Sioux Falls, SD, United States
| | - Jouke Jan Hottenga
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Thomas Hankemeier
- Division of Analytical Biosciences, Leiden Academic Center for Drug Research, Leiden University, Leiden, Netherlands
- The Netherlands Metabolomics Centre, Leiden, Netherlands
| | - Meike Bartels
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, Netherlands
- Amsterdam Neuroscience, Amsterdam, Netherlands
| | - Robert R. J. M. Vermeiren
- Curium-LUMC, Department of Child and Adolescent Psychiatry, Leiden University Medical Center, Leiden, Netherlands
| | - Dorret I. Boomsma
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, Netherlands
- Amsterdam Neuroscience, Amsterdam, Netherlands
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