1
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Liu J, Qin M, Shi Y, Jiang R, Wang Z, Zhang L, Zhao Y, Gao H, Li M, Huang C. Volatile carbonyl metabolites analysis of nanoparticle exposed lung cells in an organ-on-a-chip system. Talanta 2024; 274:126066. [PMID: 38599125 DOI: 10.1016/j.talanta.2024.126066] [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: 12/29/2023] [Revised: 03/29/2024] [Accepted: 04/05/2024] [Indexed: 04/12/2024]
Abstract
The evaluation of nanoparticles (NPs) cytotoxicity is crucial for advancing nanotechnology and assessing environmental pollution. However, existing methods for NPs cytotoxicity evaluation suffer from limited accuracy and inadequate information content. In the study, we developed a novel detection platform that enables the identification of cellular carbonyl metabolites at the organ level. The platform is integrated with a cell co-culture lung organ chip (LOC) and a micropillar concentrator. Notably, our work represents the successful measurement of the amounts of cellular metabolites on LOC system. The volatile carbonyl metabolites (VCMs) generated by cells exposure to various types of NPs with different concentrations were captured and detected by high-resolution mass spectrometry (MS). Compared with conventional cell viability and reactive oxygen species (ROS) analysis, our method discerns the toxicological impact of NPs at low concentrations by analyzed VCM at levels as low as ppb level. The LOC system based metabolic gas detection confirmed that low concentrations of NPs have a toxic effect on the cell model, which was not reflected in the fluorescence detection, and the effect of NP material is more significant than the size effect. Furthermore, this method can distinguish different NPs acting on cell models through cluster analysis of multiple VCMs.
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Affiliation(s)
- Jinlong Liu
- Institute of Microelectronics of the Chinese Academy of Sciences, China; University of Chinese Academy of Science, China
| | - Meiyan Qin
- Institute of Microelectronics of the Chinese Academy of Sciences, China; University of Chinese Academy of Science, China
| | - Yimin Shi
- Institute of Microelectronics of the Chinese Academy of Sciences, China; University of Chinese Academy of Science, China
| | - Rui Jiang
- Institute of Microelectronics of the Chinese Academy of Sciences, China; University of Chinese Academy of Science, China
| | - Zizhen Wang
- Institute of Microelectronics of the Chinese Academy of Sciences, China; University of Chinese Academy of Science, China
| | - Lingqian Zhang
- Institute of Microelectronics of the Chinese Academy of Sciences, China
| | - Yang Zhao
- Institute of Microelectronics of the Chinese Academy of Sciences, China
| | - Hang Gao
- Institute of Microelectronics of the Chinese Academy of Sciences, China
| | - Mingxiao Li
- Institute of Microelectronics of the Chinese Academy of Sciences, China.
| | - Chengjun Huang
- Institute of Microelectronics of the Chinese Academy of Sciences, China; University of Chinese Academy of Science, China
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2
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Lin W, Mellinghaus K, Rodriguez-Mateos A, Globisch D. Identification of nutritional biomarkers through highly sensitive and chemoselective metabolomics. Food Chem 2023; 425:136481. [PMID: 37276670 DOI: 10.1016/j.foodchem.2023.136481] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 04/19/2023] [Accepted: 05/26/2023] [Indexed: 06/07/2023]
Abstract
The importance of a healthy diet for humans is known for decades. The elucidation of key molecules responsible for the beneficial and adverse dietary effects is slowly developing as the tools are missing. Carbonyl-containing metabolites are a common bioproducts through conversion of diet by the microbiome. In here, we have utilized our recently developed mass spectrometric methodology based on chemoselective conjugation of carbonyl-metabolites. The method has been applied for urine sample analysis from a dietary (poly)phenol intervention study (N = 78 individuals) for the first time. We have identified a series of carbonyl-metabolites of dietary origin and the chemical structure was validated for 30 metabolites. Our sensitive analysis led to the discovery of four unknown dietary markers with high sensitivity and selectivity (AUC > 0.91). Our chemical metabolomics method has been successfully applied for large-scale analysis and provides the basis for targeted metabolomics to identify unknown nutritional and disease-related biomarkers.
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Affiliation(s)
- Weifeng Lin
- Department of Chemistry - BMC, Science for Life Laboratory, Uppsala University, Box 576, SE-75124 Uppsala, Sweden
| | - Kiana Mellinghaus
- Department of Chemistry - BMC, Science for Life Laboratory, Uppsala University, Box 576, SE-75124 Uppsala, Sweden
| | - Ana Rodriguez-Mateos
- Department of Nutritional Sciences, School of Life Course and Population Sciences, Faculty of Life Sciences and Medicine, King's College London, UK
| | - Daniel Globisch
- Department of Chemistry - BMC, Science for Life Laboratory, Uppsala University, Box 576, SE-75124 Uppsala, Sweden.
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3
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Kaur A, Lin W, Dovhalyuk V, Driutti L, Di Martino ML, Vujasinovic M, Löhr JM, Sellin ME, Globisch D. Chemoselective bicyclobutane-based mass spectrometric detection of biological thiols uncovers human and bacterial metabolites. Chem Sci 2023; 14:5291-5301. [PMID: 37234898 PMCID: PMC10207876 DOI: 10.1039/d3sc00224a] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 04/05/2023] [Indexed: 05/28/2023] Open
Abstract
Sulfur is an essential element of life. Thiol-containing metabolites in all organisms are involved in the regulation of diverse biological processes. Especially, the microbiome produces bioactive metabolites or biological intermediates of this compound class. The analysis of thiol-containing metabolites is challenging due to the lack of specific tools, making these compounds difficult to investigate selectively. We have now developed a new methodology comprising bicyclobutane for chemoselective and irreversible capturing of this metabolite class. We utilized this new chemical biology tool immobilized onto magnetic beads for the investigation of human plasma, fecal samples, and bacterial cultures. Our mass spectrometric investigation detected a broad range of human, dietary and bacterial thiol-containing metabolites and we even captured the reactive sulfur species cysteine persulfide in both fecal and bacterial samples. The described comprehensive methodology represents a new mass spectrometric strategy for the discovery of bioactive thiol-containing metabolites in humans and the microbiome.
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Affiliation(s)
- Amanpreet Kaur
- Department of Chemistry - BMC, Science for Life Laboratory, Uppsala University 75124 Uppsala Sweden
| | - Weifeng Lin
- Department of Chemistry - BMC, Science for Life Laboratory, Uppsala University 75124 Uppsala Sweden
| | - Vladyslav Dovhalyuk
- Department of Chemistry - BMC, Science for Life Laboratory, Uppsala University 75124 Uppsala Sweden
| | - Léna Driutti
- Department of Chemistry - BMC, Science for Life Laboratory, Uppsala University 75124 Uppsala Sweden
| | - Maria Letizia Di Martino
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University 75123 Uppsala Sweden
| | - Miroslav Vujasinovic
- Department for Digestive Diseases, Karolinska University Hospital Stockholm Sweden
| | - J-Matthias Löhr
- Department for Digestive Diseases, Karolinska University Hospital Stockholm Sweden
- Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institute Stockholm Sweden
| | - Mikael E Sellin
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University 75123 Uppsala Sweden
| | - Daniel Globisch
- Department of Chemistry - BMC, Science for Life Laboratory, Uppsala University 75124 Uppsala Sweden
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4
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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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Zhang M, Lai Z, Zhang R, Liu S, Tian H, Qiu Y, Li D, Zhou J, Li Z. Polyurea-Modified Magnetic Particles with Versatile Probes for Chemoselective Capture of Carbonyl Metabolites and Biomarker Discovery. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2204734. [PMID: 36354199 DOI: 10.1002/smll.202204734] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 10/11/2022] [Indexed: 06/16/2023]
Abstract
Playing a great role in human physiologies and pathologies, carbonyl metabolites are intimately associated with a variety of diseases, though the effective analysis method of them remains a challenge. A hydrazide-terminated polyurea-modified magnetic particle (HPMP) with versatile probes is developed to address this issue. The capture ability of HPMPs for carbonyl metabolite is more than 1200 µmol g-1 , which is increased by 4 orders of magnitude via the introduction of polyurea. With a broad linear range of over 4 orders of magnitude, remarkably improved sensitivity, and limit of detection at attomole quantities, HPMPs are applied in relative quantification of more than 1500 carbonyl metabolites in 113 human serum samples with high throughput and high coverage. The combined indicators of these metabolites demonstrates a great diagnostic accuracy for distinguishing between health and disease subjects as well as differentiating the patients with benign lung disease and lung cancer. Combining powerful capture ability, low-cost preparation, and convenient operation, the HPMPs demonstrate extensive application in biomarker discovery and the detailed study of the biochemical landscape.
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Affiliation(s)
- Mo Zhang
- Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
| | - Zhizhen Lai
- Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
| | - Renjun Zhang
- Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
| | - Shuai Liu
- Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
| | - Hongtao Tian
- Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
| | - Yuming Qiu
- Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
| | - Dan Li
- Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
| | - Jiang Zhou
- Analytical Instrumentation Center, College of Chemistry and Molecular Engineering, Peking University, 292 Chengfu Road, Beijing, 100871, China
| | - Zhili Li
- Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
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6
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Wang SY, Liu H, Zhu JH, Zhou SS, Xu JD, Zhou J, Mao Q, Kong M, Li SL, Zhu H. 2,4-dinitrophenylhydrazine capturing combined with mass defect filtering strategy to identify aliphatic aldehydes in biological samples. J Chromatogr A 2022; 1679:463405. [DOI: 10.1016/j.chroma.2022.463405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 08/03/2022] [Accepted: 08/05/2022] [Indexed: 10/15/2022]
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7
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Wei YB, Luo D, Xiong X, Huang YL, Xie M, Lu W, Li D. Biomimetic mimicry of formaldehyde-induced DNA-protein crosslinks in the confined space of a metal-organic framework. Chem Sci 2022; 13:4813-4820. [PMID: 35655868 PMCID: PMC9067591 DOI: 10.1039/d2sc00188h] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 03/18/2022] [Indexed: 02/05/2023] Open
Abstract
DNA-protein crosslinks (DPCs) are highly toxic DNA lesions induced by crosslinking agents such as formaldehyde (HCHO). Building artificial models to simulate the crosslinking process would advance our understanding of the underlying mechanisms and therefore develop coping strategies accordingly. Herein we report the design and synthesis of a Zn-based metal-organic framework with mixed ligands of 2,6-diaminopurine and amine-functionalized dicarboxylate, representing DNA and protein residues, respectively. Combined characterization techniques allow us to demonstrate the unusual efficiency of HCHO-crosslinking within the confined space of the titled MOF. Particularly, in situ single-crystal X-ray diffraction studies reveal a sequential methylene-knitting process upon HCHO addition, along with strong fluorescence that was not interfered with by other metabolites, glycine, and Tris. This work has successfully constructed a purine-based metal-organic framework with unoccupied Watson-Crick sites, serving as a crystalline model for HCHO-induced DPCs by mimicking the confinement effect of protein/DNA interactions.
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Affiliation(s)
- Yu-Bai Wei
- College of Chemistry and Materials Science, Guangdong Provincial Key Laboratory of Functional Supramolecular Coordination Materials and Applications, Jinan University Guangzhou 510632 P. R. China
| | - Dong Luo
- College of Chemistry and Materials Science, Guangdong Provincial Key Laboratory of Functional Supramolecular Coordination Materials and Applications, Jinan University Guangzhou 510632 P. R. China
| | - Xiao Xiong
- College of Chemistry and Materials Science, Guangdong Provincial Key Laboratory of Functional Supramolecular Coordination Materials and Applications, Jinan University Guangzhou 510632 P. R. China
| | - Yong-Liang Huang
- Department of Chemistry, Shantou University Medical College Shantou Guangdong 515041 P. R. China
| | - Mo Xie
- College of Chemistry and Materials Science, Guangdong Provincial Key Laboratory of Functional Supramolecular Coordination Materials and Applications, Jinan University Guangzhou 510632 P. R. China
| | - Weigang Lu
- College of Chemistry and Materials Science, Guangdong Provincial Key Laboratory of Functional Supramolecular Coordination Materials and Applications, Jinan University Guangzhou 510632 P. R. China
| | - Dan Li
- College of Chemistry and Materials Science, Guangdong Provincial Key Laboratory of Functional Supramolecular Coordination Materials and Applications, Jinan University Guangzhou 510632 P. R. China
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8
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Müller MJ, Dorst A, Paulus C, Khan I, Sieber S. Catch-enrich-release approach for amine-containing natural products. Chem Commun (Camb) 2022; 58:12560-12563. [DOI: 10.1039/d2cc04905h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Chemoselective approach to extract amine-containing natural products from complex matrices. The enzymatic release from the probe affords the underivatised compounds as products.
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Affiliation(s)
| | - Andrea Dorst
- Department of Chemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Constanze Paulus
- Department of Chemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Imran Khan
- Department of Chemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Simon Sieber
- Department of Chemistry, University of Zurich, 8057 Zurich, Switzerland
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9
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Vallianatou T, Bèchet NB, Correia MSP, Lundgaard I, Globisch D. Regional Brain Analysis of Modified Amino Acids and Dipeptides during the Sleep/Wake Cycle. Metabolites 2021; 12:metabo12010021. [PMID: 35050142 PMCID: PMC8780251 DOI: 10.3390/metabo12010021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 12/19/2021] [Accepted: 12/22/2021] [Indexed: 12/18/2022] Open
Abstract
Sleep is a state in which important restorative and anabolic processes occur. Understanding changes of these metabolic processes during the circadian rhythm in the brain is crucial to elucidate neurophysiological mechanisms important for sleep function. Investigation of amino acid modifications and dipeptides has recently emerged as a valuable approach in the metabolic profiling of the central nervous system. Nonetheless, very little is known about the effects of sleep on the brain levels of amino acid analogues. In the present study, we examined brain regional sleep-induced alterations selective for modified amino acids and dipeptides using Ultra-high performance liquid chromatography-MS/MS (UHPLC-MS/MS) based metabolomics. Our approach enabled the detection and identification of numerous amino acid-containing metabolites in the cortex, the hippocampus, the midbrain, and the cerebellum. In particular, analogues of the aromatic amino acids phenylalanine, tyrosine and tryptophan were significantly altered during sleep in the investigated brain regions. Cortical levels of medium and long chain N-acyl glycines were higher during sleep. Regional specific changes were also detected, especially related to tyrosine analogues in the hippocampus and the cerebellum. Our findings demonstrate a strong correlation between circadian rhythms and amino acid metabolism specific for different brain regions that provide previously unknown insights in brain metabolism.
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Affiliation(s)
- Theodosia Vallianatou
- Science for Life Laboratory, Department of Chemistry-BMC, Uppsala University, Box 599, SE-75124 Uppsala, Sweden; (T.V.); (M.S.P.C.)
| | - Nicholas B. Bèchet
- Department of Experimental Medical Science, Lund University, SE-22362 Lund, Sweden; (N.B.B.); (I.L.)
- Wallenberg Centre for Molecular Medicine, Lund University, SE-22362 Lund, Sweden
| | - Mario S. P. Correia
- Science for Life Laboratory, Department of Chemistry-BMC, Uppsala University, Box 599, SE-75124 Uppsala, Sweden; (T.V.); (M.S.P.C.)
| | - Iben Lundgaard
- Department of Experimental Medical Science, Lund University, SE-22362 Lund, Sweden; (N.B.B.); (I.L.)
- Wallenberg Centre for Molecular Medicine, Lund University, SE-22362 Lund, Sweden
| | - Daniel Globisch
- Science for Life Laboratory, Department of Chemistry-BMC, Uppsala University, Box 599, SE-75124 Uppsala, Sweden; (T.V.); (M.S.P.C.)
- Correspondence:
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10
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Lin W, Conway LP, Vujasinovic M, Löhr J, Globisch D. Chemoselective and Highly Sensitive Quantification of Gut Microbiome and Human Metabolites. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202107101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Weifeng Lin
- Department of Chemistry—BMC Science for Life Laboratory Uppsala University, Box 599 75124 Uppsala Sweden
| | - Louis P. Conway
- Department of Chemistry—BMC Science for Life Laboratory Uppsala University, Box 599 75124 Uppsala Sweden
| | - Miroslav Vujasinovic
- Department for Digestive Diseases Karolinska University Hospital Stockholm Sweden
| | - J.‐Matthias Löhr
- Department for Digestive Diseases Karolinska University Hospital Stockholm Sweden
- Department of Clinical Science Intervention and Technology (CLINTEC) Karolinska Institute Stockholm Sweden
| | - Daniel Globisch
- Department of Chemistry—BMC Science for Life Laboratory Uppsala University, Box 599 75124 Uppsala Sweden
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11
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Progress and Challenges in Quantifying Carbonyl-Metabolomic Phenomes with LC-MS/MS. Molecules 2021; 26:molecules26206147. [PMID: 34684729 PMCID: PMC8541004 DOI: 10.3390/molecules26206147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 09/30/2021] [Accepted: 10/01/2021] [Indexed: 12/17/2022] Open
Abstract
Carbonyl-containing metabolites widely exist in biological samples and have important physiological functions. Thus, accurate and sensitive quantitative analysis of carbonyl-containing metabolites is crucial to provide insight into metabolic pathways as well as disease mechanisms. Although reversed phase liquid chromatography electrospray ionization mass spectrometry (RPLC-ESI-MS) is widely used due to the powerful separation capability of RPLC and high specificity and sensitivity of MS, but it is often challenging to directly analyze carbonyl-containing metabolites using RPLC-ESI-MS due to the poor ionization efficiency of neutral carbonyl groups in ESI. Modification of carbonyl-containing metabolites by a chemical derivatization strategy can overcome the obstacle of sensitivity; however, it is insufficient to achieve accurate quantification due to instrument drift and matrix effects. The emergence of stable isotope-coded derivatization (ICD) provides a good solution to the problems encountered above. Thus, LC-MS methods that utilize ICD have been applied in metabolomics including quantitative targeted analysis and untargeted profiling analysis. In addition, ICD makes multiplex or multichannel submetabolome analysis possible, which not only reduces instrument running time but also avoids the variation of MS response. In this review, representative derivatization reagents and typical applications in absolute quantification and submetabolome profiling are discussed to highlight the superiority of the ICD strategy for detection of carbonyl-containing metabolites.
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12
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Lin W, Yang Z, Kaur A, Block A, Vujasinovic M, Löhr JM, Globisch D. Squaric acid as a new chemoselective moiety for mass spectrometry-based metabolomics analysis of amines. RSC Chem Biol 2021; 2:1479-1483. [PMID: 34704052 PMCID: PMC8496035 DOI: 10.1039/d1cb00132a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 08/10/2021] [Indexed: 12/24/2022] Open
Abstract
The investigation of microbiome-derived metabolites is important to understand metabolic interactions with their human host. New methodologies for mass spectrometric discovery of undetected metabolites with unknown bioactivity are required. Herein, we introduce squaric acid as a new chemoselective moiety for amine metabolite analysis in human fecal samples.
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Affiliation(s)
- Weifeng Lin
- Department of Chemistry-BMC, Science for Life Laboratory, Uppsala University, Box 599 Uppsala SE-75124 Sweden
| | - Zhen Yang
- Department of Chemistry-BMC, Science for Life Laboratory, Uppsala University, Box 599 Uppsala SE-75124 Sweden
| | - Amanpreet Kaur
- Department of Chemistry-BMC, Science for Life Laboratory, Uppsala University, Box 599 Uppsala SE-75124 Sweden
| | - Annika Block
- Department of Chemistry-BMC, Science for Life Laboratory, Uppsala University, Box 599 Uppsala SE-75124 Sweden
| | - Miroslav Vujasinovic
- Department for Digestive Diseases, Karolinska University Hospital Stockholm Sweden
| | - J-Matthias Löhr
- Department for Digestive Diseases, Karolinska University Hospital Stockholm Sweden
- Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institute Stockholm Sweden
| | - Daniel Globisch
- Department of Chemistry-BMC, Science for Life Laboratory, Uppsala University, Box 599 Uppsala SE-75124 Sweden
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13
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Kijewska M, Koch T, Waliczek M, Konieczny A, Stefanowicz P, Szewczuk Z. Selective ESI-MS detection of carbonyl containing compounds by aminooxyacetic acid immobilized on a resin. Anal Chim Acta 2021; 1176:338767. [PMID: 34399903 DOI: 10.1016/j.aca.2021.338767] [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: 04/22/2021] [Revised: 05/28/2021] [Accepted: 06/14/2021] [Indexed: 10/21/2022]
Abstract
There are numerous examples of bioactive compounds containing carbonyl groups including modified proteins with oxidation of side chain of amino acid residues to aldehyde/ketone groups which are frequently considered as markers of oxidative stress. The carbonyl unit can be also distinguished as a substructure in many illegal drugs including anabolic steroids as well as cations derivatives. Based on chemoselective formation of oximes by solid phase immobilized hydroxylamine derivatives we proposed the protocol for derivatization and selective detection of carbonylated compounds in human serum albumin hydrolysate as a complex peptide mixture and of testosterone in urine samples. This allowed for the removal of the matrix and the qualitative and quantitative analysis of the derivatized analyte by LC-MS/MS (or LC-MRM). Herein we report the preparation and chemical characterization of a novel, ChemMatrix - based resin functionalized with aminooxyacetic acid (AOA). The hydroxylamine moiety in this resin is combined with a peptide linker (GRG) containing an arginine residue to enhance the ionization efficiency. Application of an isotopically labeled carbonylated peptide ((H-Leu-Val-Thr(O)-Asp-Leu-Thr-Lys [13C6,15N2]-OH and testosterone-d3 allowed us to carry out quantitative analyses of detected compounds. Our method is general and may be applied for analysis of carbonylated compounds in biological samples. Our method based on application of functionalized resin allowed to quantify the level of free testosterone in small sample (0.5 mL) of urine, while the non-derivatized testosterone from urine sample was not detected during direct LC-MRM analysis.
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Affiliation(s)
- Monika Kijewska
- Faculty of Chemistry, University of Wrocław, Joliot-Curie 14, 50-383, Wrocław, Poland.
| | - Tomasz Koch
- Faculty of Chemistry, University of Wrocław, Joliot-Curie 14, 50-383, Wrocław, Poland
| | - Mateusz Waliczek
- Faculty of Chemistry, University of Wrocław, Joliot-Curie 14, 50-383, Wrocław, Poland
| | - Andrzej Konieczny
- Department of Nephrology and Transplantation Medicine, Wrocław Medical University, Borowska 213, 50-556, Wrocław, Poland
| | - Piotr Stefanowicz
- Faculty of Chemistry, University of Wrocław, Joliot-Curie 14, 50-383, Wrocław, Poland
| | - Zbigniew Szewczuk
- Faculty of Chemistry, University of Wrocław, Joliot-Curie 14, 50-383, Wrocław, Poland
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Lin W, Conway LP, Vujasinovic M, Löhr JM, Globisch D. Chemoselective and highly sensitive quantification of gut microbiome and human metabolites. Angew Chem Int Ed Engl 2021; 60:23232-23240. [PMID: 34339587 PMCID: PMC8597006 DOI: 10.1002/anie.202107101] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 07/15/2021] [Indexed: 11/18/2022]
Abstract
The microbiome has a fundamental impact on the human host's physiology through the production of highly reactive compounds that can lead to disease development. One class of such compounds are carbonyl‐containing metabolites, which are involved in diverse biochemical processes. Mass spectrometry is the method of choice for analysis of metabolites but carbonyls are analytically challenging. Herein, we have developed a new chemical biology tool using chemoselective modification to overcome analytical limitations. Two isotopic probes allow for the simultaneous and semi‐quantitative analysis at the femtomole level as well as qualitative analysis at attomole quantities that allows for detection of more than 200 metabolites in human fecal, urine and plasma samples. This comprehensive mass spectrometric analysis enhances the scope of metabolomics‐driven biomarker discovery. We anticipate that our chemical biology tool will be of general use in metabolomics analysis to obtain a better understanding of microbial interactions with the human host and disease development.
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Affiliation(s)
- Weifeng Lin
- Uppsala University: Uppsala Universitet, Dept. Chemistry - BMC, Uppsala, SWEDEN
| | - Louis P Conway
- Uppsala University: Uppsala Universitet, Dept. Chem. - BMC, 75421, Uppsala, SWEDEN
| | - Miroslav Vujasinovic
- Karolinska University Hospital: Karolinska Universitetssjukhuset, Dept. for Digestive Diseases, Stockholm, SWEDEN
| | - J-Matthias Löhr
- Karolinska Institute: Karolinska Institutet, Dept. Clinical Science, Intervention and Technology, Stockholm, SWEDEN
| | - Daniel Globisch
- Uppsala University, Department of Medicinal Chemistry, Husaragatan 3, Biomedical Center, Box 574, 75123, Uppsala, SWEDEN
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15
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Beard HA, Korovesis D, Chen S, Verhelst SHL. Cleavable linkers and their application in MS-based target identification. Mol Omics 2021; 17:197-209. [PMID: 33507200 DOI: 10.1039/d0mo00181c] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Covalent chemical probes are important tools in chemical biology. They range from post-translational modification (PTM)-derived metabolic probes, to activity-based probes and photoaffinity labels. Identification of the probe targets is often performed by tandem mass spectrometry-based proteomics methods. In the past fifteen years, cleavable linker technologies have been implemented in these workflows in order to identify probe targets with lower background and higher confidence. In addition, the linkers have enabled identification of modification sites. Overall, this has led to an increased knowledge of PTMs, enzyme function and drug action. This review gives an overview of the different types of cleavable linkers, and their benefits and limitations. Their applicability in target identification is also illustrated by several specific examples.
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Affiliation(s)
- Hester A Beard
- KU Leuven, Department of Cellular and Molecular Medicine, Laboratory of Chemical Biology, Herestr. 49 box 802, 3000 Leuven, Belgium.
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Correia MSP, Lin W, Aria AJ, Jain A, Globisch D. Rapid Preparation of a Large Sulfated Metabolite Library for Structure Validation in Human Samples. Metabolites 2020; 10:metabo10100415. [PMID: 33081284 PMCID: PMC7603051 DOI: 10.3390/metabo10100415] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 10/04/2020] [Accepted: 10/13/2020] [Indexed: 12/12/2022] Open
Abstract
Metabolomics analysis of biological samples is widely applied in medical and natural sciences. Assigning the correct chemical structure in the metabolite identification process is required to draw the correct biological conclusions and still remains a major challenge in this research field. Several metabolite tandem mass spectrometry (MS/MS) fragmentation spectra libraries have been developed that are either based on computational methods or authentic libraries. These libraries are limited due to the high number of structurally diverse metabolites, low commercial availability of these compounds, and the increasing number of newly discovered metabolites. Phase II modification of xenobiotics is a compound class that is underrepresented in these databases despite their importance in diet, drug, or microbiome metabolism. The O-sulfated metabolites have been described as a signature for the co-metabolism of bacteria and their human host. Herein, we have developed a straightforward chemical synthesis method for rapid preparation of sulfated metabolite standards to obtain mass spectrometric fragmentation pattern and retention time information. We report the preparation of 38 O-sulfated alcohols and phenols for the determination of their MS/MS fragmentation pattern and chromatographic properties. Many of these metabolites are regioisomers that cannot be distinguished solely by their fragmentation pattern. We demonstrate that the versatility of this method is comparable to standard chemical synthesis. This comprehensive metabolite library can be applied for co-injection experiments to validate metabolites in different human sample types to explore microbiota-host co-metabolism, xenobiotic, and diet metabolism.
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