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Liu P, Cai Y, Qiu S, Yang Q, Xie Y, Zhang A. Critical roles of functional molecule metabolites. Front Mol Biosci 2023; 10:1119588. [PMID: 36876048 PMCID: PMC9975730 DOI: 10.3389/fmolb.2023.1119588] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 01/10/2023] [Indexed: 02/17/2023] Open
Affiliation(s)
- Peng Liu
- International Advanced Functional Omics Platform, Scientific Experiment Center, Hainan Medical University, Haikou, China.,Experimental Center and Graduate School, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Ying Cai
- Experimental Center and Graduate School, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Shi Qiu
- International Advanced Functional Omics Platform, Scientific Experiment Center, Hainan Medical University, Haikou, China
| | - Qiang Yang
- Experimental Center and Graduate School, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Yiqiang Xie
- International Advanced Functional Omics Platform, Scientific Experiment Center, Hainan Medical University, Haikou, China
| | - Aihua Zhang
- International Advanced Functional Omics Platform, Scientific Experiment Center, Hainan Medical University, Haikou, China.,Experimental Center and Graduate School, Heilongjiang University of Chinese Medicine, Harbin, China
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Zhang Y, Wang D, Lv B, Hou X, Liu Q, Liao C, Xu R, Zhang Y, Xu F, Zhang P. Oleic Acid and Insulin as Key Characteristics of T2D Promote Colorectal Cancer Deterioration in Xenograft Mice Revealed by Functional Metabolomics. Front Oncol 2021; 11:685059. [PMID: 34434893 PMCID: PMC8381473 DOI: 10.3389/fonc.2021.685059] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 07/19/2021] [Indexed: 11/13/2022] Open
Abstract
Colorectal cancer (CRC) is one of the most commonly diagnosed cancers with high mortality worldwide. Type 2 diabetes mellitus (T2D), known as a risk factor of CRC, can promote the deterioration of CRC, but the underlying mechanism is elusive. In this study, we aimed to reveal the relationship between CRC and T2D from the perspective of small-molecule metabolism. First, a list of common dysregulated metabolites in CRC and T2D was obtained by retrieving existing metabolomics publications. Among these metabolites, oleic acid (OA) was found to be able to promote the proliferation and migration of colon carcinoma cell HCT116. Further experiments proved that insulin could significantly strengthen this promotion and showed a synergistic effect with OA. Mechanism study found that OA and insulin acted synergistically through the extracellular signal-regulated kinase (ERK)1/2/c-Myc/cyclin D1 pathway. In addition, the combination of ERK1/2 inhibitor SCH772984 and cyclin-dependent kinase (CDK)4/6 inhibitor palbociclib showed a remarkable inhibitory effect on tumor growth in vivo. Taken together, the current study found that OA plays an important role in CRC development by using a functional metabolomics approach. More importantly, insulin and OA were confirmed to synergistically promote the deterioration of CRC in vitro and in vivo via ERK1/2/c-Myc/cyclin D1 pathway. Our findings may shed light on CRC treatment among the T2D population.
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Affiliation(s)
- Ying Zhang
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), State Key Laboratory of Natural Medicine, China Pharmaceutical University, Nanjing, China
| | - Di Wang
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), State Key Laboratory of Natural Medicine, China Pharmaceutical University, Nanjing, China
| | - Bo Lv
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), State Key Laboratory of Natural Medicine, China Pharmaceutical University, Nanjing, China
| | - Xiaoying Hou
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), State Key Laboratory of Natural Medicine, China Pharmaceutical University, Nanjing, China
| | - Qiwei Liu
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), State Key Laboratory of Natural Medicine, China Pharmaceutical University, Nanjing, China
| | - Chuyao Liao
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), State Key Laboratory of Natural Medicine, China Pharmaceutical University, Nanjing, China
| | - Ruijie Xu
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), State Key Laboratory of Natural Medicine, China Pharmaceutical University, Nanjing, China
| | - Yuxin Zhang
- Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Fengguo Xu
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), State Key Laboratory of Natural Medicine, China Pharmaceutical University, Nanjing, China
| | - Pei Zhang
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), State Key Laboratory of Natural Medicine, China Pharmaceutical University, Nanjing, China
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Hu L, Liu J, Zhang W, Wang T, Zhang N, Lee YH, Lu H. FUNCTIONAL METABOLOMICS DECIPHER BIOCHEMICAL FUNCTIONS AND ASSOCIATED MECHANISMS UNDERLIE SMALL-MOLECULE METABOLISM. Mass Spectrom Rev 2020; 39:417-433. [PMID: 31682024 DOI: 10.1002/mas.21611] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Revised: 10/08/2019] [Accepted: 10/10/2019] [Indexed: 06/10/2023]
Abstract
Metabolism is the collection of biochemical reactions enabled by chemically diverse metabolites, which facilitate different physiological processes to exchange substances and synthesize energy in diverse living organisms. Metabolomics has emerged as a cutting-edge method to qualify and quantify the metabolites in different biological matrixes, and it has the extraordinary capacity to interrogate the biological significance that underlies metabolic modification and modulation. Liquid chromatography combined with mass spectrometry (LC/MS), as a robust platform for metabolomics analysis, has increased in popularity over the past 10 years due to its excellent sensitivity, throughput, and versatility. However, metabolomics investigation currently provides us with only phenotype data without revealing the biochemical functions and associated mechanisms. This limitation indeed weakens the core value of metabolomics data in a broad spectrum of the life sciences. In recent years, the scientific community has actively explored the functional features of metabolomics and translated this cutting-edge approach to be used to solve key multifaceted questions, such as disease pathogenesis, the therapeutic discovery of drugs, nutritional issues, agricultural problems, environmental toxicology, and microbial evolution. Here, we are the first to briefly review the history and applicable progression of LC/MS-based metabolomics, with an emphasis on the applications of metabolic phenotyping. Furthermore, we specifically highlight the next era of LC/MS-based metabolomics to target functional metabolomes, through which we can answer phenotype-related questions to elucidate biochemical functions and associated mechanisms implicated in dysregulated metabolism. Finally, we propose many strategies to enhance the research capacity of functional metabolomics by enabling the combination of contemporary omics technologies and cutting-edge biochemical techniques. The main purpose of this review is to improve the understanding of LC/MS-based metabolomics, extending beyond the conventional metabolic phenotype toward biochemical functions and associated mechanisms, to enhance research capability and to enlarge the applicable scope of functional metabolomics in small-molecule metabolism in different living organisms.
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Affiliation(s)
- Longlong Hu
- Laboratory for Functional Metabolomics Science, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jingjing Liu
- Laboratory for Functional Metabolomics Science, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Wenhua Zhang
- Laboratory for Functional Metabolomics Science, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China
- Department of Pharmacognosy, College of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin, 150040, China
| | - Tianyu Wang
- Laboratory for Functional Metabolomics Science, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Ning Zhang
- Department of Pharmacognosy, College of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin, 150040, China
- Department of Pharmaceutical Analysis, College of Jiamusi, Heilongjiang University of Chinese Medicine, Harbin, 121000, China
| | - Yie Hou Lee
- Translational 'Omics and Biomarkers Group, KK Research Centre, KK Women's and Children's Hospital, Singapore, 229899, Singapore
- OBGYN-Academic Clinical Program, Duke-NUS Medical School, Singapore, 169857, Singapore
| | - Haitao Lu
- Laboratory for Functional Metabolomics Science, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China
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Fernández-García M, Rey-Stolle F, Boccard J, Reddy VP, García A, Cumming BM, Steyn AJC, Rudaz S, Barbas C. Comprehensive Examination of the Mouse Lung Metabolome Following Mycobacterium tuberculosis Infection Using a Multiplatform Mass Spectrometry Approach. J Proteome Res 2020; 19:2053-2070. [PMID: 32285670 PMCID: PMC7199213 DOI: 10.1021/acs.jproteome.9b00868] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Indexed: 02/08/2023]
Abstract
The mechanisms whereby Mycobacterium tuberculosis (Mtb) rewires the host metabolism in vivo are surprisingly unexplored. Here, we used three high-resolution mass spectrometry platforms to track altered lung metabolic changes associated with Mtb infection of mice. The multiplatform data sets were merged using consensus orthogonal partial least squares-discriminant analysis (cOPLS-DA), an algorithm that allows for the joint interpretation of the results from a single multivariate analysis. We show that Mtb infection triggers a temporal and progressive catabolic state to satisfy the continuously changing energy demand to control infection. This causes dysregulation of metabolic and oxido-reductive pathways culminating in Mtb-associated wasting. Notably, high abundances of trimethylamine-N-oxide (TMAO), produced by the host from the bacterial metabolite trimethylamine upon infection, suggest that Mtb could exploit TMAO as an electron acceptor under anaerobic conditions. Overall, these new pathway alterations advance our understanding of the link between Mtb pathogenesis and metabolic dysregulation and could serve as a foundation for new therapeutic intervention strategies. Mass spectrometry data has been deposited in the Metabolomics Workbench repository (data-set identifier: ST001328).
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Affiliation(s)
- Miguel Fernández-García
- Centro
de Metabolómica y Bioanálisis (CEMBIO), Facultad de
Farmacia, Universidad San Pablo-CEU, CEU
Universities, Urbanización Montepríncipe, Boadilla del Monte 28660, Spain
| | - Fernanda Rey-Stolle
- Centro
de Metabolómica y Bioanálisis (CEMBIO), Facultad de
Farmacia, Universidad San Pablo-CEU, CEU
Universities, Urbanización Montepríncipe, Boadilla del Monte 28660, Spain
| | - Julien Boccard
- School
of Pharmaceutical Sciences, University of
Lausanne and University of Geneva, Geneva 1211, Switzerland
| | - Vineel P. Reddy
- Department
of Microbiology, University of Alabama at
Birmingham, Birmingham, Alabama 35294, United States
| | - Antonia García
- Centro
de Metabolómica y Bioanálisis (CEMBIO), Facultad de
Farmacia, Universidad San Pablo-CEU, CEU
Universities, Urbanización Montepríncipe, Boadilla del Monte 28660, Spain
| | | | - Adrie J. C. Steyn
- Department
of Microbiology, University of Alabama at
Birmingham, Birmingham, Alabama 35294, United States
- Africa
Health Research Institute, Durban 4001, South Africa
- UAB
Centers for AIDS Research and Free Radical Biology, University of Alabama at Birmingham, Birmingham, Alabama 35294, United States
| | - Serge Rudaz
- School
of Pharmaceutical Sciences, University of
Lausanne and University of Geneva, Geneva 1211, Switzerland
| | - Coral Barbas
- Centro
de Metabolómica y Bioanálisis (CEMBIO), Facultad de
Farmacia, Universidad San Pablo-CEU, CEU
Universities, Urbanización Montepríncipe, Boadilla del Monte 28660, Spain
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Mülleder M, Calvani E, Alam MT, Wang RK, Eckerstorfer F, Zelezniak A, Ralser M. Functional Metabolomics Describes the Yeast Biosynthetic Regulome. Cell 2016; 167:553-565.e12. [PMID: 27693354 PMCID: PMC5055083 DOI: 10.1016/j.cell.2016.09.007] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 06/23/2016] [Accepted: 09/02/2016] [Indexed: 11/16/2022]
Abstract
Genome-metabolism interactions enable cell growth. To probe the extent of these interactions and delineate their functional contributions, we quantified the Saccharomyces amino acid metabolome and its response to systematic gene deletion. Over one-third of coding genes, in particular those important for chromatin dynamics, translation, and transport, contribute to biosynthetic metabolism. Specific amino acid signatures characterize genes of similar function. This enabled us to exploit functional metabolomics to connect metabolic regulators to their effectors, as exemplified by TORC1, whose inhibition in exponentially growing cells is shown to match an interruption in endomembrane transport. Providing orthogonal information compared to physical and genetic interaction networks, metabolomic signatures cluster more than half of the so far uncharacterized yeast genes and provide functional annotation for them. A major part of coding genes is therefore participating in gene-metabolism interactions that expose the metabolism regulatory network and enable access to an underexplored space in gene function. One-third of coding genes significantly impact yeast biosynthetic metabolism The amino acid metabolome is most sensitive to chromatin and transport proteins TORC1 affects biosynthetic amino acid metabolism via vesicle-mediated transport Metabolic signatures are gene specific and cluster 3,923 genes according to function
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Affiliation(s)
- Michael Mülleder
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge CB2 1GA, UK; The Francis Crick Institute, Mill Hill Laboratory, Mill Hill, London NW7 1AA, UK
| | - Enrica Calvani
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge CB2 1GA, UK; The Francis Crick Institute, Mill Hill Laboratory, Mill Hill, London NW7 1AA, UK
| | - Mohammad Tauqeer Alam
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge CB2 1GA, UK
| | - Richard Kangda Wang
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge CB2 1GA, UK
| | - Florian Eckerstorfer
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge CB2 1GA, UK
| | - Aleksej Zelezniak
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge CB2 1GA, UK; The Francis Crick Institute, Mill Hill Laboratory, Mill Hill, London NW7 1AA, UK
| | - Markus Ralser
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge CB2 1GA, UK; The Francis Crick Institute, Mill Hill Laboratory, Mill Hill, London NW7 1AA, UK.
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