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Meiser J, Frezza C. Presenting metabolomics analyses: what's in a number? EMBO J 2024:10.1038/s44318-024-00098-1. [PMID: 38664540 DOI: 10.1038/s44318-024-00098-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 03/20/2024] [Accepted: 03/20/2024] [Indexed: 05/09/2024] Open
Affiliation(s)
- Johannes Meiser
- Cancer Metabolism Group, Department of Cancer Research, Luxembourg Institute of Health, Luxembourg, Luxembourg.
| | - Christian Frezza
- Cluster of Excellence Cellular Stress Responses in Aging-associated Diseases (CECAD), University Hospital Cologne, Cologne, Germany.
- Institute of Genetics, Faculty of Mathematics and Natural Sciences, Faculty of Medicine, University of Cologne, Cologne, Germany.
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52
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Yang C, Yu H, Li W, Lin H, Wu H, Deng C. High-Throughput Metabolic Pattern Screening Strategy for Early Colorectal and Gastric Cancers Based on Covalent Organic Frameworks-Assisted Laser Desorption/Ionization Mass Spectrometry. Anal Chem 2024; 96:6264-6274. [PMID: 38600676 DOI: 10.1021/acs.analchem.3c05527] [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: 04/12/2024]
Abstract
Precise early diagnosis and staging are conducive to improving the prognosis of colorectal cancer (CRC) and gastric cancer (GC) patients. However, due to intrusive inspections and limited sensitivity, the prevailing diagnostic methods impede precisely large-scale screening. In this work, we reported a high-throughput serum metabolic patterns (SMP) screening strategy based on covalent organic frameworks-assisted laser desorption/ionization mass spectrometry (hf-COFsLDI-MS) for early diagnosis and staging of CRC and GC. Notably, 473 high-quality SMP were extracted without any tedious sample pretreatment and coupled with multiple machine learning algorithms; the area under the curve (AUC) value is 0.938 with 96.9% sensitivity for early CRC diagnosis, and the AUC value is 0.974 with 100% sensitivity for early GC diagnosis. Besides, the discrimination of CRC and GC is accomplished with an AUC value of 0.966 for the validation set. Also, the screened-out features were identified by MS/MS experiments, and 8 metabolites were identified as the biomarkers for CRC and GC. Finally, the corresponding disordered metabolic pathways were revealed, and the staging of CRC and GC was completed. This work provides an alternative high-throughput screening strategy for CRC and GC and highlights the potential of metabolic molecular diagnosis in clinical applications.
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Affiliation(s)
- Chenjie Yang
- Department of Chemistry, Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
| | - Hailong Yu
- Department of Chemistry, Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
| | - Weihong Li
- Department of Chemistry, Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
| | - Hairu Lin
- Department of Chemistry, Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
| | - Hao Wu
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Chunhui Deng
- Department of Chemistry, Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
- School of Chemistry and Chemical Engineering, Nanchang University, Nanchang 330031, China
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53
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Chen J, Wang W, Hu X, Yue Y, Lu X, Wang C, Wei B, Zhang H, Wang H. Medium-sized peptides from microbial sources with potential for antibacterial drug development. Nat Prod Rep 2024. [PMID: 38651516 DOI: 10.1039/d4np00002a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
Covering: 1993 to the end of 2022As the rapid development of antibiotic resistance shrinks the number of clinically available antibiotics, there is an urgent need for novel options to fill the existing antibiotic pipeline. In recent years, antimicrobial peptides have attracted increased interest due to their impressive broad-spectrum antimicrobial activity and low probability of antibiotic resistance. However, macromolecular antimicrobial peptides of plant and animal origin face obstacles in antibiotic development because of their extremely short elimination half-life and poor chemical stability. Herein, we focus on medium-sized antibacterial peptides (MAPs) of microbial origin with molecular weights below 2000 Da. The low molecular weight is not sufficient to form complex protein conformations and is also associated to a better chemical stability and easier modifications. Microbially-produced peptides are often composed of a variety of non-protein amino acids and terminal modifications, which contribute to improving the elimination half-life of compounds. Therefore, MAPs have great potential for drug discovery and are likely to become key players in the development of next-generation antibiotics. In this review, we provide a detailed exploration of the modes of action demonstrated by 45 MAPs and offer a concise summary of the structure-activity relationships observed in these MAPs.
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Affiliation(s)
- Jianwei Chen
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Wei Wang
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Xubin Hu
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Yujie Yue
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Xingyue Lu
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Chenjie Wang
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Bin Wei
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Huawei Zhang
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Hong Wang
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
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Lu H, Zheng S, Ma C, Gao X, Ji J, Luo J, Hua H, Cui J. Integrated Omics Analysis Reveals Key Pathways in Cotton Defense against Mirid Bug ( Adelphocoris suturalis Jakovlev) Feeding. INSECTS 2024; 15:254. [PMID: 38667384 PMCID: PMC11049813 DOI: 10.3390/insects15040254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 04/05/2024] [Accepted: 04/06/2024] [Indexed: 04/28/2024]
Abstract
The recent dominance of Adelphocoris suturalis Jakovlev as the primary cotton field pest in Bt-cotton-cultivated areas has generated significant interest in cotton pest control research. This study addresses the limited understanding of cotton defense mechanisms triggered by A. suturalis feeding. Utilizing LC-QTOF-MS, we analyzed cotton metabolomic changes induced by A. suturalis, and identified 496 differential positive ions (374 upregulated, 122 downregulated) across 11 categories, such as terpenoids, alkaloids, phenylpropanoids, flavonoids, isoflavones, etc. Subsequent iTRAQ-LC-MS/MS analysis of the cotton proteome revealed 1569 differential proteins enriched in 35 metabolic pathways. Integrated metabolome and proteome analysis highlighted significant upregulation of 17 (89%) proteases in the α-linolenic acid (ALA) metabolism pathway, concomitant with a significant increase in 14 (88%) associated metabolites. Conversely, 19 (73%) proteases in the fructose and mannose biosynthesis pathway were downregulated, with 7 (27%) upregulated proteases corresponding to the downregulation of 8 pathway-associated metabolites. Expression analysis of key regulators in the ALA pathway, including allene oxidase synthase (AOS), phospholipase A (PLA), allene oxidative cyclase (AOC), and 12-oxophytodienoate reductase3 (OPR3), demonstrated significant responses to A. suturalis feeding. Finally, this study pioneers the exploration of molecular mechanisms in the plant-insect relationship, thereby offering insights into potential novel control strategies against this cotton pest.
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Affiliation(s)
- Hui Lu
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Chinese Academy of Agricultural Sciences, No. 38, Huanghe Road, Anyang 455000, China; (H.L.); (J.J.); (J.L.)
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant, Science and Technology, Huazhong Agricultural University, Wuhan 430070, China;
- Green Agricultural Products Safety and Warning Laboratory, Research Center of Soil Resource Comprehensive Utilization and Ecological Environment in Western Inner Mongolia, Hetao College, Bayannur 015000, China
| | - Shuaichao Zheng
- Henan Institute of Science and Technology, College of Life Science, Hualan St. 90, Xinxiang 453003, China;
| | - Chao Ma
- Anhui Provincial Center for Disease Control and Prevention, Hefei 230601, China;
| | - Xueke Gao
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Chinese Academy of Agricultural Sciences, No. 38, Huanghe Road, Anyang 455000, China; (H.L.); (J.J.); (J.L.)
| | - Jichao Ji
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Chinese Academy of Agricultural Sciences, No. 38, Huanghe Road, Anyang 455000, China; (H.L.); (J.J.); (J.L.)
| | - Junyu Luo
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Chinese Academy of Agricultural Sciences, No. 38, Huanghe Road, Anyang 455000, China; (H.L.); (J.J.); (J.L.)
| | - Hongxia Hua
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant, Science and Technology, Huazhong Agricultural University, Wuhan 430070, China;
| | - Jinjie Cui
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Chinese Academy of Agricultural Sciences, No. 38, Huanghe Road, Anyang 455000, China; (H.L.); (J.J.); (J.L.)
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Li S, Looby N, Chandran V, Kulasingam V. Challenges in the Metabolomics-Based Biomarker Validation Pipeline. Metabolites 2024; 14:200. [PMID: 38668328 PMCID: PMC11051909 DOI: 10.3390/metabo14040200] [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: 03/01/2024] [Revised: 03/27/2024] [Accepted: 03/31/2024] [Indexed: 04/28/2024] Open
Abstract
As end-products of the intersection between the genome and environmental influences, metabolites represent a promising approach to the discovery of novel biomarkers for diseases. However, many potential biomarker candidates identified by metabolomics studies fail to progress beyond analytical validation for routine implementation in clinics. Awareness of the challenges present can facilitate the development and advancement of innovative strategies that allow improved and more efficient applications of metabolite-based markers in clinical settings. This minireview provides a comprehensive summary of the pre-analytical factors, required analytical validation studies, and kit development challenges that must be resolved before the successful translation of novel metabolite biomarkers originating from research. We discuss the necessity for strict protocols for sample collection, storage, and the regulatory requirements to be fulfilled for a bioanalytical method to be considered as analytically validated. We focus especially on the blood as a biological matrix and liquid chromatography coupled with tandem mass spectrometry as the analytical platform for biomarker validation. Furthermore, we examine the challenges of developing a commercially viable metabolomics kit for distribution. To bridge the gap between the research lab and clinical implementation and utility of relevant metabolites, the understanding of the translational challenges for a biomarker panel is crucial for more efficient development of metabolomics-based precision medicine.
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Affiliation(s)
- Shenghan Li
- Division of Rheumatology, Psoriatic Arthritis Program, Schroeder Arthritis Program, University Health Network, Toronto, ON M5T 0S8, Canada; (S.L.); (N.L.)
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A1, Canada
- Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada
| | - Nikita Looby
- Division of Rheumatology, Psoriatic Arthritis Program, Schroeder Arthritis Program, University Health Network, Toronto, ON M5T 0S8, Canada; (S.L.); (N.L.)
- Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada
- Division of Orthopaedic Surgery, Osteoarthritis Research Program, Schroeder Arthritis Institute, University Health Network, Toronto, ON M5T 0S8, Canada
| | - Vinod Chandran
- Division of Rheumatology, Psoriatic Arthritis Program, Schroeder Arthritis Program, University Health Network, Toronto, ON M5T 0S8, Canada; (S.L.); (N.L.)
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A1, Canada
- Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada
- Division of Rheumatology, Department of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Vathany Kulasingam
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A1, Canada
- Division of Clinical Biochemistry, Laboratory Medicine Program, University Health Network, Toronto, ON M5G 2C4, Canada
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56
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Liu Y, Zhang X, Wang Y, Wang J, Wei H, Zhang C, Zhang Q. Cyclocodon lancifolius fruit prolongs the lifespan of Caenorhabditis elegans via antioxidation and regulation of purine metabolism. Food Funct 2024; 15:3353-3364. [PMID: 38481358 DOI: 10.1039/d3fo02931j] [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: 04/04/2024]
Abstract
Cyclocodon lancifolius fruit is a promising commercial fruit with antioxidant activity and is rich in polyphenolic compounds. In this study, the anti-aging activity of C. lancifolius fruit extract (CF) on Caenorhabditis elegans (C. elegans) was evaluated by observing the longevity, stress response, reproduction, oscillation, lipofuscin, and antioxidant enzymes of worms. Moreover, the effects and potential mechanisms of CF on delaying C. elegans senescence at the mRNA and metabolite levels were investigated. The results showed that CF treatment significantly increased the lifespan and stress resistance, decreased the levels of lipofuscin and reactive oxygen species (ROS), and improved the antioxidant system of C. elegans. The extension of the lifespan of C. elegans was remarkably correlated with the upregulation of mtl-1 and Hsp-16.2, along with the downregulation of age-1, daf-2, and akt-1. Metabolomics analysis revealed that purine metabolism is a key regulatory pathway for CF to exert anti-aging effects. The present study suggests that C. lancifolius fruit has potential for use as a functional food to enhance antioxidant capacity and delay aging.
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Affiliation(s)
- Yihan Liu
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling 712100, China.
| | - Xudong Zhang
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling 712100, China.
| | - Yan Wang
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling 712100, China.
| | - Jianxia Wang
- School of Pharmaceutical Sciences, Jishou University, Jishou 416000, China
| | - Hua Wei
- School of Pharmaceutical Sciences, Jishou University, Jishou 416000, China
| | - Cunli Zhang
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling 712100, China.
| | - Qiang Zhang
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling 712100, China.
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Mukherjee A, Abraham S, Singh A, Balaji S, Mukunthan KS. From Data to Cure: A Comprehensive Exploration of Multi-omics Data Analysis for Targeted Therapies. Mol Biotechnol 2024:10.1007/s12033-024-01133-6. [PMID: 38565775 DOI: 10.1007/s12033-024-01133-6] [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: 12/27/2023] [Accepted: 02/27/2024] [Indexed: 04/04/2024]
Abstract
In the dynamic landscape of targeted therapeutics, drug discovery has pivoted towards understanding underlying disease mechanisms, placing a strong emphasis on molecular perturbations and target identification. This paradigm shift, crucial for drug discovery, is underpinned by big data, a transformative force in the current era. Omics data, characterized by its heterogeneity and enormity, has ushered biological and biomedical research into the big data domain. Acknowledging the significance of integrating diverse omics data strata, known as multi-omics studies, researchers delve into the intricate interrelationships among various omics layers. This review navigates the expansive omics landscape, showcasing tailored assays for each molecular layer through genomes to metabolomes. The sheer volume of data generated necessitates sophisticated informatics techniques, with machine-learning (ML) algorithms emerging as robust tools. These datasets not only refine disease classification but also enhance diagnostics and foster the development of targeted therapeutic strategies. Through the integration of high-throughput data, the review focuses on targeting and modeling multiple disease-regulated networks, validating interactions with multiple targets, and enhancing therapeutic potential using network pharmacology approaches. Ultimately, this exploration aims to illuminate the transformative impact of multi-omics in the big data era, shaping the future of biological research.
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Affiliation(s)
- Arnab Mukherjee
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, India
| | - Suzanna Abraham
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, India
| | - Akshita Singh
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, India
| | - S Balaji
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, India
| | - K S Mukunthan
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, India.
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58
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Jiang W, Yang L, Dang Y, Jiang X, Wu L, Tong X, Guo J, Bao Y. Metabolomic profiling of deep vein thrombosis. Phlebology 2024; 39:154-168. [PMID: 37992130 PMCID: PMC10938490 DOI: 10.1177/02683555231215199] [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] [Indexed: 11/24/2023]
Abstract
Deep vein thrombosis (DVT) of the lower extremities is one of the most common peripheral vascular diseases, with significant complications and sequelae. Metabolomics aims to identify small molecules in biological samples. It can serve as a promising method for screening compounds that can be used for early disease detection, diagnosis, treatment response prediction, and prognosis. In addition, high-throughput metabolomics screening can yield significant insights into the pathophysiological pathways of DVT. Currently, the metabolomic profiles of DVT have yielded inconsistent expression patterns. This article examines the recent advancements in metabolomic studies of DVT and analyzes the factors that may influence the results.
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Affiliation(s)
- Weiguang Jiang
- Chifeng Clinical Medical College of Inner Mongolia Medical University, Chifeng, China
- Department of Vascular Surgery, Chifeng Municipal Hospital, Chifeng, China
| | - Liu Yang
- Department of Vascular Surgery, Chifeng Municipal Hospital, Chifeng, China
| | - Yongkang Dang
- Department of Vascular Surgery, Chifeng Municipal Hospital, Chifeng, China
| | - Xuechao Jiang
- Department of Vascular Surgery, Chifeng Municipal Hospital, Chifeng, China
| | - Lan Wu
- Department of Vascular Surgery, Chifeng Municipal Hospital, Chifeng, China
| | - Xiangyang Tong
- Department of Vascular Surgery, Chifeng Municipal Hospital, Chifeng, China
| | - Jianquan Guo
- Department of Vascular Surgery, Chifeng Municipal Hospital, Chifeng, China
| | - Yongtao Bao
- Department of Vascular Surgery, Chifeng Municipal Hospital, Chifeng, China
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59
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Ho PY, Nguyen TH, Sanchez JM, DeFelice BC, Huang KC. Resource competition predicts assembly of gut bacterial communities in vitro. Nat Microbiol 2024; 9:1036-1048. [PMID: 38486074 DOI: 10.1038/s41564-024-01625-w] [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: 04/30/2023] [Accepted: 01/26/2024] [Indexed: 04/06/2024]
Abstract
Microbial community dynamics arise through interspecies interactions, including resource competition, cross-feeding and pH modulation. The individual contributions of these mechanisms to community structure are challenging to untangle. Here we develop a framework to estimate multispecies niche overlaps by combining metabolomics data of individual species, growth measurements in spent media and mathematical models. We applied our framework to an in vitro model system comprising 15 human gut commensals in complex media and showed that a simple model of resource competition accounted for most pairwise interactions. Next, we built a coarse-grained consumer-resource model by grouping metabolomic features depleted by the same set of species and showed that this model predicted the composition of 2-member to 15-member communities with reasonable accuracy. Furthermore, we found that incorporation of cross-feeding and pH-mediated interactions improved model predictions of species coexistence. Our theoretical model and experimental framework can be applied to characterize interspecies interactions in bacterial communities in vitro.
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Affiliation(s)
- Po-Yi Ho
- Department of Bioengineering, Stanford University, Stanford, CA, USA.
- School of Engineering, Westlake University, Hangzhou, China.
| | - Taylor H Nguyen
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | | | | | - Kerwyn Casey Huang
- Department of Bioengineering, Stanford University, Stanford, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA.
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60
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Çiçek SS, Mangoni A, Hanschen FS, Agerbirk N, Zidorn C. Essentials in the acquisition, interpretation, and reporting of plant metabolite profiles. PHYTOCHEMISTRY 2024; 220:114004. [PMID: 38331135 DOI: 10.1016/j.phytochem.2024.114004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 01/22/2024] [Accepted: 01/23/2024] [Indexed: 02/10/2024]
Abstract
Plant metabolite profiling reveals the diversity of secondary or specialized metabolites in the plant kingdom with its hundreds of thousands of species. Specialized plant metabolites constitute a vast class of chemicals posing significant challenges in analytical chemistry. In order to be of maximum scientific relevance, reports dealing with these compounds and their source species must be transparent, make use of standards and reference materials, and be based on correctly and traceably identified plant material. Essential aspects in qualitative plant metabolite profiling include: (i) critical review of previous literature and a reasoned sampling strategy; (ii) transparent plant sampling with wild material documented by vouchers in public herbaria and, optimally, seed banks; (iii) if possible, inclusion of generally available reference plant material; (iv) transparent, documented state-of-the art chemical analysis, ideally including chemical reference standards; (v) testing for artefacts during preparative extraction and isolation, using gentle analytical methods; (vi) careful chemical data interpretation, avoiding over- and misinterpretation and taking into account phytochemical complexity when assigning identification confidence levels, and (vii) taking all previous scientific knowledge into account in reporting the scientific data. From the current stage of the phytochemical literature, selected comments and suggestions are given. In the past, proposed revisions of botanical taxonomy were sometimes based on metabolite profiles, but this approach ("chemosystematics" or "chemotaxonomy") is outdated due to the advent of DNA sequence-based phylogenies. In contrast, systematic comparisons of plant metabolite profiles in a known phylogenetic framework remain relevant. This approach, known as chemophenetics, allows characterizing species and clades based on their array of specialized metabolites, aids in deducing the evolution of biosynthetic pathways and coevolution, and can serve in identifying new sources of rare and economically interesting natural products.
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Affiliation(s)
- Serhat S Çiçek
- Department of Biotechnology, Hamburg University of Applied Sciences, Ulmenliet 20, 21033, Hamburg, Germany
| | - Alfonso Mangoni
- Dipartimento di Farmacia, Università di Napoli Federico II, Via Domenico Montesano 49, 80131, Napoli, Italy
| | - Franziska S Hanschen
- Plant Quality and Food Security, Leibniz Institute of Vegetable and Ornamental Crops (IGZ) e. V., Theodor-Echtermeyer-Weg 1, 14979, Grossbeeren, Germany
| | - Niels Agerbirk
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
| | - Christian Zidorn
- Pharmazeutisches Institut, Abteilung Pharmazeutische Biologie, Christian-Albrechts- Universität zu Kiel, Gutenbergstraße 76, 24118, Kiel, Germany.
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61
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Lazar SM, Challman TD, Myers SM. Etiologic Evaluation of Children with Autism Spectrum Disorder. Pediatr Clin North Am 2024; 71:179-197. [PMID: 38423715 DOI: 10.1016/j.pcl.2023.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
Autism spectrum disorder (ASD) is clinically and etiologically heterogeneous. A causal genetic variant can be identified in approximately 20% to 25% of affected individuals with current clinical genetic testing, and all patients with an ASD diagnosis should be offered genetic etiologic evaluation. We suggest that exome sequencing with copy number variant coverage should be the first-line etiologic evaluation for ASD. Neuroimaging, neurophysiologic, metabolic, and other biochemical evaluations can provide insight into the pathophysiology of ASD but should be recommended in the appropriate clinical circumstances.
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Affiliation(s)
- Steven M Lazar
- Section of Pediatric Neurology and Developmental Neuroscience, Meyer Center for Developmental Pediatrics & Autism, Baylor College of Medicine - Texas Children's Hospital, 6701 Fannin Street Suite 1250, Houston, TX 77030, USA.
| | - Thomas D Challman
- Geisinger Autism & Developmental Medicine Institute, Geisinger Commonwealth School of Medicine, 120 Hamm Drive, Suite 2A, Lewisburg, PA 17837, USA
| | - Scott M Myers
- Geisinger Autism & Developmental Medicine Institute, Geisinger Commonwealth School of Medicine, 120 Hamm Drive, Suite 2A, Lewisburg, PA 17837, USA
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62
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Tkalec Ž, Antignac JP, Bandow N, Béen FM, Belova L, Bessems J, Le Bizec B, Brack W, Cano-Sancho G, Chaker J, Covaci A, Creusot N, David A, Debrauwer L, Dervilly G, Duca RC, Fessard V, Grimalt JO, Guerin T, Habchi B, Hecht H, Hollender J, Jamin EL, Klánová J, Kosjek T, Krauss M, Lamoree M, Lavison-Bompard G, Meijer J, Moeller R, Mol H, Mompelat S, Van Nieuwenhuyse A, Oberacher H, Parinet J, Van Poucke C, Roškar R, Togola A, Trontelj J, Price EJ. Innovative analytical methodologies for characterizing chemical exposure with a view to next-generation risk assessment. ENVIRONMENT INTERNATIONAL 2024; 186:108585. [PMID: 38521044 DOI: 10.1016/j.envint.2024.108585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 03/14/2024] [Accepted: 03/15/2024] [Indexed: 03/25/2024]
Abstract
The chemical burden on the environment and human population is increasing. Consequently, regulatory risk assessment must keep pace to manage, reduce, and prevent adverse impacts on human and environmental health associated with hazardous chemicals. Surveillance of chemicals of known, emerging, or potential future concern, entering the environment-food-human continuum is needed to document the reality of risks posed by chemicals on ecosystem and human health from a one health perspective, feed into early warning systems and support public policies for exposure mitigation provisions and safe and sustainable by design strategies. The use of less-conventional sampling strategies and integration of full-scan, high-resolution mass spectrometry and effect-directed analysis in environmental and human monitoring programmes have the potential to enhance the screening and identification of a wider range of chemicals of known, emerging or potential future concern. Here, we outline the key needs and recommendations identified within the European Partnership for Assessment of Risks from Chemicals (PARC) project for leveraging these innovative methodologies to support the development of next-generation chemical risk assessment.
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Affiliation(s)
- Žiga Tkalec
- RECETOX, Faculty of Science, Masaryk University, Kotlarska 2, Brno, Czech Republic; Jožef Stefan Institute, Department of Environmental Sciences, Ljubljana, Slovenia.
| | | | - Nicole Bandow
- German Environment Agency, Laboratory for Water Analysis, Colditzstraße 34, 12099 Berlin, Germany.
| | - Frederic M Béen
- Vrije Universiteit Amsterdam, Amsterdam Institute for Life and Environment (A-LIFE), Section Chemistry for Environment and Health, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands; KWR Water Research Institute, Nieuwegein, The Netherlands.
| | - Lidia Belova
- Toxicological Center, University of Antwerp, 2610 Wilrijk, Belgium.
| | - Jos Bessems
- Flemish Institute for Technological Research (VITO), Mol, Belgium.
| | | | - Werner Brack
- Helmholtz Centre for Environmental Research GmbH - UFZ, Department of Effect-Directed Analysis, Permoserstraße 15, 04318 Leipzig, Germany; Goethe University Frankfurt, Department of Evolutionary Ecology and Environmental Toxicology, Max-von-Laue-Strasse 13, 60438 Frankfurt, Germany.
| | | | - Jade Chaker
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, Rennes, France.
| | - Adrian Covaci
- Toxicological Center, University of Antwerp, 2610 Wilrijk, Belgium.
| | - Nicolas Creusot
- INRAE, French National Research Institute For Agriculture, Food & Environment, UR1454 EABX, Bordeaux Metabolome, MetaboHub, Gazinet Cestas, France.
| | - Arthur David
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, Rennes, France.
| | - Laurent Debrauwer
- Toxalim (Research Centre in Food Toxicology), INRAE UMR 1331, ENVT, INP-Purpan, Paul Sabatier University (UPS), Toulouse, France.
| | | | - Radu Corneliu Duca
- Unit Environmental Hygiene and Human Biological Monitoring, Department of Health Protection, Laboratoire National de Santé (LNS), 1 Rue Louis Rech, L-3555 Dudelange, Luxembourg; Environment and Health, Department of Public Health and Primary Care, Katholieke Universiteit of Leuven (KU Leuven), 3000 Leuven, Belgium.
| | - Valérie Fessard
- ANSES, French Agency for Food, Environmental and Occupational Health & Safety, Laboratory of Fougères, Toxicology of Contaminants Unit, 35306 Fougères, France.
| | - Joan O Grimalt
- Institute of Environmental Assessment and Water Research (IDAEA-CSIC), Barcelona, Catalonia, Spain.
| | - Thierry Guerin
- ANSES, French Agency for Food, Environmental and Occupational Health & Safety, Strategy and Programs Department, F-94701 Maisons-Alfort, France.
| | - Baninia Habchi
- INRS, Département Toxicologie et Biométrologie Laboratoire Biométrologie 1, rue du Morvan - CS 60027 - 54519, Vandoeuvre Cedex, France.
| | - Helge Hecht
- RECETOX, Faculty of Science, Masaryk University, Kotlarska 2, Brno, Czech Republic.
| | - Juliane Hollender
- Swiss Federal Institute of Aquatic Science and Technology - Eawag, 8600 Dübendorf, Switzerland; Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich, 8092 Zürich, Switzerland.
| | - Emilien L Jamin
- Toxalim (Research Centre in Food Toxicology), INRAE UMR 1331, ENVT, INP-Purpan, Paul Sabatier University (UPS), Toulouse, France.
| | - Jana Klánová
- RECETOX, Faculty of Science, Masaryk University, Kotlarska 2, Brno, Czech Republic.
| | - Tina Kosjek
- Jožef Stefan Institute, Department of Environmental Sciences, Ljubljana, Slovenia.
| | - Martin Krauss
- Helmholtz Centre for Environmental Research GmbH - UFZ, Department of Effect-Directed Analysis, Permoserstraße 15, 04318 Leipzig, Germany.
| | - Marja Lamoree
- Vrije Universiteit Amsterdam, Amsterdam Institute for Life and Environment (A-LIFE), Section Chemistry for Environment and Health, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands.
| | - Gwenaelle Lavison-Bompard
- ANSES, French Agency for Food, Environmental and Occupational Health & Safety, Laboratory for Food Safety, Pesticides and Marine Biotoxins Unit, F-94701 Maisons-Alfort, France.
| | - Jeroen Meijer
- Vrije Universiteit Amsterdam, Amsterdam Institute for Life and Environment (A-LIFE), Section Chemistry for Environment and Health, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands.
| | - Ruth Moeller
- Unit Medical Expertise and Data Intelligence, Department of Health Protection, Laboratoire National de Santé (LNS), 1 Rue Louis Rech, L-3555 Dudelange, Luxembourg.
| | - Hans Mol
- Wageningen Food Safety Research - Part of Wageningen University and Research, Akkermaalsbos 2, 6708 WB, Wageningen, The Netherlands.
| | - Sophie Mompelat
- ANSES, French Agency for Food, Environmental and Occupational Health & Safety, Laboratory of Fougères, Toxicology of Contaminants Unit, 35306 Fougères, France.
| | - An Van Nieuwenhuyse
- Environment and Health, Department of Public Health and Primary Care, Katholieke Universiteit of Leuven (KU Leuven), 3000 Leuven, Belgium; Department of Health Protection, Laboratoire National de Santé (LNS), 1 Rue Louis Rech, L-3555 Dudelange, Luxembourg.
| | - Herbert Oberacher
- Institute of Legal Medicine and Core Facility Metabolomics, Medical University of Insbruck, 6020 Innsbruck, Austria.
| | - Julien Parinet
- ANSES, French Agency for Food, Environmental and Occupational Health & Safety, Laboratory for Food Safety, Pesticides and Marine Biotoxins Unit, F-94701 Maisons-Alfort, France.
| | - Christof Van Poucke
- Flanders Research Institute for Agriculture, Fisheries And Food (ILVO), Brusselsesteenweg 370, 9090 Melle, Belgium.
| | - Robert Roškar
- University of Ljubljana, Faculty of Pharmacy, Slovenia.
| | - Anne Togola
- BRGM, 3 avenue Claude Guillemin, 45060 Orléans, France.
| | | | - Elliott J Price
- RECETOX, Faculty of Science, Masaryk University, Kotlarska 2, Brno, Czech Republic.
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Jiang J, Hu D, Pei E. Integrated omics analysis reveals a correlation between gut microbiota and egg production in captive African penguins (Spheniscus demersus). Anim Reprod Sci 2024; 263:107448. [PMID: 38428346 DOI: 10.1016/j.anireprosci.2024.107448] [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: 11/02/2023] [Revised: 01/24/2024] [Accepted: 02/21/2024] [Indexed: 03/03/2024]
Abstract
The egg production of captive African penguins differs considerably between individuals. An understanding of the physiological differences in African penguins with relatively greater and lesser egg production is meaningful for the captive breeding program of this endangered species. The objective of this study was to investigate differential microbial composition and metabolites in captive African penguins with different egg production. Fecal samples were collected from captive female African penguins during the breeding season. The results of 16 S rRNA gene sequencing showed that African penguins with different egg production had similar microbial diversities, whereas a significant difference was observed between their microbial community structure. African penguins with relatively greater egg production exhibited a higher relative abundance of Alphaproteobacteria, Rhizobiales, Bradyrhizobiaceae, Bradyrhizobium and Bosea. Meanwhile, penguins with relatively lesser egg production had an increased proportion of Klebsiella and Plesiomonas. We further identified a total of 1858 metabolites in female African penguins by liquid chromatography-mass spectrometry analysis. Among these metabolites, 13 kinds of metabolites were found to be significantly differential between African penguins with different egg production. In addition, the correlation analysis revealed that the egg production had significant correlations with most of the differential microbial bacteria and metabolites. Our findings might aid in understanding the potential mechanism underlying the phenomenon of abnormal egg production in captive African penguins, and provide novel insights into the relationship between gut microbiota and reproduction in penguins.
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Affiliation(s)
- Jingle Jiang
- Shanghai Endangered Species Conservation and Research Centre, Shanghai Zoo, Shanghai 200335, China
| | - Di Hu
- Shanghai Endangered Species Conservation and Research Centre, Shanghai Zoo, Shanghai 200335, China
| | - Enle Pei
- Shanghai Endangered Species Conservation and Research Centre, Shanghai Zoo, Shanghai 200335, China.
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64
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Olanrewaju OS, Glick BR, Babalola OO. Metabolomics-guided utilization of beneficial microbes for climate-resilient crops. Curr Opin Chem Biol 2024; 79:102427. [PMID: 38290195 DOI: 10.1016/j.cbpa.2024.102427] [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: 04/26/2023] [Revised: 01/04/2024] [Accepted: 01/05/2024] [Indexed: 02/01/2024]
Abstract
In the rhizosphere, plants and microbes communicate chemically, especially under environmental stress. Over millions of years, plants and their microbiome have coevolved, sharing various chemicals, including signaling molecules. This mutual exchange impacts bacterial communication and influences plant metabolism. Inter-kingdom signal crosstalk affects bacterial colonization and plant fitness. Beneficial microbes and their metabolomes offer eco-friendly ways to enhance plant resilience and agriculture. Plant metabolites are pivotal in this dynamic interaction between host plants and their interacting beneficial microbes. Understanding these associations is key to engineering a robust microbiome for stress mitigation and improved plant growth. This review explores mechanisms behind plant-microbe interactions, the role of beneficial microbes and metabolomics, and the practical applications for addressing climate change's impact on agriculture. Integrating beneficial microbes' activities and metabolomics' application to study metabolome-driven interaction between host plants and their corresponding beneficial microbes holds promise for enhancing crop resilience and productivity.
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Affiliation(s)
- Oluwaseyi Samuel Olanrewaju
- Unit for Environmental Sciences and Management, Potchefstroom Campus, North-West University, Private Bag X6001, Potchefstroom 2520, South Africa
| | - Bernard R Glick
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Olubukola Oluranti Babalola
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho 2735, South Africa.
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65
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Liu X, Song L, Xue B, Chi Z, Wang Y, Wen S, Lv W, Hu Q, Guo Q, Wang S, Wu D, Liang G, Jing D. Organic acid and sugar components accumulation and flavor associated metabolites dynamic changes in yellow- and white-fleshed seedless loquats ( Eriobotrya japonica). Food Chem X 2024; 21:101046. [PMID: 38173902 PMCID: PMC10762357 DOI: 10.1016/j.fochx.2023.101046] [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: 08/08/2023] [Revised: 11/27/2023] [Accepted: 12/03/2023] [Indexed: 01/05/2024] Open
Abstract
Triploid loquats are divided into yellow- and white-fleshed cultivars. To better understand taste variations in triploid loquat fruits, we used a UPLC-ESI-QTRAP-MS/MS-based widely targeted metabolomic analysis to examine the metabolic composition of two different color fleshed triploid loquats with a sample size of 54 and external validation method within a confidence level of P<0.05. We identified key flavor-related differentially accumulated metabolites using the variable importance in projection (VIP) value (VIP ≥ 1.0) and fold change ≥ 2 or ≤ 0.5. Furthermore, the results of the HPLC analysis showed that white-fleshed loquats had a low malic acid content. We also performed the UPLC-MS/MS system to investigate the carotenoids contents and lipidome in four triploid cultivars. In the fruits of white-fleshed varieties, the carotenoids contents were significantly downregulated, but the contents of most glycerolphospholipids were increased. Our results reveal the metabolomic changes between the yellow- and white-fleshed cultivars.
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Affiliation(s)
- Xinya Liu
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing 400715, China
- Academy of Agricultural Sciences of Southwest University, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Beibei, Chongqing 400715, China
| | - Liqin Song
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing 400715, China
- Academy of Agricultural Sciences of Southwest University, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Beibei, Chongqing 400715, China
| | - Baogui Xue
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing 400715, China
- Academy of Agricultural Sciences of Southwest University, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Beibei, Chongqing 400715, China
- Jiuquan Forest Fruit Service Center, Jiuquan, Gansu 735000, China
| | - Zhuoheng Chi
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing 400715, China
- Academy of Agricultural Sciences of Southwest University, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Beibei, Chongqing 400715, China
| | - Yuan Wang
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing 400715, China
- Academy of Agricultural Sciences of Southwest University, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Beibei, Chongqing 400715, China
| | - Songqin Wen
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing 400715, China
- Academy of Agricultural Sciences of Southwest University, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Beibei, Chongqing 400715, China
| | - Wenjuan Lv
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing 400715, China
- Academy of Agricultural Sciences of Southwest University, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Beibei, Chongqing 400715, China
| | - Qiankun Hu
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing 400715, China
- Academy of Agricultural Sciences of Southwest University, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Beibei, Chongqing 400715, China
| | - Qigao Guo
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing 400715, China
- Academy of Agricultural Sciences of Southwest University, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Beibei, Chongqing 400715, China
| | - Shuming Wang
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing 400715, China
- Academy of Agricultural Sciences of Southwest University, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Beibei, Chongqing 400715, China
| | - Di Wu
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing 400715, China
- Academy of Agricultural Sciences of Southwest University, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Beibei, Chongqing 400715, China
| | - Guolu Liang
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing 400715, China
- Academy of Agricultural Sciences of Southwest University, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Beibei, Chongqing 400715, China
| | - Danlong Jing
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing 400715, China
- Academy of Agricultural Sciences of Southwest University, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Beibei, Chongqing 400715, China
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P. Gomes PW, Mannochio-Russo H, Mao J, Zhao HN, Ancira J, Tipton CD, Dorrestein PC, Li M. Co-occurrence network analysis reveals the alterations of the skin microbiome and metabolome in adults with mild to moderate atopic dermatitis. mSystems 2024; 9:e0111923. [PMID: 38319107 PMCID: PMC10949451 DOI: 10.1128/msystems.01119-23] [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: 10/19/2023] [Accepted: 01/04/2024] [Indexed: 02/07/2024] Open
Abstract
Skin microbiome can be altered in patients with atopic dermatitis (AD). An understanding of the changes from healthy to atopic skin can help develop new targets for treatment by identifying microbial and molecular biomarkers. This study investigates the skin microbiome and metabolome of healthy adult subjects and lesion (ADL) and non-lesion (ADNL) of AD patients by 16S rRNA gene sequencing and mass spectrometry, respectively. Samples from AD patients showed alterations in the diversity and composition of the skin microbiome, with ADL skin having the greatest divergence. Staphylococcus species, especially S. aureus, were significantly increased in AD patients. Metabolomic profiles were also different between the groups. Dipeptide derivatives are more abundant in ADL, which may be related to skin inflammation. Co-occurrence network analysis of the microbiome and metabolomics data revealed higher co-occurrence of metabolites and bacteria in healthy ADNL compared to ADL. S. aureus co-occurred with dipeptide derivatives in ADL, while phytosphingosine-derived compounds showed co-occurrences with commensal bacteria, for example, Paracoccus sp., Pseudomonas sp., Prevotella bivia, Lactobacillus iners, Anaerococcus sp., Micrococcus sp., Corynebacterium ureicelerivorans, Corynebacterium massiliense, Streptococcus thermophilus, and Roseomonas mucosa, in healthy and ADNL groups. Therefore, these findings provide valuable insights into how AD affects the human skin metabolome and microbiome.IMPORTANCEThis study provides valuable insight into changes in the skin microbiome and associated metabolomic profiles in an adult population with mild to moderate atopic dermatitis. It also identifies new therapeutic targets that may be useful for developing personalized treatments for individuals with atopic dermatitis based on their unique skin microbiome and metabolic profiles.
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Affiliation(s)
- Paulo Wender P. Gomes
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, USA
| | - Helena Mannochio-Russo
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, USA
| | - Junhong Mao
- Colgate−Palmolive Company, Piscataway, New Jersey, USA
| | - Haoqi Nina Zhao
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, USA
| | | | | | - Pieter C. Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, USA
- Department of Pediatrics, University of California, San Diego, California, USA
| | - Min Li
- Colgate−Palmolive Company, Piscataway, New Jersey, USA
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67
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Calabrese V, Brunet TA, Degli-Esposti D, Chaumot A, Geffard O, Salvador A, Clément Y, Ayciriex S. Electron-activated dissociation (EAD) for the complementary annotation of metabolites and lipids through data-dependent acquisition analysis and feature-based molecular networking, applied to the sentinel amphipod Gammarus fossarum. Anal Bioanal Chem 2024:10.1007/s00216-024-05232-w. [PMID: 38492024 DOI: 10.1007/s00216-024-05232-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 02/23/2024] [Accepted: 02/27/2024] [Indexed: 03/18/2024]
Abstract
The past decades have marked the rise of metabolomics and lipidomics as the -omics sciences which reflect the most phenotypes in living systems. Mass spectrometry-based approaches are acknowledged for both quantification and identification of molecular signatures, the latter relying primarily on fragmentation spectra interpretation. However, the high structural diversity of biological small molecules poses a considerable challenge in compound annotation. Feature-based molecular networking (FBMN) combined with database searches currently sets the gold standard for annotation of large datasets. Nevertheless, FBMN is usually based on collision-induced dissociation (CID) data, which may lead to unsatisfying information. The use of alternative fragmentation methods, such as electron-activated dissociation (EAD), is undergoing a re-evaluation for the annotation of small molecules, as it gives access to additional fragmentation routes. In this study, we apply the performances of data-dependent acquisition mass spectrometry (DDA-MS) under CID and EAD fragmentation along with FBMN construction, to perform extensive compound annotation in the crude extracts of the freshwater sentinel organism Gammarus fossarum. We discuss the analytical aspects of the use of the two fragmentation modes, perform a general comparison of the information delivered, and compare the CID and EAD fragmentation pathways for specific classes of compounds, including previously unstudied species. In addition, we discuss the potential use of FBMN constructed with EAD fragmentation spectra to improve lipid annotation, compared to the classic CID-based networks. Our approach has enabled higher confidence annotations and finer structure characterization of 823 features, including both metabolites and lipids detected in G. fossarum extracts.
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Affiliation(s)
- Valentina Calabrese
- Universite Claude Bernard Lyon1, ISA, UMR 5280, CNRS, 5 Rue de La Doua, 69100, Villeurbanne, France.
| | - Thomas Alexandre Brunet
- Universite Claude Bernard Lyon1, ISA, UMR 5280, CNRS, 5 Rue de La Doua, 69100, Villeurbanne, France
| | | | - Arnaud Chaumot
- Laboratoire d'écotoxicologie, INRAE, UR RiverLy, 69625, Villeurbanne, France
| | - Olivier Geffard
- Laboratoire d'écotoxicologie, INRAE, UR RiverLy, 69625, Villeurbanne, France
| | - Arnaud Salvador
- Universite Claude Bernard Lyon1, ISA, UMR 5280, CNRS, 5 Rue de La Doua, 69100, Villeurbanne, France
| | - Yohann Clément
- Universite Claude Bernard Lyon1, ISA, UMR 5280, CNRS, 5 Rue de La Doua, 69100, Villeurbanne, France
| | - Sophie Ayciriex
- Universite Claude Bernard Lyon1, ISA, UMR 5280, CNRS, 5 Rue de La Doua, 69100, Villeurbanne, France.
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68
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Horn PJ, Chapman KD. Imaging plant metabolism in situ. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:1654-1670. [PMID: 37889862 PMCID: PMC10938046 DOI: 10.1093/jxb/erad423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 10/25/2023] [Indexed: 10/29/2023]
Abstract
Mass spectrometry imaging (MSI) has emerged as an invaluable analytical technique for investigating the spatial distribution of molecules within biological systems. In the realm of plant science, MSI is increasingly employed to explore metabolic processes across a wide array of plant tissues, including those in leaves, fruits, stems, roots, and seeds, spanning various plant systems such as model species, staple and energy crops, and medicinal plants. By generating spatial maps of metabolites, MSI has elucidated the distribution patterns of diverse metabolites and phytochemicals, encompassing lipids, carbohydrates, amino acids, organic acids, phenolics, terpenes, alkaloids, vitamins, pigments, and others, thereby providing insights into their metabolic pathways and functional roles. In this review, we present recent MSI studies that demonstrate the advances made in visualizing the plant spatial metabolome. Moreover, we emphasize the technical progress that enhances the identification and interpretation of spatial metabolite maps. Within a mere decade since the inception of plant MSI studies, this robust technology is poised to continue as a vital tool for tackling complex challenges in plant metabolism.
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Affiliation(s)
- Patrick J Horn
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton TX 76203, USA
| | - Kent D Chapman
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton TX 76203, USA
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69
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Martínez-Rivas FJ, Fernie AR. Metabolomics to understand metabolic regulation underpinning fruit ripening, development, and quality. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:1726-1740. [PMID: 37864494 PMCID: PMC10938048 DOI: 10.1093/jxb/erad384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 09/28/2023] [Indexed: 10/23/2023]
Abstract
Classically fruit ripening and development was studied using genetic approaches, with understanding of metabolic changes that occurred in concert largely focused on a handful of metabolites including sugars, organic acids, cell wall components, and phytohormones. The advent and widespread application of metabolomics has, however, led to far greater understanding of metabolic components that play a crucial role not only in this process but also in influencing the organoleptic and nutritive properties of the fruits. Here we review how the study of natural variation, mutants, transgenics, and gene-edited fruits has led to a considerable increase in our understanding of these aspects. We focus on fleshy fruits such as tomato but also review berries, receptacle fruits, and stone-bearing fruits. Finally, we offer a perspective as to how comparative analyses and machine learning will likely further improve our comprehension of the functional importance of various metabolites in the future.
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Affiliation(s)
- Félix Juan Martínez-Rivas
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) – Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain
- Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, Edificio Severo Ochoa, Campus de Rabanales, E-14014, Córdoba, Spain
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
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70
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Gouveia GJ, Head T, Cheng LL, Clendinen CS, Cort JR, Du X, Edison AS, Fleischer CC, Hoch J, Mercaldo N, Pathmasiri W, Raftery D, Schock TB, Sumner LW, Takis PG, Copié V, Eghbalnia HR, Powers R. Perspective: use and reuse of NMR-based metabolomics data: what works and what remains challenging. Metabolomics 2024; 20:41. [PMID: 38480600 DOI: 10.1007/s11306-024-02090-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 01/12/2024] [Indexed: 04/20/2024]
Abstract
BACKGROUND The National Cancer Institute issued a Request for Information (RFI; NOT-CA-23-007) in October 2022, soliciting input on using and reusing metabolomics data. This RFI aimed to gather input on best practices for metabolomics data storage, management, and use/reuse. AIM OF REVIEW The nuclear magnetic resonance (NMR) Interest Group within the Metabolomics Association of North America (MANA) prepared a set of recommendations regarding the deposition, archiving, use, and reuse of NMR-based and, to a lesser extent, mass spectrometry (MS)-based metabolomics datasets. These recommendations were built on the collective experiences of metabolomics researchers within MANA who are generating, handling, and analyzing diverse metabolomics datasets spanning experimental (sample handling and preparation, NMR/MS metabolomics data acquisition, processing, and spectral analyses) to computational (automation of spectral processing, univariate and multivariate statistical analysis, metabolite prediction and identification, multi-omics data integration, etc.) studies. KEY SCIENTIFIC CONCEPTS OF REVIEW We provide a synopsis of our collective view regarding the use and reuse of metabolomics data and articulate several recommendations regarding best practices, which are aimed at encouraging researchers to strengthen efforts toward maximizing the utility of metabolomics data, multi-omics data integration, and enhancing the overall scientific impact of metabolomics studies.
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Affiliation(s)
- Goncalo Jorge Gouveia
- Metabolomics Association of North America (MANA), NMR Special Interest Group, Edmonton, Canada
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology, University of Maryland, Gudelsky Drive, Rockville, MD, 20850, USA
| | - Thomas Head
- Metabolomics Association of North America (MANA), NMR Special Interest Group, Edmonton, Canada
- University of British Columbia, Kelowna, BC, V1V 1V7, Canada
| | - Leo L Cheng
- Metabolomics Association of North America (MANA), NMR Special Interest Group, Edmonton, Canada
- Department of Pathology and Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Chaevien S Clendinen
- Metabolomics Association of North America (MANA), NMR Special Interest Group, Edmonton, Canada
- Earth and Biological Sciences Directorate, Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - John R Cort
- Metabolomics Association of North America (MANA), NMR Special Interest Group, Edmonton, Canada
- Earth and Biological Sciences Directorate, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Xiuxia Du
- Metabolomics Association of North America (MANA), NMR Special Interest Group, Edmonton, Canada
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, 9291 University City Blvd, Charlotte, NC, 28223, USA
| | - Arthur S Edison
- Metabolomics Association of North America (MANA), NMR Special Interest Group, Edmonton, Canada
- Department of Biochemistry, University of Georgia, Athens, GA, USA
| | - Candace C Fleischer
- Metabolomics Association of North America (MANA), NMR Special Interest Group, Edmonton, Canada
- Department of Radiology and Imaging Sciences, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Jeffrey Hoch
- Metabolomics Association of North America (MANA), NMR Special Interest Group, Edmonton, Canada
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, 06030-3305, USA
| | - Nathaniel Mercaldo
- Metabolomics Association of North America (MANA), NMR Special Interest Group, Edmonton, Canada
- Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Wimal Pathmasiri
- Metabolomics Association of North America (MANA), NMR Special Interest Group, Edmonton, Canada
- Department of Nutrition, School of Public Health, Nutrition Research Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Daniel Raftery
- Metabolomics Association of North America (MANA), NMR Special Interest Group, Edmonton, Canada
- Department of Anesthesia and Pain Medicine, University of Washington, Seattle, WA, 98109, USA
| | - Tracey B Schock
- Metabolomics Association of North America (MANA), NMR Special Interest Group, Edmonton, Canada
- Chemical Sciences Division, National Institute of Standards and Technology (NIST), Charleston, SC, 29412, USA
| | - Lloyd W Sumner
- Metabolomics Association of North America (MANA), NMR Special Interest Group, Edmonton, Canada
- Department of Biochemistry, MU Metabolomics Center, Bond Life Sciences Center, Interdisciplinary Plant Group, University of Missouri, Columbia, MO, 65211, USA
| | - Panteleimon G Takis
- Metabolomics Association of North America (MANA), NMR Special Interest Group, Edmonton, Canada
- Section of Bioanalytical Chemistry, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, SW7 2AZ, UK
- Department of Metabolism, Digestion and Reproduction, National Phenome Centre, Imperial College London, London, W12 0NN, UK
| | - Valérie Copié
- Metabolomics Association of North America (MANA), NMR Special Interest Group, Edmonton, Canada
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717-3400, USA
| | - Hamid R Eghbalnia
- Metabolomics Association of North America (MANA), NMR Special Interest Group, Edmonton, Canada
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, 06030-3305, USA
| | - Robert Powers
- Metabolomics Association of North America (MANA), NMR Special Interest Group, Edmonton, Canada.
- Department of Chemistry, Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, 722 Hamilton Hall, Lincoln, NE, 68588-0304, USA.
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Chakraborty N. Metabolites: a converging node of host and microbe to explain meta-organism. Front Microbiol 2024; 15:1337368. [PMID: 38505556 PMCID: PMC10949987 DOI: 10.3389/fmicb.2024.1337368] [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: 11/15/2023] [Accepted: 02/13/2024] [Indexed: 03/21/2024] Open
Abstract
Meta-organisms encompassing the host and resident microbiota play a significant role in combatting diseases and responding to stress. Hence, there is growing traction to build a knowledge base about this ecosystem, particularly to characterize the bidirectional relationship between the host and microbiota. In this context, metabolomics has emerged as the major converging node of this entire ecosystem. Systematic comprehension of this resourceful omics component can elucidate the organism-specific response trajectory and the communication grid across the ecosystem embodying meta-organisms. Translating this knowledge into designing nutraceuticals and next-generation therapy are ongoing. Its major hindrance is a significant knowledge gap about the underlying mechanisms maintaining a delicate balance within this ecosystem. To bridge this knowledge gap, a holistic picture of the available information has been presented with a primary focus on the microbiota-metabolite relationship dynamics. The central theme of this article is the gut-brain axis and the participating microbial metabolites that impact cerebral functions.
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Affiliation(s)
- Nabarun Chakraborty
- Medical Readiness Systems Biology, CMPN, WRAIR, Silver Spring, MD, United States
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Wang Z, Guo S, Cai Y, Yang Q, Wang Y, Yu X, Sun W, Qiu S, Li X, Guo Y, Xie Y, Zhang A, Zheng S. Decoding active compounds and molecular targets of herbal medicine by high-throughput metabolomics technology: A systematic review. Bioorg Chem 2024; 144:107090. [PMID: 38218070 DOI: 10.1016/j.bioorg.2023.107090] [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: 06/26/2023] [Revised: 12/19/2023] [Accepted: 12/31/2023] [Indexed: 01/15/2024]
Abstract
Clinical experiences of herbal medicine (HM) have been used to treat a variety of human intractable diseases. As the treatment of diseases using HM is characterized by multi-components and multi-targets, it is difficult to determine the bio-active components, explore the molecular targets and reveal the mechanisms of action. Metabolomics is frequently used to characterize the effect of external disturbances on organisms because of its unique advantages on detecting changes in endogenous small-molecule metabolites. Its systematicity and integrity are consistent with the effective characteristics of HM. After HM intervention, metabolomics can accurately capture and describe the behavior of endogenous metabolites under the disturbance of functional compounds, which will be used to decode the bioactive ingredients of HM and expound the molecular targets. Metabolomics can provide an approach for explaining HM, addressing unclear clinical efficacy and undefined mechanisms of action. In this review, the metabolomics strategy and its applications in HM are systematically introduced, which offers valuable insights for metabolomics methods to characterizing the pharmacological effects and molecular targets of HM.
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Affiliation(s)
- Zhibo Wang
- Scientific Experiment Center, Hainan General Hospital, International Advanced Functional Omics Platform, International Joint Research Center on Traditional Chinese and Modern Medicine, Key Laboratory of Tropical Cardiovascular Diseases Research of Hainan Province, Hainan Engineering Research Center for Biological Sample Resources of Major Diseases, Hainan Medical University, Xueyuan Road 3, Haikou 571199, China; Graduate School, Heilongjiang University of Chinese Medicine, Harbin 150040, China
| | - Sifan Guo
- Scientific Experiment Center, Hainan General Hospital, International Advanced Functional Omics Platform, International Joint Research Center on Traditional Chinese and Modern Medicine, Key Laboratory of Tropical Cardiovascular Diseases Research of Hainan Province, Hainan Engineering Research Center for Biological Sample Resources of Major Diseases, Hainan Medical University, Xueyuan Road 3, Haikou 571199, China
| | - Ying Cai
- Scientific Experiment Center, Hainan General Hospital, International Advanced Functional Omics Platform, International Joint Research Center on Traditional Chinese and Modern Medicine, Key Laboratory of Tropical Cardiovascular Diseases Research of Hainan Province, Hainan Engineering Research Center for Biological Sample Resources of Major Diseases, Hainan Medical University, Xueyuan Road 3, Haikou 571199, China; Graduate School, Heilongjiang University of Chinese Medicine, Harbin 150040, China
| | - Qiang Yang
- Graduate School, Heilongjiang University of Chinese Medicine, Harbin 150040, China
| | - Yan Wang
- Scientific Experiment Center, Hainan General Hospital, International Advanced Functional Omics Platform, International Joint Research Center on Traditional Chinese and Modern Medicine, Key Laboratory of Tropical Cardiovascular Diseases Research of Hainan Province, Hainan Engineering Research Center for Biological Sample Resources of Major Diseases, Hainan Medical University, Xueyuan Road 3, Haikou 571199, China
| | - Xiaodan Yu
- Scientific Experiment Center, Hainan General Hospital, International Advanced Functional Omics Platform, International Joint Research Center on Traditional Chinese and Modern Medicine, Key Laboratory of Tropical Cardiovascular Diseases Research of Hainan Province, Hainan Engineering Research Center for Biological Sample Resources of Major Diseases, Hainan Medical University, Xueyuan Road 3, Haikou 571199, China
| | - Wanying Sun
- Scientific Experiment Center, Hainan General Hospital, International Advanced Functional Omics Platform, International Joint Research Center on Traditional Chinese and Modern Medicine, Key Laboratory of Tropical Cardiovascular Diseases Research of Hainan Province, Hainan Engineering Research Center for Biological Sample Resources of Major Diseases, Hainan Medical University, Xueyuan Road 3, Haikou 571199, China
| | - Shi Qiu
- Scientific Experiment Center, Hainan General Hospital, International Advanced Functional Omics Platform, International Joint Research Center on Traditional Chinese and Modern Medicine, Key Laboratory of Tropical Cardiovascular Diseases Research of Hainan Province, Hainan Engineering Research Center for Biological Sample Resources of Major Diseases, Hainan Medical University, Xueyuan Road 3, Haikou 571199, China.
| | - Xiancai Li
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Xingke Road 723, Guangzhou 510650, China.
| | - Yu Guo
- Scientific Experiment Center, Hainan General Hospital, International Advanced Functional Omics Platform, International Joint Research Center on Traditional Chinese and Modern Medicine, Key Laboratory of Tropical Cardiovascular Diseases Research of Hainan Province, Hainan Engineering Research Center for Biological Sample Resources of Major Diseases, Hainan Medical University, Xueyuan Road 3, Haikou 571199, China.
| | - Yiqiang Xie
- Scientific Experiment Center, Hainan General Hospital, International Advanced Functional Omics Platform, International Joint Research Center on Traditional Chinese and Modern Medicine, Key Laboratory of Tropical Cardiovascular Diseases Research of Hainan Province, Hainan Engineering Research Center for Biological Sample Resources of Major Diseases, Hainan Medical University, Xueyuan Road 3, Haikou 571199, China.
| | - Aihua Zhang
- Scientific Experiment Center, Hainan General Hospital, International Advanced Functional Omics Platform, International Joint Research Center on Traditional Chinese and Modern Medicine, Key Laboratory of Tropical Cardiovascular Diseases Research of Hainan Province, Hainan Engineering Research Center for Biological Sample Resources of Major Diseases, Hainan Medical University, Xueyuan Road 3, Haikou 571199, China; Graduate School, Heilongjiang University of Chinese Medicine, Harbin 150040, China.
| | - Shaojiang Zheng
- Medical Research Center of The First Affiliated Hospital, Hainan Women and Children Medical Center, Key Laboratory of Emergency and Trauma of Ministry of Education, Hainan Medical University, Haikou 571199, China.
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73
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Kumari M, Yagnik KN, Gupta V, Singh IK, Gupta R, Verma PK, Singh A. Metabolomics-driven investigation of plant defense response against pest and pathogen attack. PHYSIOLOGIA PLANTARUM 2024; 176:e14270. [PMID: 38566280 DOI: 10.1111/ppl.14270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 02/27/2024] [Accepted: 02/29/2024] [Indexed: 04/04/2024]
Abstract
The advancement of metabolomics has assisted in the identification of various bewildering characteristics of the biological system. Metabolomics is a standard approach, facilitating crucial aspects of system biology with absolute quantification of metabolites using minimum samples, based on liquid/gas chromatography, mass spectrometry and nuclear magnetic resonance. The metabolome profiling has narrowed the wide gaps of missing information and has enhanced the understanding of a wide spectrum of plant-environment interactions by highlighting the complex pathways regulating biochemical reactions and cellular physiology under a particular set of conditions. This high throughput technique also plays a prominent role in combined analyses of plant metabolomics and other omics datasets. Plant metabolomics has opened a wide paradigm of opportunities for developing stress-tolerant plants, ensuring better food quality and quantity. However, despite advantageous methods and databases, the technique has a few limitations, such as ineffective 3D capturing of metabolites, low comprehensiveness, and lack of cell-based sampling. In the future, an expansion of plant-pathogen and plant-pest response towards the metabolite architecture is necessary to understand the intricacies of plant defence against invaders, elucidation of metabolic pathway operational during defence and developing a direct correlation between metabolites and biotic stresses. Our aim is to provide an overview of metabolomics and its utilities for the identification of biomarkers or key metabolites associated with biotic stress, devising improved diagnostic methods to efficiently assess pest and pathogen attack and generating improved crop varieties with the help of combined application of analytical and molecular tools.
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Affiliation(s)
- Megha Kumari
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
- Department of Botany, Hansraj College, University of Delhi, Delhi, India
| | - Kalpesh Nath Yagnik
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
- Department of Botany, Hansraj College, University of Delhi, Delhi, India
| | - Vaishali Gupta
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | - Indrakant K Singh
- Molecular Biology Research Lab, Department of Zoology, Deshbandhu College, University of Delhi, New Delhi, India
| | - Ravi Gupta
- College of General Education, Kookmin University, Seoul, Republic of Korea
| | - Praveen K Verma
- Plant-Immunity Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Archana Singh
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
- Department of Botany, Hansraj College, University of Delhi, Delhi, India
- Delhi School of Climate Change and Sustainability, Institution of Eminence, Maharishi Karnad Bhawan, University of Delhi, India
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Cajka T, Hricko J, Rakusanova S, Brejchova K, Novakova M, Rudl Kulhava L, Hola V, Paucova M, Fiehn O, Kuda O. Hydrophilic Interaction Liquid Chromatography-Hydrogen/Deuterium Exchange-Mass Spectrometry (HILIC-HDX-MS) for Untargeted Metabolomics. Int J Mol Sci 2024; 25:2899. [PMID: 38474147 DOI: 10.3390/ijms25052899] [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: 01/15/2024] [Revised: 02/17/2024] [Accepted: 02/26/2024] [Indexed: 03/14/2024] Open
Abstract
Liquid chromatography with mass spectrometry (LC-MS)-based metabolomics detects thousands of molecular features (retention time-m/z pairs) in biological samples per analysis, yet the metabolite annotation rate remains low, with 90% of signals classified as unknowns. To enhance the metabolite annotation rates, researchers employ tandem mass spectral libraries and challenging in silico fragmentation software. Hydrogen/deuterium exchange mass spectrometry (HDX-MS) may offer an additional layer of structural information in untargeted metabolomics, especially for identifying specific unidentified metabolites that are revealed to be statistically significant. Here, we investigate the potential of hydrophilic interaction liquid chromatography (HILIC)-HDX-MS in untargeted metabolomics. Specifically, we evaluate the effectiveness of two approaches using hypothetical targets: the post-column addition of deuterium oxide (D2O) and the on-column HILIC-HDX-MS method. To illustrate the practical application of HILIC-HDX-MS, we apply this methodology using the in silico fragmentation software MS-FINDER to an unknown compound detected in various biological samples, including plasma, serum, tissues, and feces during HILIC-MS profiling, subsequently identified as N1-acetylspermidine.
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Affiliation(s)
- Tomas Cajka
- Institute of Physiology of the Czech Academy of Sciences, Videnska 1083, 14200 Prague, Czech Republic
| | - Jiri Hricko
- Institute of Physiology of the Czech Academy of Sciences, Videnska 1083, 14200 Prague, Czech Republic
| | - Stanislava Rakusanova
- Institute of Physiology of the Czech Academy of Sciences, Videnska 1083, 14200 Prague, Czech Republic
| | - Kristyna Brejchova
- Institute of Physiology of the Czech Academy of Sciences, Videnska 1083, 14200 Prague, Czech Republic
| | - Michaela Novakova
- Institute of Physiology of the Czech Academy of Sciences, Videnska 1083, 14200 Prague, Czech Republic
| | - Lucie Rudl Kulhava
- Institute of Physiology of the Czech Academy of Sciences, Videnska 1083, 14200 Prague, Czech Republic
| | - Veronika Hola
- Institute of Physiology of the Czech Academy of Sciences, Videnska 1083, 14200 Prague, Czech Republic
| | - Michaela Paucova
- Institute of Physiology of the Czech Academy of Sciences, Videnska 1083, 14200 Prague, Czech Republic
| | - Oliver Fiehn
- West Coast Metabolomics Center, University of California, Davis, 451 Health Sciences Drive, Davis, CA 95616, USA
| | - Ondrej Kuda
- Institute of Physiology of the Czech Academy of Sciences, Videnska 1083, 14200 Prague, Czech Republic
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Zhang N, Zhang H, Lv Z, Bai B, Ren J, Shi X, Kang S, Zhao X, Yu H, Zhao T. Integrative multi-omics analysis reveals the crucial biological pathways involved in the adaptive response to NaCl stress in peanut seedlings. PHYSIOLOGIA PLANTARUM 2024; 176:e14266. [PMID: 38558467 DOI: 10.1111/ppl.14266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 03/02/2024] [Accepted: 03/05/2024] [Indexed: 04/04/2024]
Abstract
Plant growth is restricted by salt stress, which is a significant abiotic factor, particularly during the seedling stage. The aim of this study was to investigate the mechanisms underlying peanut adaptation to salt stress by transcriptomic and metabolomic analysis during the seedling stage. In this study, phenotypic variations of FH23 and NH5, two peanut varieties with contrasting tolerance to salt, changed obviously, with the strongest differences observed at 24 h. FH23 leaves wilted and the membrane system was seriously damaged. A total of 1470 metabolites were identified, with flavonoids being the most common (21.22%). Multi-omics analyses demonstrated that flavonoid biosynthesis (ko00941), isoflavones biosynthesis (ko00943), and plant hormone signal transduction (ko04075) were key metabolic pathways. The comparison of metabolites in isoflavone biosynthesis pathways of peanut varieties with different salt tolerant levels demonstrated that the accumulation of naringenin and formononetin may be the key metabolite leading to their different tolerance. Using our transcriptomic data, we identified three possible reasons for the difference in salt tolerance between the two varieties: (1) differential expression of LOC112715558 (HIDH) and LOC112709716 (HCT), (2) differential expression of LOC112719763 (PYR/PYL) and LOC112764051 (ABF) in the abscisic acid (ABA) signal transduction pathway, then (3) differential expression of genes encoding JAZ proteins (LOC112696383 and LOC112790545). Key metabolites and candidate genes related to improving the salt tolerance in peanuts were screened to promote the study of the responses of peanuts to NaCl stress and guide their genetic improvement.
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Affiliation(s)
- Nan Zhang
- College of Agriculture, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - He Zhang
- College of Agriculture, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Zhenghao Lv
- College of Agriculture, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Baiyi Bai
- School of Agriculture and Horticulture, Liaoning Agriculture Vocational and Technical College, Yingkou, Liaoning, China
| | - Jingyao Ren
- College of Agriculture, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Xiaolong Shi
- College of Agriculture, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Shuli Kang
- College of Agriculture, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Xinhua Zhao
- College of Agriculture, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Haiqiu Yu
- College of Agriculture, Shenyang Agricultural University, Shenyang, Liaoning, China
- School of Agriculture and Horticulture, Liaoning Agriculture Vocational and Technical College, Yingkou, Liaoning, China
| | - Tianhong Zhao
- College of Agriculture, Shenyang Agricultural University, Shenyang, Liaoning, China
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76
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Kant K, Rigó G, Faragó D, Benyó D, Tengölics R, Szabados L, Zsigmond L. Mutation in Arabidopsis mitochondrial Pentatricopeptide repeat 40 gene affects tolerance to water deficit. PLANTA 2024; 259:78. [PMID: 38427069 PMCID: PMC10907415 DOI: 10.1007/s00425-024-04354-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 01/26/2024] [Indexed: 03/02/2024]
Abstract
MAIN CONCLUSION The Arabidopsis Pentatricopeptide repeat 40 (PPR40) insertion mutants have increased tolerance to water deficit compared to wild-type plants. Tolerance is likely the consequence of ABA hypersensitivity of the mutants. Plant growth and development depend on multiple environmental factors whose alterations can disrupt plant homeostasis and trigger complex molecular and physiological responses. Water deficit is one of the factors which can seriously restrict plant growth and viability. Mitochondria play an important role in cellular metabolism, energy production, and redox homeostasis. During drought and salinity stress, mitochondrial dysfunction can lead to ROS overproduction and oxidative stress, affecting plant growth and survival. Alternative oxidases (AOXs) and stabilization of mitochondrial electron transport chain help mitigate ROS damage. The mitochondrial Pentatricopeptide repeat 40 (PPR40) protein was implicated in stress regulation as ppr40 mutants were found to be hypersensitive to ABA and high salinity during germination. This study investigated the tolerance of the knockout ppr40-1 and knockdown ppr40-2 mutants to water deprivation. Our results show that these mutants display an enhanced tolerance to water deficit. The mutants had higher relative water content, reduced level of oxidative damage, and better photosynthetic parameters in water-limited conditions compared to wild-type plants. ppr40 mutants had considerable differences in metabolic profiles and expression of a number of stress-related genes, suggesting important metabolic reprogramming. Tolerance to water deficit was also manifested in higher survival rates and alleviated growth reduction when watering was suspended. Enhanced sensitivity to ABA and fast stomata closure was suggested to lead to improved capacity for water conservation in such environment. Overall, this study highlights the importance of mitochondrial functions and in particular PPR40 in plant responses to abiotic stress, particularly drought.
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Affiliation(s)
- Kamal Kant
- Institute of Plant Biology, HUN-REN Biological Research Centre, Temesvári Krt. 62, 6726, Szeged, Hungary
| | - Gábor Rigó
- Institute of Plant Biology, HUN-REN Biological Research Centre, Temesvári Krt. 62, 6726, Szeged, Hungary
| | - Dóra Faragó
- Institute of Plant Biology, HUN-REN Biological Research Centre, Temesvári Krt. 62, 6726, Szeged, Hungary
| | - Dániel Benyó
- Institute of Plant Biology, HUN-REN Biological Research Centre, Temesvári Krt. 62, 6726, Szeged, Hungary
| | - Roland Tengölics
- Institute of Biochemistry, HUN-REN Biological Research Centre, Temesvári Krt. 62, 6726, Szeged, Hungary
| | - László Szabados
- Institute of Plant Biology, HUN-REN Biological Research Centre, Temesvári Krt. 62, 6726, Szeged, Hungary.
| | - Laura Zsigmond
- Institute of Plant Biology, HUN-REN Biological Research Centre, Temesvári Krt. 62, 6726, Szeged, Hungary
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77
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Cooper B, Yang R. An assessment of AcquireX and Compound Discoverer software 3.3 for non-targeted metabolomics. Sci Rep 2024; 14:4841. [PMID: 38418855 PMCID: PMC10902394 DOI: 10.1038/s41598-024-55356-3] [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: 10/20/2023] [Accepted: 02/22/2024] [Indexed: 03/02/2024] Open
Abstract
We used the Exploris 240 mass spectrometer for non-targeted metabolomics on Saccharomyces cerevisiae strain BY4741 and tested AcquireX software for increasing the number of detectable compounds and Compound Discoverer 3.3 software for identifying compounds by MS2 spectral library matching. AcquireX increased the number of potentially identifiable compounds by 50% through six iterations of MS2 acquisition. On the basis of high-scoring MS2 matches made by Compound Discoverer, there were 483 compounds putatively identified from nearly 8000 candidate spectra. Comparisons to 20 amino acid standards, however, revealed instances whereby compound matches could be incorrect despite strong scores. Situations included the candidate with the top score not being the correct compound, matching the same compound at two different chromatographic peaks, assigning the highest score to a library compound much heavier than the mass for the parent ion, and grouping MS2 isomers to a single parent ion. Because the software does not calculate false positive and false discovery rates at these multiple levels where such errors can propagate, we conclude that manual examination of findings will be required post software analysis. These results will interest scientists who may use this platform for metabolomics research in diverse disciplines including medical science, environmental science, and agriculture.
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Affiliation(s)
- Bret Cooper
- Soybean Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD, 20705, USA.
| | - Ronghui Yang
- Soybean Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD, 20705, USA
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Zhu A, Liu M, Tian Z, Liu W, Hu X, Ao M, Jia J, Shi T, Liu H, Li D, Mao H, Su H, Yan W, Li Q, Lan C, Fernie AR, Chen W. Chemical-tag-based semi-annotated metabolomics facilitates gene identification and specialized metabolic pathway elucidation in wheat. THE PLANT CELL 2024; 36:540-558. [PMID: 37956052 PMCID: PMC10896294 DOI: 10.1093/plcell/koad286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 10/19/2023] [Accepted: 10/19/2023] [Indexed: 11/15/2023]
Abstract
The importance of metabolite modification and species-specific metabolic pathways has long been recognized. However, linking the chemical structure of metabolites to gene function in order to explore the genetic and biochemical basis of metabolism has not yet been reported in wheat (Triticum aestivum). Here, we profiled metabolic fragment enrichment in wheat leaves and consequently applied chemical-tag-based semi-annotated metabolomics in a genome-wide association study in accessions of wheat. The studies revealed that all 1,483 quantified metabolites have at least one known functional group whose modification is tailored in an enzyme-catalyzed manner and eventually allows efficient candidate gene mining. A Triticeae crop-specific flavonoid pathway and its underlying metabolic gene cluster were elucidated in further functional studies. Additionally, upon overexpressing the major effect gene of the cluster TraesCS2B01G460000 (TaOMT24), the pathway was reconstructed in rice (Oryza sativa), which lacks this pathway. The reported workflow represents an efficient and unbiased approach for gene mining using forward genetics in hexaploid wheat. The resultant candidate gene list contains vast molecular resources for decoding the genetic architecture of complex traits and identifying valuable breeding targets and will ultimately aid in achieving wheat crop improvement.
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Affiliation(s)
- Anting Zhu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Mengmeng Liu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Zhitao Tian
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Wei Liu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Xin Hu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Min Ao
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Jingqi Jia
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Taotao Shi
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Hongbo Liu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Dongqin Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Hailiang Mao
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Handong Su
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Wenhao Yan
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Qiang Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Caixia Lan
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Department of Root Biology and Symbiosis, Potsdam-Golm 14476, Germany
| | - Wei Chen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
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79
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Ikeda K, Takahashi M, Bamba T, Izumi Y. Comparison of Amine-Modified Polymeric Stationary Phases for Polar Metabolomic Analysis Based on Unified-Hydrophilic Interaction/Anion Exchange Liquid Chromatography/High-Resolution Mass Spectrometry (Unified-HILIC/AEX/HRMS). Mass Spectrom (Tokyo) 2024; 13:A0143. [PMID: 38410254 PMCID: PMC10894851 DOI: 10.5702/massspectrometry.a0143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 01/19/2024] [Indexed: 02/28/2024] Open
Abstract
In metabolomic analysis, one of the most commonly used techniques to support the detection sensitivity and quantitation of mass spectrometry is combining it with liquid chromatography. Recently, we developed a method that enables comprehensive single-run measurement of hydrophilic metabolites using unified-hydrophilic interaction/anion exchange liquid chromatography/high-resolution mass spectrometry (unified-HILIC/AEX/HRMS) with a polymer-based mixed amines column (Gelpack GL-HilicAex). However, the importance of stationary phase functional groups and mobile phase conditions for the separation mechanisms and sensitive detection in unified-HILIC/AEX/HRMS is not yet fully understood. This study aimed to understand the importance of the mobile and stationary phases in unified-HILIC/AEX/HRMS. Two different alkali-resistant polymer-based amines-modified columns (Gelpack GL-HilicAex, primary, secondary, tertiary, and quaternary amine-modified polyglycerol dimethacrylate gel; Asahipak NH2P-50 2D, secondary amine-modified polyvinyl alcohol gel) and two eluents (acetonitrile and ammonium bicarbonate solution, pH 9.8) were used for comparative validation. A comparison of mobile phase conditions using both columns confirmed that the two-step separation from HILIC to AEX characteristic of unified-HILIC/AEX requires a linear gradient condition from acetonitrile to nearly 50% water and AEX with up to 40 mM bicarbonate ions. We found that when alkali-resistant hydrophilic polymer packing materials are modified with amines, unified-HILIC/AEX separation can be reproduced if at least one secondary amine associated with the amine series is present in the stationary phase. Furthermore, the difference in sensitivity in the HILIC and AEX modes owing to the different columns indicates the need for further improvements in the mobile phase composition and stationary phase.
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Affiliation(s)
- Kazuki Ikeda
- Department of Systems Life Sciences, Graduate School of Systems Life Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Masatomo Takahashi
- Department of Systems Life Sciences, Graduate School of Systems Life Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
- Division of Metabolomics/Mass Spectrometry Center, Medical Research Center for High Depth Omics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Takeshi Bamba
- Department of Systems Life Sciences, Graduate School of Systems Life Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
- Division of Metabolomics/Mass Spectrometry Center, Medical Research Center for High Depth Omics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Yoshihiro Izumi
- Department of Systems Life Sciences, Graduate School of Systems Life Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
- Division of Metabolomics/Mass Spectrometry Center, Medical Research Center for High Depth Omics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
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80
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Liu D, Nagana Gowda GA, Jiang Z, Alemdjrodo K, Zhang M, Zhang D, Raftery D. Modeling blood metabolite homeostatic levels reduces sample heterogeneity across cohorts. Proc Natl Acad Sci U S A 2024; 121:e2307430121. [PMID: 38359289 PMCID: PMC10895372 DOI: 10.1073/pnas.2307430121] [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: 05/06/2023] [Accepted: 12/05/2023] [Indexed: 02/17/2024] Open
Abstract
Blood metabolite levels are affected by numerous factors, including preanalytical factors such as collection methods and geographical sites. These perturbations have caused deleterious consequences for many metabolomics studies and represent a major challenge in the metabolomics field. It is important to understand these factors and develop models to reduce their perturbations. However, to date, the lack of suitable mathematical models for blood metabolite levels under homeostasis has hindered progress. In this study, we develop quantitative models of blood metabolite levels in healthy adults based on multisite sample cohorts that mimic the current challenge. Five cohorts of samples obtained across four geographically distinct sites were investigated, focusing on approximately 50 metabolites that were quantified using 1H NMR spectroscopy. More than one-third of the variation in these metabolite profiles is due to cross-cohort variation. A dramatic reduction in the variation of metabolite levels (90%), especially their site-to-site variation (95%), was achieved by modeling each metabolite using demographic and clinical factors and especially other metabolites, as observed in the top principal components. The results also reveal that several metabolites contribute disproportionately to such variation, which could be explained by their association with biological pathways including biosynthesis and degradation. The study demonstrates an intriguing network effect of metabolites that can be utilized to better define homeostatic metabolite levels, which may have implications for improved health monitoring. As an example of the potential utility of the approach, we show that modeling gender-related metabolic differences retains the interesting variance while reducing unwanted (site-related) variance.
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Affiliation(s)
- Danni Liu
- Department of Statistics, Purdue University, West Lafayette, IN47907
| | - G. A. Nagana Gowda
- Department of Anesthesiology and Pain Medicine, Northwest Metabolomics Research Center, University of Washington, Seattle, WA98109
| | - Zhongli Jiang
- Department of Statistics, Purdue University, West Lafayette, IN47907
| | - Kangni Alemdjrodo
- Department of Statistics, Purdue University, West Lafayette, IN47907
| | - Min Zhang
- Department of Statistics, Purdue University, West Lafayette, IN47907
- Department of Epidemiology and Biostatistics, University of California, Irvine, CA92697
| | - Dabao Zhang
- Department of Statistics, Purdue University, West Lafayette, IN47907
- Department of Epidemiology and Biostatistics, University of California, Irvine, CA92697
| | - Daniel Raftery
- Department of Anesthesiology and Pain Medicine, Northwest Metabolomics Research Center, University of Washington, Seattle, WA98109
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81
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Kambhampati S, Hubbard AH, Koley S, Gomez JD, Marsolais F, Evans BS, Young JD, Allen DK. SIMPEL: using stable isotopes to elucidate dynamics of context specific metabolism. Commun Biol 2024; 7:172. [PMID: 38347116 PMCID: PMC10861564 DOI: 10.1038/s42003-024-05844-z] [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: 08/03/2022] [Accepted: 01/23/2024] [Indexed: 02/15/2024] Open
Abstract
The capacity to leverage high resolution mass spectrometry (HRMS) with transient isotope labeling experiments is an untapped opportunity to derive insights on context-specific metabolism, that is difficult to assess quantitatively. Tools are needed to comprehensively mine isotopologue information in an automated, high-throughput way without errors. We describe a tool, Stable Isotope-assisted Metabolomics for Pathway Elucidation (SIMPEL), to simplify analysis and interpretation of isotope-enriched HRMS datasets. The efficacy of SIMPEL is demonstrated through examples of central carbon and lipid metabolism. In the first description, a dual-isotope labeling experiment is paired with SIMPEL and isotopically nonstationary metabolic flux analysis (INST-MFA) to resolve fluxes in central metabolism that would be otherwise challenging to quantify. In the second example, SIMPEL was paired with HRMS-based lipidomics data to describe lipid metabolism based on a single labeling experiment. Available as an R package, SIMPEL extends metabolomics analyses to include isotopologue signatures necessary to quantify metabolic flux.
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Affiliation(s)
- Shrikaar Kambhampati
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA.
- Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA.
| | - Allen H Hubbard
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | - Somnath Koley
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | - Javier D Gomez
- Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, 37235, USA
| | - Frédéric Marsolais
- London Research and Development Center, London, ON, N5V 4T3, Canada
- Department of Biology, University of Western Ontario, London, ON, N6A 5B7, Canada
| | - Bradley S Evans
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | - Jamey D Young
- Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, 37235, USA
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37235, USA
| | - Doug K Allen
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA.
- Agricultural Research Service, US Department of Agriculture, St. Louis, MO, 63132, USA.
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82
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Shafer CC, Neumann EK. Optimized combination of MALDI MSI and immunofluorescence for neuroimaging of lipids within cellular microenvironments. Front Chem 2024; 12:1334209. [PMID: 38406559 PMCID: PMC10884125 DOI: 10.3389/fchem.2024.1334209] [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: 11/06/2023] [Accepted: 01/25/2024] [Indexed: 02/27/2024] Open
Abstract
Proper neurological function relies on the cellular and molecular microenvironment of the brain, with perturbations of this environment leading to neurological disorders. However, studying the microenvironments of neurological tissue has proven difficult because of its inherent complexity. Both the cell type and metabolomic underpinnings of the cell have crucial functional roles, thus making multimodal characterization methods key to acquiring a holistic view of the brain's microenvironment. This study investigates methods for combining matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI) and immunofluorescence (IF) microscopy to enable the concurrent investigation of cell types and lipid profiles on the same sample. In brief, 1,5-diaminonaphthalene (DAN), α-cyano-4-hydroxy-cinnamic acid (CHCA), and 2,5-dihydroxybenzoic acid (DHB) were tested in addition to instrument-specific parameters for compatibility with IF. Alternatively, the effects of IF protocols on MALDI MSI were also tested, showing significant signal loss with all tested permutations. Ultimately, the use of CHCA for MALDI MSI resulted in the best IF images, while the use of DAN gave the lowest quality IF images. Overall, increasing the laser power and number of shots per laser burst resulted in the most tissue ablation. However, optimized parameter settings allowed for minimal tissue ablation while maintaining sufficient MALDI MSI signal.
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Affiliation(s)
| | - Elizabeth K. Neumann
- Department of Chemistry, University of California Davis, Davis, CA, United States
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83
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Engler Hart C, Kind T, Dorrestein PC, Healey D, Domingo-Fernández D. Weighting Low-Intensity MS/MS Ions and m/ z Frequency for Spectral Library Annotation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:266-274. [PMID: 38271611 PMCID: PMC10854760 DOI: 10.1021/jasms.3c00353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 12/29/2023] [Accepted: 01/05/2024] [Indexed: 01/27/2024]
Abstract
Calculating spectral similarity is a fundamental step in MS/MS data analysis in untargeted metabolomics experiments, as it facilitates the identification of related spectra and the annotation of compounds. To improve matching accuracy when querying an experimental mass spectrum against a spectral library, previous approaches have proposed increasing peak intensities for high m/z ranges. These high m/z values tend to be smaller in magnitude, yet they offer more crucial information for identifying the chemical structure. Here, we evaluate the impact of using these weights for identifying structurally related compounds and mass spectral library searches. Additionally, we propose a weighting approach that (i) takes into account the frequency of the m/z values within a spectral library in order to assign higher importance to the most common peaks and (ii) increases the intensity of lower peaks, similar to previous approaches. To demonstrate our approach, we applied weighting preprocessing to modified cosine, entropy, and fidelity distance metrics and benchmarked it against previously reported weights. Our results demonstrate how weighting-based preprocessing can assist in annotating the structure of unknown spectra as well as identifying structurally similar compounds. Finally, we examined scenarios in which the utilization of weights resulted in diminished performance, pinpointing spectral features where the application of weights might be detrimental.
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Affiliation(s)
- Chloe Engler Hart
- Enveda Biosciences, 5700 Flatiron Parkway, Boulder, Colorado 80301, United States
| | - Tobias Kind
- Enveda Biosciences, 5700 Flatiron Parkway, Boulder, Colorado 80301, United States
| | - Pieter C. Dorrestein
- Collaborative
Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and
Pharmaceutical Sciences, University of California
San Diego, La Jolla, California 92093, United States
| | - David Healey
- Enveda Biosciences, 5700 Flatiron Parkway, Boulder, Colorado 80301, United States
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84
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Wang W, Zhen S, Ping Y, Wang L, Zhang Y. Metabolomic biomarkers in liquid biopsy: accurate cancer diagnosis and prognosis monitoring. Front Oncol 2024; 14:1331215. [PMID: 38384814 PMCID: PMC10879439 DOI: 10.3389/fonc.2024.1331215] [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: 10/31/2023] [Accepted: 01/26/2024] [Indexed: 02/23/2024] Open
Abstract
Liquid biopsy, a novel detection method, has recently become an active research area in clinical cancer owing to its unique advantages. Studies on circulating free DNA, circulating tumor cells, and exosomes obtained by liquid biopsy have shown great advances and they have entered clinical practice as new cancer biomarkers. The metabolism of the body is dynamic as cancer originates and progresses. Metabolic abnormalities caused by cancer can be detected in the blood, sputum, urine, and other biological fluids via systemic or local circulation. A considerable number of recent studies have focused on the roles of metabolic molecules in cancer. The purpose of this review is to provide an overview of metabolic markers from various biological fluids in the latest clinical studies, which may contribute to cancer screening and diagnosis, differentiation of cancer typing, grading and staging, and prediction of therapeutic response and prognosis.
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Affiliation(s)
- Wenqian Wang
- Biotherapy Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Key Laboratory for Tumor Immunology and Biotherapy of Henan Province, Zhengzhou, Henan, China
| | - Shanshan Zhen
- Biotherapy Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Key Laboratory for Tumor Immunology and Biotherapy of Henan Province, Zhengzhou, Henan, China
| | - Yu Ping
- Biotherapy Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Key Laboratory for Tumor Immunology and Biotherapy of Henan Province, Zhengzhou, Henan, China
| | - Liping Wang
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Yi Zhang
- Biotherapy Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Key Laboratory for Tumor Immunology and Biotherapy of Henan Province, Zhengzhou, Henan, China
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou, Henan, China
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85
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Evans SE, Franks AE, Bergman ME, Sethna NS, Currie MA, Phillips MA. Plastid ancestors lacked a complete Entner-Doudoroff pathway, limiting plants to glycolysis and the pentose phosphate pathway. Nat Commun 2024; 15:1102. [PMID: 38321044 PMCID: PMC10847513 DOI: 10.1038/s41467-024-45384-y] [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: 08/17/2023] [Accepted: 01/20/2024] [Indexed: 02/08/2024] Open
Abstract
The Entner-Doudoroff (ED) pathway provides an alternative to glycolysis. It converts 6-phosphogluconate (6-PG) to glyceraldehyde-3-phosphate and pyruvate in two steps consisting of a dehydratase (EDD) and an aldolase (EDA). Here, we investigate its distribution and significance in higher plants and determine the ED pathway is restricted to prokaryotes due to the absence of EDD genes in eukaryotes. EDDs share a common origin with dihydroxy-acid dehydratases (DHADs) of the branched chain amino acid pathway (BCAA). Each dehydratase features strict substrate specificity. E. coli EDD dehydrates 6-PG to 2-keto-3-deoxy-6-phosphogluconate, while DHAD only dehydrates substrates from the BCAA pathway. Structural modeling identifies two divergent domains which account for their non-overlapping substrate affinities. Coupled enzyme assays confirm only EDD participates in the ED pathway. Plastid ancestors lacked EDD but transferred metabolically promiscuous EDA, which explains the absence of the ED pathway from the Viridiplantae and sporadic persistence of EDA genes across the plant kingdom.
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Affiliation(s)
- Sonia E Evans
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, M5S 3G5, Canada
| | - Anya E Franks
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, M5S 3G5, Canada
| | - Matthew E Bergman
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, M5S 3G5, Canada
| | - Nasha S Sethna
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, M5S 3G5, Canada
| | - Mark A Currie
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, M5S 3G5, Canada
- Department of Biology, University of Toronto-Mississauga, Mississauga, ON, L5L 1C6, Canada
| | - Michael A Phillips
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, M5S 3G5, Canada.
- Department of Biology, University of Toronto-Mississauga, Mississauga, ON, L5L 1C6, Canada.
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86
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Pautova AK. Metabolic Profiling of Aromatic Compounds. Metabolites 2024; 14:107. [PMID: 38392999 PMCID: PMC10890443 DOI: 10.3390/metabo14020107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 02/02/2024] [Indexed: 02/25/2024] Open
Abstract
Metabolic profiling is a powerful modern tool in searching for novel biomarkers and indicators of normal or pathological processes in the body [...].
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Affiliation(s)
- Alisa K Pautova
- Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, 25-2 Petrovka Str., 107031 Moscow, Russia
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87
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Olkowicz M, Ramadan K, Rosales-Solano H, Yu M, Wang A, Cypel M, Pawliszyn J. Mapping the metabolic responses to oxaliplatin-based chemotherapy with in vivo spatiotemporal metabolomics. J Pharm Anal 2024; 14:196-210. [PMID: 38464782 PMCID: PMC10921245 DOI: 10.1016/j.jpha.2023.08.001] [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: 04/15/2023] [Revised: 07/14/2023] [Accepted: 08/07/2023] [Indexed: 03/12/2024] Open
Abstract
Adjuvant chemotherapy improves the survival outlook for patients undergoing operations for lung metastases caused by colorectal cancer (CRC). However, a multidisciplinary approach that evaluates several factors related to patient and tumor characteristics is necessary for managing chemotherapy treatment in metastatic CRC patients with lung disease, as such factors dictate the timing and drug regimen, which may affect treatment response and prognosis. In this study, we explore the potential of spatial metabolomics for evaluating metabolic phenotypes and therapy outcomes during the local delivery of the anticancer drug, oxaliplatin, to the lung. 12 male Yorkshire pigs underwent a 3 h left lung in vivo lung perfusion (IVLP) with various doses of oxaliplatin (7.5, 10, 20, 40, and 80 mg/L), which were administered to the perfusion circuit reservoir as a bolus. Biocompatible solid-phase microextraction (SPME) microprobes were combined with global metabolite profiling to obtain spatiotemporal information about the activity of the drug, determine toxic doses that exceed therapeutic efficacy, and conduct a mechanistic exploration of associated lung injury. Mild and subclinical lung injury was observed at 40 mg/L of oxaliplatin, and significant compromise of the hemodynamic lung function was found at 80 mg/L. This result was associated with massive alterations in metabolic patterns of lung tissue and perfusate, resulting in a total of 139 discriminant compounds. Uncontrolled inflammatory response, abnormalities in energy metabolism, and mitochondrial dysfunction next to accelerated kynurenine and aldosterone production were recognized as distinct features of dysregulated metabolipidome. Spatial pharmacometabolomics may be a promising tool for identifying pathological responses to chemotherapy.
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Affiliation(s)
- Mariola Olkowicz
- Department of Chemistry, University of Waterloo, Waterloo, ON, Canada
- Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, Krakow, Poland
| | - Khaled Ramadan
- Latner Thoracic Surgery Research Laboratories, Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
| | | | - Miao Yu
- The Jackson Laboratory, JAX Genomic Medicine, Farmington, CT, USA
| | - Aizhou Wang
- Latner Thoracic Surgery Research Laboratories, Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
| | - Marcelo Cypel
- Latner Thoracic Surgery Research Laboratories, Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
- Division of Thoracic Surgery, Department of Surgery, University Health Network, University of Toronto, Toronto Lung Transplant Program, Toronto, ON, Canada
| | - Janusz Pawliszyn
- Department of Chemistry, University of Waterloo, Waterloo, ON, Canada
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88
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Mahmud I, Wei B, Veillon L, Tan L, Martinez S, Tran B, Raskind A, de Jong F, Akbani R, Weinstein JN, Beecher C, Lorenzi PL. An IROA Workflow for correction and normalization of ion suppression in mass spectrometry-based metabolomic profiling data. RESEARCH SQUARE 2024:rs.3.rs-3914827. [PMID: 38352620 PMCID: PMC10862963 DOI: 10.21203/rs.3.rs-3914827/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Ion suppression is a major problem in mass spectrometry (MS)-based metabolomics; it can dramatically decrease measurement accuracy, precision, and signal-to-noise sensitivity. Here we report a new method, the IROA TruQuant Workflow, that uses a stable isotope-labeled internal standard (IROA-IS) plus novel companion algorithms to 1) measure and correct for ion suppression, and 2) perform Dual MSTUS normalization of MS metabolomic data. We have evaluated the method across ion chromatography (IC), hydrophilic interaction liquid chromatography (HILIC), and reverse phase liquid chromatography (RPLC)-MS systems in both positive and negative ionization modes, with clean and unclean ion sources, and across different biological matrices. Across the broad range of conditions tested, all detected metabolites exhibited ion suppression ranging from 1% to 90+% and coefficient of variations ranging from 1% to 20%, but the Workflow and companion algorithms were highly effective at nulling out that suppression and error. Overall, the Workflow corrects ion suppression across diverse analytical conditions and produces robust normalization of non-targeted metabolomic data.
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89
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Boutoub O, Jadhav S, Zheng X, El Ghadraoui L, Al Babili S, Fernie AR, Figueiredo AC, Miguel MG, Borghi M. Biochemical characterization of Euphorbia resinifera floral cyathia. JOURNAL OF PLANT PHYSIOLOGY 2024; 293:154184. [PMID: 38295538 DOI: 10.1016/j.jplph.2024.154184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 01/17/2024] [Accepted: 01/18/2024] [Indexed: 02/02/2024]
Abstract
Euphorbia resinifera O. Berg is a plant endemic to the Northern and Central regions of Morocco known since the ancient Roman and Greek times for secreting a poisonous latex containing resiniferatoxin. However, E. resinifera pseudo-inflorescences called cyathia are devoid of laticifers and, therefore, do not secrete latex. Instead, they exudate nectar that local honey bees collect and craft into honey. Honey and cyathium water extracts find a broad range of applications in the traditional medicine of Northern Africa as ointments and water decoctions. Moreover, E. resinifera monofloral honey has received the Protected Geographic Indication certification for its outstanding qualities. Given the relevance of E. resinifera cyathia for bee nutrition, honey production, and the health benefit of cyathium-derived products, this study aimed to screen metabolites synthesized and accumulated in its pseudo-inflorescences. Our analyses revealed that E. resinifera cyathia accumulate primary metabolites in considerable abundance, including hexoses, amino acids and vitamins that honey bees may collect from nectar and craft into honey. Cyathia also synthesize volatile organic compounds of the class of benzenoids and terpenes, which are emitted by flowers pollinated by honey bees and bumblebees. Many specialized metabolites, including carotenoids, flavonoids, and polyamines, were also detected, which, while protecting the reproductive organs against abiotic stresses, also confer antioxidant properties to water decoctions. In conclusion, our analyses revealed that E. resinifera cyathia are a great source of antioxidant molecules and a good food source for the local foraging honeybees, revealing the central role of the flowers from this species in mediating interactions with local pollinators and the conferral of medicinal properties to plant extracts.
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Affiliation(s)
- Oumaima Boutoub
- Department of Biology, Utah State University, Logan, UT, 84321-5305, USA; Faculty of Science and Technology, University of Algarve, Campus of Gambelas, 8005-139, Faro, Portugal; Laboratory of Functional Ecology and Environment, Faculty of Science and Technology, BP 2202, University Sidi Mohamed Ben Abdallah, Fez, 20000, Morocco
| | - Sagar Jadhav
- Department of Biology, Utah State University, Logan, UT, 84321-5305, USA
| | - Xiongjie Zheng
- The Bioactives Lab, Biological and Environmental Sciences and Engineering Division, King Abdullahuniversity of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Lahsen El Ghadraoui
- Laboratory of Functional Ecology and Environment, Faculty of Science and Technology, BP 2202, University Sidi Mohamed Ben Abdallah, Fez, 20000, Morocco
| | - Salim Al Babili
- The Bioactives Lab, Biological and Environmental Sciences and Engineering Division, King Abdullahuniversity of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Ana Cristina Figueiredo
- Centro de Estudos do Ambiente e do Mar Lisboa (CESAM Ciências), Faculdade de Ciências da Universidade de Lisboa, Biotecnologia Vegetal (BV), DBV, C2, Campo Grande, 1749-016, Lisboa, Portugal
| | - Maria Graça Miguel
- Faculty of Science and Technology, University of Algarve, Campus of Gambelas, 8005-139, Faro, Portugal; Mediterranean Institute for Agriculture, Environment and Development, Campus de Gambelas, University of Algarve, 8005-139, Faro, Portugal
| | - Monica Borghi
- Department of Biology, Utah State University, Logan, UT, 84321-5305, USA.
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90
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Liu L, Zhang L, Zhang X, Dong X, Jiang X, Huang X, Li W, Xie X, Qiu X. Analysis of cellular response to drugs with a microfluidic single-cell platform based on hyperspectral imaging. Anal Chim Acta 2024; 1288:342158. [PMID: 38220290 DOI: 10.1016/j.aca.2023.342158] [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: 10/07/2023] [Revised: 12/07/2023] [Accepted: 12/16/2023] [Indexed: 01/16/2024]
Abstract
BACKGROUND Cellular response to pharmacological action of drugs is significant for drug development. Traditional detection method for cellular response to drugs normally rely on cell proliferation assay and metabolomics examination. In principle, these analytical methods often required cell labeling, invasion analysis, and hours of co-culture with drugs, which are relatively complex and time-consuming. Moreover, these methods can only indicate the drug effectiveness on cell colony rather than single cells. Thus, to meet the requirements of personal precision medicine, the development of drug response analysis on the high resolution of single cell is demanded. RESULTS To provide precise result for drug response on single-cell level, a microfluidic platform coupled with the label-free hyperspectral imaging was developed. With the help of horizontal single-cell trapping sieves, hundreds of single cells were trapped independently in microfluidic channels for the purposes of real-time drug delivery and single-cell hyperspectral image recording. To significantly identify the cellular hyperspectral change after drug stimulation, the differenced single-cell spectrum was proposed. Compared with the deep learning classification method based on hyperspectral images, an optimal performance can be achieved by the classification strategy based on differenced spectra. And the cellular response to different reagents, for example, K+, Epidermal Growth Factor (EGF), and Gefitinib at different concentrations can be accurately characterized by the differenced single-cell spectra analysis. SIGNIFICANCE AND NOVELTY The high-throughput, rapid analysis of cellular response to drugs at the single-cell level can be accurately performed by our platform. After systematically analyzing the materials and the structures of the single-cell microfluidic chip, the optimal single-cell trapping method was proposed to contribute to the further application of hyperspectral imaging on microfluidic single-cell analysis. And the hyperspectral characterization of single-cell with cancer drug stimulation proved the application potential of our method in personal cancer medication.
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Affiliation(s)
- Luyao Liu
- Institute of Microfluidic Chip Development in Biomedical Engineering, School of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Lulu Zhang
- Institute of Microfluidic Chip Development in Biomedical Engineering, School of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Xueyu Zhang
- School of Information and Electronics, Beijing Institute of Technology, Beijing, 100081, China
| | - Xiaobin Dong
- Institute of Microfluidic Chip Development in Biomedical Engineering, School of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Xiaodan Jiang
- Institute of Microfluidic Chip Development in Biomedical Engineering, School of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Xiaoqi Huang
- School of Information and Electronics, Beijing Institute of Technology, Beijing, 100081, China
| | - Wei Li
- School of Information and Electronics, Beijing Institute of Technology, Beijing, 100081, China
| | - Xiaoming Xie
- School of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Xianbo Qiu
- Institute of Microfluidic Chip Development in Biomedical Engineering, School of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China.
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91
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Chen Q, Lu Q, Zhang L, Zhang C, Zhang J, Gu Y, Huang Q, Tang H. A novel endogenous retention-index for minimizing retention-time variations in metabolomic analysis with reversed-phase ultrahigh-performance liquid-chromatography and mass spectrometry. Talanta 2024; 268:125318. [PMID: 37875029 DOI: 10.1016/j.talanta.2023.125318] [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: 06/06/2023] [Revised: 10/07/2023] [Accepted: 10/14/2023] [Indexed: 10/26/2023]
Abstract
Consistent retention time (tR) of metabolites is vital for identification in metabolomic analysis with ultrahigh-performance liquid-chromatography (UPLC). To minimize inter-experimental tR variations from the reversed-phase UPLC-MS, we developed an endogenous retention-index (endoRI) using in-sample straight-chain acylcarnitines with different chain-length (LC, C0-C26) without additives. The endoRI-corrections reduced the tR variations caused by the combined changes of mobile phases, gradients, flow-rates, elution time, columns and temperature from up to 5.1 min-0.2 min for most metabolites in a model metabolome consisting of 91 metabolites and multiple biological matrices including human serum, plasma, fecal, urine, A549 cells and rabbit liver extracts. The endoRI-corrections also reduced the inter-batch and inter-platform tR variations from 1.5 min to 0.15 min for 95 % of detected features in the above biological samples. We further established a quantitative model between tR and LC for predicting tR values of acylcarnitines when absent in samples. This makes it possible to compare metabolites' tR from different tR databases and the UPLC-based metabolomic data from different batches.
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Affiliation(s)
- Qinsheng Chen
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Metabonomics and Systems Biology Laboratory at Shanghai International Centre for Molecular Phenomics, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Qinwei Lu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Metabonomics and Systems Biology Laboratory at Shanghai International Centre for Molecular Phenomics, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Lianglong Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Metabonomics and Systems Biology Laboratory at Shanghai International Centre for Molecular Phenomics, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Chenhan Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Metabonomics and Systems Biology Laboratory at Shanghai International Centre for Molecular Phenomics, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Jingxian Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Metabonomics and Systems Biology Laboratory at Shanghai International Centre for Molecular Phenomics, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Yu Gu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Metabonomics and Systems Biology Laboratory at Shanghai International Centre for Molecular Phenomics, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Qingxia Huang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Metabonomics and Systems Biology Laboratory at Shanghai International Centre for Molecular Phenomics, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.
| | - Huiru Tang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Metabonomics and Systems Biology Laboratory at Shanghai International Centre for Molecular Phenomics, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.
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92
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Roach J, Mital R, Haffner JJ, Colwell N, Coats R, Palacios HM, Liu Z, Godinho JLP, Ness M, Peramuna T, McCall LI. Microbiome metabolite quantification methods enabling insights into human health and disease. Methods 2024; 222:81-99. [PMID: 38185226 DOI: 10.1016/j.ymeth.2023.12.007] [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: 07/07/2023] [Revised: 10/27/2023] [Accepted: 12/13/2023] [Indexed: 01/09/2024] Open
Abstract
Many of the health-associated impacts of the microbiome are mediated by its chemical activity, producing and modifying small molecules (metabolites). Thus, microbiome metabolite quantification has a central role in efforts to elucidate and measure microbiome function. In this review, we cover general considerations when designing experiments to quantify microbiome metabolites, including sample preparation, data acquisition and data processing, since these are critical to downstream data quality. We then discuss data analysis and experimental steps to demonstrate that a given metabolite feature is of microbial origin. We further discuss techniques used to quantify common microbial metabolites, including short-chain fatty acids (SCFA), secondary bile acids (BAs), tryptophan derivatives, N-acyl amides and trimethylamine N-oxide (TMAO). Lastly, we conclude with challenges and future directions for the field.
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Affiliation(s)
- Jarrod Roach
- Department of Chemistry and Biochemistry, University of Oklahoma
| | - Rohit Mital
- Department of Biology, University of Oklahoma
| | - Jacob J Haffner
- Department of Anthropology, University of Oklahoma; Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma
| | - Nathan Colwell
- Department of Chemistry and Biochemistry, University of Oklahoma
| | - Randy Coats
- Department of Chemistry and Biochemistry, University of Oklahoma
| | - Horvey M Palacios
- Department of Anthropology, University of Oklahoma; Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma
| | - Zongyuan Liu
- Department of Chemistry and Biochemistry, University of Oklahoma
| | | | - Monica Ness
- Department of Chemistry and Biochemistry, University of Oklahoma
| | - Thilini Peramuna
- Department of Chemistry and Biochemistry, University of Oklahoma
| | - Laura-Isobel McCall
- Department of Chemistry and Biochemistry, University of Oklahoma; Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma; Department of Chemistry and Biochemistry, San Diego State University.
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93
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Chen Z, Bai Y, Lou C, Wu B. Serum metabolome responses induced by long-term inoculation of suspended PM2.5 in chicken. Poult Sci 2024; 103:103283. [PMID: 38086244 PMCID: PMC10733702 DOI: 10.1016/j.psj.2023.103283] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 10/28/2023] [Accepted: 11/13/2023] [Indexed: 12/24/2023] Open
Abstract
The adverse effects of exposure to fine particulate matter (PM2.5) on body health have attracted global public attention. However, there is limited research on PM2.5 in animal houses. Numerous studies have indicated that long-term exposure to high levels of PM2.5 can cause damage to multiple systems in animals. Poultry houses are one of the primary sources of PM2.5 emissions. However, there is limited research on the effects of PM2.5 exposure on poultry organisms. This study analyzed the histopathological changes in the lung tissue of poultry under PM2.5 exposure conditions. It used the LC-MS method to analyze the alterations in the serum metabolomic profile of poultry. This study confirmed that long-term exposure to high levels of PM2.5 had significantly reduced the growth performance of poultry. Histopathological slides of the lung tissue in chickens exposed to long-term retention of PM2.5 clearly showed significant damage. Furthermore, the serum metabolome analysis revealed significant changes in the serum metabolic profile of chickens exposed to long-term PM2.5 exposure. Specifically, there were notable alterations in the Glycerophospholipid metabolism, Steroid hormone biosynthesis, and Phenylalanine, tyrosine, and tryptophan biosynthesis pathways.
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Affiliation(s)
- Zhuo Chen
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528225, China
| | - Yu Bai
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528225, China
| | - Cheng Lou
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528225, China
| | - Bo Wu
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528225, China.
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94
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Wang X, Sun X, Wang F, Wei C, Zheng F, Zhang X, Zhao X, Zhao C, Lu X, Xu G. Enhancing Metabolome Annotation by Electron Impact Excitation of Ions from Organics-Molecular Networking. Anal Chem 2024; 96:1444-1453. [PMID: 38240194 DOI: 10.1021/acs.analchem.3c03443] [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: 01/31/2024]
Abstract
Liquid chromatography-high-resolution mass spectrometry (LC-HRMS) is widely used in untargeted metabolomics, but large-scale and high-accuracy metabolite annotation remains a challenge due to the complex nature of biological samples. Recently introduced electron impact excitation of ions from organics (EIEIO) fragmentation can generate information-rich fragment ions. However, effective utilization of EIEIO tandem mass spectrometry (MS/MS) is hindered by the lack of reference spectral databases. Molecular networking (MN) shows great promise in large-scale metabolome annotation, but enhancing the correlation between spectral and structural similarity is essential to fully exploring the benefits of MN annotation. In this study, a novel approach was proposed to enhance metabolite annotation in untargeted metabolomics using EIEIO and MN. MS/MS spectra were acquired in EIEIO and collision-induced dissociation (CID) modes for over 400 reference metabolites. The study revealed a stronger correlation between the EIEIO spectra and metabolite structure. Moreover, the EIEIO spectral network outperformed the CID spectral network in capturing structural analogues. The annotation performance of the structural similarity network for untargeted LC-MS/MS was evaluated. For the spiked NIST SRM 1950 human plasma, the annotation coverage and accuracy were 72.94 and 74.19%, respectively. A total of 2337 metabolite features were successfully annotated in NIST SRM 1950 human plasma, which was twice that of LC-CID MS/MS. Finally, the developed method was applied to investigate prostate cancer. A total of 87 significantly differential metabolites were annotated. This study combining EIEIO and MN makes a valuable contribution to improving metabolome annotation.
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Affiliation(s)
- Xinxin Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
- Liaoning Province Key Laboratory of Metabolomics, Dalian 116023, P. R. China
| | - Xiaoshan Sun
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
- Liaoning Province Key Laboratory of Metabolomics, Dalian 116023, P. R. China
| | - Fubo Wang
- Center for Genomic and Personalized Medicine, Guangxi key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning 530021, P. R. China
- Department of Urology, Institute of Urology and Nephrology, First Affiliated Hospital of Guangxi Medical University, Nanning 530021, P. R. China
| | - Chunmeng Wei
- Center for Genomic and Personalized Medicine, Guangxi key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning 530021, P. R. China
- Department of Urology, Institute of Urology and Nephrology, First Affiliated Hospital of Guangxi Medical University, Nanning 530021, P. R. China
| | - Fujian Zheng
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
- Liaoning Province Key Laboratory of Metabolomics, Dalian 116023, P. R. China
| | - Xiuqiong Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
- Liaoning Province Key Laboratory of Metabolomics, Dalian 116023, P. R. China
| | - Xinjie Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
- Liaoning Province Key Laboratory of Metabolomics, Dalian 116023, P. R. China
| | - Chunxia Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
- Liaoning Province Key Laboratory of Metabolomics, Dalian 116023, P. R. China
| | - Xin Lu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
- Liaoning Province Key Laboratory of Metabolomics, Dalian 116023, P. R. China
| | - Guowang Xu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
- Liaoning Province Key Laboratory of Metabolomics, Dalian 116023, P. R. China
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95
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Liu Z, Jiang A, Lv X, Zhou C, Tan Z. Metabolic Changes in Serum and Milk of Holstein Cows in Their First to Fourth Parity Revealed by Biochemical Analysis and Untargeted Metabolomics. Animals (Basel) 2024; 14:407. [PMID: 38338048 PMCID: PMC10854930 DOI: 10.3390/ani14030407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 01/17/2024] [Accepted: 01/23/2024] [Indexed: 02/12/2024] Open
Abstract
The performance of dairy cows is closely tied to the metabolic state, and this performance varies depending on the number of times the cows have given birth. However, there is still a lack of research on the relationship between the metabolic state of Holstein cows and the performance of lactation across multiple parities. In this study, biochemical analyses and metabolomics studies were performed on the serum and milk from Holstein cows of parities 1-4 (H1, N = 10; H2, N = 7; H3, N = 9; H4, N = 9) in mid-lactation (DIM of 141 ± 4 days) to investigate the link between performance and metabolic changes. The results of the milk quality analysis showed that the lactose levels were highest in H1 (p = 0.036). The total protein content in the serum increased with increasing parity (p = 0.013). Additionally, the lipase activity was found to be lowest in H1 (p = 0.022). There was no difference in the composition of the hydrolyzed amino acids in the milk among H1 to H4. However, the free amino acids histidine and glutamate in the serum were lowest in H1 and highest in H3 (p < 0.001), while glycine was higher in H4 (p = 0.031). The metabolomics analysis revealed that 53 and 118 differential metabolites were identified in the milk and serum, respectively. The differential metabolites in the cows' milk were classified into seven categories based on KEGG. Most of the differential metabolites in the cows' milk were found to be more abundant in H1, and these metabolites were enriched in two impact pathways. The differential metabolites in the serum could be classified into nine categories and enriched in six metabolic pathways. A total of six shared metabolites were identified in the serum and milk, among which cholesterol and citric acid were closely related to amino acid metabolism in the serum. These findings indicate a significant influence of blood metabolites on the energy and amino acid metabolism during the milk production process in the Holstein cows across 1-4 lactations, and that an in-depth understanding of the metabolic changes that occur in Holstein cows during different lactations is essential for precision farming, and that it is worthwhile to further investigate these key metabolites that have an impact through controlled experiments.
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Affiliation(s)
- Zixin Liu
- CAS Key Laboratory for Agri-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution CON and Waste Utilization in Livestock and Poultry Production, Hunan Provincial Key Laboratory of Animal Nutrition Physiology and Metabolic Process, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China; (Z.L.); (A.J.); (X.L.); (Z.T.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Aoyu Jiang
- CAS Key Laboratory for Agri-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution CON and Waste Utilization in Livestock and Poultry Production, Hunan Provincial Key Laboratory of Animal Nutrition Physiology and Metabolic Process, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China; (Z.L.); (A.J.); (X.L.); (Z.T.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaokang Lv
- CAS Key Laboratory for Agri-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution CON and Waste Utilization in Livestock and Poultry Production, Hunan Provincial Key Laboratory of Animal Nutrition Physiology and Metabolic Process, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China; (Z.L.); (A.J.); (X.L.); (Z.T.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- College of Animal Science, Anhui Science and Technology University, Bengbu 233100, China
| | - Chuanshe Zhou
- CAS Key Laboratory for Agri-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution CON and Waste Utilization in Livestock and Poultry Production, Hunan Provincial Key Laboratory of Animal Nutrition Physiology and Metabolic Process, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China; (Z.L.); (A.J.); (X.L.); (Z.T.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhiliang Tan
- CAS Key Laboratory for Agri-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution CON and Waste Utilization in Livestock and Poultry Production, Hunan Provincial Key Laboratory of Animal Nutrition Physiology and Metabolic Process, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China; (Z.L.); (A.J.); (X.L.); (Z.T.)
- University of Chinese Academy of Sciences, Beijing 100049, China
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96
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Zhang N, Chen Q, Zhang P, Zhou K, Liu Y, Wang H, Duan S, Xie Y, Yu W, Kong Z, Ren L, Hou W, Yang J, Gong X, Dong L, Fang X, Shi L, Yu Y, Zheng Y. Quartet metabolite reference materials for inter-laboratory proficiency test and data integration of metabolomics profiling. Genome Biol 2024; 25:34. [PMID: 38268000 PMCID: PMC10809448 DOI: 10.1186/s13059-024-03168-z] [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: 11/08/2022] [Accepted: 01/09/2024] [Indexed: 01/26/2024] Open
Abstract
BACKGROUND Various laboratory-developed metabolomic methods lead to big challenges in inter-laboratory comparability and effective integration of diverse datasets. RESULTS As part of the Quartet Project, we establish a publicly available suite of four metabolite reference materials derived from B lymphoblastoid cell lines from a family of parents and monozygotic twin daughters. We generate comprehensive LC-MS-based metabolomic data from the Quartet reference materials using targeted and untargeted strategies in different laboratories. The Quartet multi-sample-based signal-to-noise ratio enables objective assessment of the reliability of intra-batch and cross-batch metabolomics profiling in detecting intrinsic biological differences among the four groups of samples. Significant variations in the reliability of the metabolomics profiling are identified across laboratories. Importantly, ratio-based metabolomics profiling, by scaling the absolute values of a study sample relative to those of a common reference sample, enables cross-laboratory quantitative data integration. Thus, we construct the ratio-based high-confidence reference datasets between two reference samples, providing "ground truth" for inter-laboratory accuracy assessment, which enables objective evaluation of quantitative metabolomics profiling using various instruments and protocols. CONCLUSIONS Our study provides the community with rich resources and best practices for inter-laboratory proficiency tests and data integration, ensuring reliability of large-scale and longitudinal metabolomic studies.
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Affiliation(s)
- Naixin Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Qiaochu Chen
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Peipei Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Kejun Zhou
- Human Metabolomics Institute, Inc., Shenzhen, Guangdong, China
| | - Yaqing Liu
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Haiyan Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Shumeng Duan
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Yongming Xie
- Shanghai Applied Protein Technology Co. Ltd, Shanghai, China
| | - Wenxiang Yu
- Novogene Bioinformatics Institute, Beijing, China
| | - Ziqing Kong
- Calibra Diagnostics, Hangzhou, Zhejiang, China
| | - Luyao Ren
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Wanwan Hou
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Jingcheng Yang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
- Greater Bay Area Institute of Precision Medicine, Guangzhou, Guangdong, China
| | | | | | - Xiang Fang
- National Institute of Metrology, Beijing, China
| | - Leming Shi
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
- International Human Phenome Institute, Shanghai, China
| | - Ying Yu
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China.
| | - Yuanting Zheng
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China.
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97
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Ahmad F, Javed K, Tahir A, Khan MUG, Abbas M, Rabbani M, Shabbir MZ. Identifying key soil characteristics for Francisella tularensis classification with optimized Machine learning models. Sci Rep 2024; 14:1743. [PMID: 38242908 PMCID: PMC10799052 DOI: 10.1038/s41598-024-51502-z] [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: 02/15/2023] [Accepted: 01/05/2024] [Indexed: 01/21/2024] Open
Abstract
Francisella tularensis (Ft) poses a significant threat to both animal and human populations, given its potential as a bioweapon. Current research on the classification of this pathogen and its relationship with soil physical-chemical characteristics often relies on traditional statistical methods. In this study, we leverage advanced machine learning models to enhance the prediction of epidemiological models for soil-based microbes. Our model employs a two-stage feature ranking process to identify crucial soil attributes and hyperparameter optimization for accurate pathogen classification using a unique soil attribute dataset. Optimization involves various classification algorithms, including Support Vector Machines (SVM), Ensemble Models (EM), and Neural Networks (NN), utilizing Bayesian and Random search techniques. Results indicate the significance of soil features such as clay, nitrogen, soluble salts, silt, organic matter, and zinc , while identifying the least significant ones as potassium, calcium, copper, sodium, iron, and phosphorus. Bayesian optimization yields the best results, achieving an accuracy of 86.5% for SVM, 81.8% for EM, and 83.8% for NN. Notably, SVM emerges as the top-performing classifier, with an accuracy of 86.5% for both Bayesian and Random Search optimizations. The insights gained from employing machine learning techniques enhance our understanding of the environmental factors influencing Ft's persistence in soil. This, in turn, reduces the risk of false classifications, contributing to better pandemic control and mitigating socio-economic impacts on communities.
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Affiliation(s)
- Fareed Ahmad
- Department of Computer Science, University of Engineering and Technology, Lahore, Pakistan.
- Quality Operations Laboratory, Institute of Microbiology, University of Veterinary and Animal Sciences, Lahore, Pakistan.
| | - Kashif Javed
- Department of Electrical Engineering, University of Engineering and Technology, Lahore, Pakistan
| | - Ahsen Tahir
- Department of Electrical Engineering, University of Engineering and Technology, Lahore, Pakistan
| | | | - Mateen Abbas
- Quality Operations Laboratory, Institute of Microbiology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Masood Rabbani
- Institute of Microbiology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Muhammad Zubair Shabbir
- Quality Operations Laboratory, Institute of Microbiology, University of Veterinary and Animal Sciences, Lahore, Pakistan
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Wang W, Kou J, Long J, Wang T, Zhang M, Wei M, Xie Q. GC/MS and LC/MS serum metabolomic analysis of Chinese LN patients. Sci Rep 2024; 14:1523. [PMID: 38233574 PMCID: PMC10794181 DOI: 10.1038/s41598-024-52137-w] [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: 05/30/2023] [Accepted: 01/14/2024] [Indexed: 01/19/2024] Open
Abstract
China, being a densely populated nation, faces a substantial economic burden due to a high incidence of lupus nephritis (LN) cases. The concealed onset of LN has resulted in many individuals have missed the optimal timing for treatment. The aim of the research is to study the serum metabolomics of Chinese LN patients using gas chromatography (GC)/mass spectrometry (MS) and liquid chromatography (LC)/MS to identify potential diagnostic markers. Fifty LN patients and fifty normal controls, matched for Body Mass Index (BMI) and age, were selected. Serum analysis was conducted using GC/MS and LC/MS, followed by multivariate statistical analysis. Various multidimensional analyses, including principal component analysis, partial least squares discrimination analysis, and orthogonal partial least squares discrimination analysis, along with one-dimensional analyses such as t-tests, were performed. Metabolites with variable importance in projection value > 1 and a p-value < 0.05 were considered critical biomarkers for LN. Furthermore, identified biomarkers delineated relevant metabolic pathways, and a metabolic pathway map was obtained from the database. Forty-one metabolites were identified as potential LN biomarkers, primarily associated with immune regulation, energy metabolism, intestinal microbial metabolism, renal damage, and oxidative stress. The potential for diagnosing LN and other diseases through metabolomics is demonstrated. Future research should explore larger sample sizes, metabolomic comparisons across different diseases and health states, and integration of metabolomics with clinical diagnostics. Such studies will enhance the understanding of metabolomics in medical diagnosis and provide robust support for its practical application.
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Affiliation(s)
- Wei Wang
- Department of Orthopedics, General Hospital of Western Theater Command, Rongdu Avenue No. 270, Chengdu, 610000, People's Republic of China
| | - Jun Kou
- Department of Ultrasound Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders (Chongqing Key Laboratory of Pediatrics), Chongqing, 400010, China
| | - Jie Long
- Department of Nephrology, Honghui Hospital, Xi'an Jiaotong University College of Medicine, No.555 Youyi East Road, Beilin District, Xi'an, 710054, Shaanxi, People's Republic of China
| | - Tao Wang
- Department of Rheumatism and Immunology, The General Hospital of Western Theater Command, Tianhui Road 270, Chengdu, 610000, People's Republic of China
| | - Mingmei Zhang
- Department of Rheumatism and Immunology, The General Hospital of Western Theater Command, Tianhui Road 270, Chengdu, 610000, People's Republic of China
| | - Meng Wei
- Department of Rheumatism and Immunology, The General Hospital of Western Theater Command, Tianhui Road 270, Chengdu, 610000, People's Republic of China.
| | - Qingyun Xie
- Department of Orthopedics, General Hospital of Western Theater Command, Rongdu Avenue No. 270, Chengdu, 610000, People's Republic of China.
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99
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Chu Z, Zhao T, Zhang Z, Chu CH, Cai K, Wu J, Wu W, Tang C. Untargeted Metabolomics Analysis of Gingival Tissue in Patients with Severe Periodontitis. J Proteome Res 2024; 23:3-15. [PMID: 38018860 DOI: 10.1021/acs.jproteome.3c00105] [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] [Indexed: 11/30/2023]
Abstract
The purpose of this study was to determine potential metabolic biomarkers and therapeutic drugs in the gingival tissue of individuals with periodontitis. Liquid chromatography-mass spectrometry (LC-MS) and gas chromatography-mass spectrometry (GC-MS) were used to analyze the gingival tissue samples from 20 patients with severe periodontitis and 20 healthy controls. Differential metabolites were identified using variable important in projection (VIP) values from the orthogonal partial least squares discrimination analysis (OPLS-DA) model and then verified for significance between groups using a two-tailed Student's t test. In total, 65 metabolites were enriched in 33 metabolic pathways, with 40 showing a significant increase and 25 expressing a significant decrease. In addition, it was found that patients with severe periodontitis have abnormalities in metabolic pathways, such as glucose metabolism, purine metabolism, amino acid metabolism, and so on. Furthermore, based on a multidimensional analysis, 12 different metabolites may be the potential biomarkers of severe periodontitis. The experiment's raw data have been uploaded to the MetaboLights database, and the project number is MTBLS8357. Moreover, osteogenesis differentiation characteristics were detected in the selected metabolites. The findings may provide a basis for the study of diagnostic biomarkers and therapeutic metabolites in severe periodontitis.
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Affiliation(s)
- Zhuangzhuang Chu
- Department of Dental Implantology, The Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing 210029, China
- Jiangsu Key Laboratory of Oral Diseases,Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing 210029, China
| | - Tong Zhao
- Department of Dental Implantology, The Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing 210029, China
- Jiangsu Key Laboratory of Oral Diseases,Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing 210029, China
| | - Zhewei Zhang
- Department of Dental Implantology, The Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing 210029, China
- Jiangsu Key Laboratory of Oral Diseases,Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing 210029, China
| | - Catherine Huihan Chu
- Department of Orthodontic, The Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing 210029, China
- Jiangsu Key Laboratory of Oral Diseases,Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing 210029, China
| | - Kunzhan Cai
- Department of Dental Implantology, The Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing 210029, China
- Jiangsu Key Laboratory of Oral Diseases,Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing 210029, China
| | - Jin Wu
- Department of Dental Implantology, The Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing 210029, China
- Jiangsu Key Laboratory of Oral Diseases,Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing 210029, China
| | - Wei Wu
- Department of Dental Implantology, The Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing 210029, China
- Jiangsu Key Laboratory of Oral Diseases,Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing 210029, China
| | - Chunbo Tang
- Department of Dental Implantology, The Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing 210029, China
- Jiangsu Key Laboratory of Oral Diseases,Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing 210029, China
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100
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Shixiong Z, Shaowei L, Zeqi Y, Miaochan X, Pingping Z, Haiyan B, Jingjing L, Yangang W. Study on the Characteristics of Traditional Chinese Medicine Syndromes in Patients with Erosive Gastritis Based on Metabolomics. Int J Anal Chem 2024; 2024:6684677. [PMID: 38204992 PMCID: PMC10776191 DOI: 10.1155/2024/6684677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 11/30/2023] [Accepted: 12/16/2023] [Indexed: 01/12/2024] Open
Abstract
According to traditional Chinese medicine theory, tongue coatings reflect changes in the body. The goal of this study was to identify a metabolite or a set of metabolites capable of classifying characteristics of traditional Chinese medicine syndromes in erosive gastritis. In this study, we collected tongue coatings of patients with erosive gastritis with damp-heat syndrome (DHS), liver depression and qi stagnation syndrome (LDQSS), and healthy volunteers. Then, we analyzed the differences in metabolic characteristics between the two groups based on metabolomics. We identified 14 potential biomarkers related to the DHS group, and six metabolic pathways were enriched. The differential pathways included pyrimidine metabolism, pantothenate and CoA biosynthesis, citrate cycle (TCA cycle), pyruvate metabolism, glycolysis/gluconeogenesis, and purine metabolism. Similarly, in the LDQSS group, we identified 25 potential biomarkers and 18 metabolic pathways were enriched. The top five pathways were the TCA cycle, sphingolipid metabolism, fatty acid biosynthesis, pantothenate and CoA biosynthesis, and the pentose phosphate pathway. In conclusion, the DHS group and the LDQSS group have different characteristics.
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Affiliation(s)
- Zhang Shixiong
- Nanjing University of Chinese Medicine, Nanjing 210046, China
| | - Liu Shaowei
- Hebei University of Chinese Medicine, Shijiazhuang 050200, China
| | - Yang Zeqi
- Hebei University of Chinese Medicine, Shijiazhuang 050200, China
| | - Xu Miaochan
- Hebei University of Chinese Medicine, Shijiazhuang 050200, China
| | - Zhou Pingping
- Hebei Hospital of Traditional Chinese Medicine, Shijiazhuang 050091, China
| | - Bai Haiyan
- Hebei Hospital of Traditional Chinese Medicine, Shijiazhuang 050091, China
| | - Lv Jingjing
- Hebei Hospital of Traditional Chinese Medicine, Shijiazhuang 050091, China
| | - Wang Yangang
- The Third Affiliated Hospital of Beijing University of Chinese Medicine, Beijing 100029, China
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