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metabolomics-centered mining of plant metabolic diversity and function:Past decade and future perspectives

Molecular Plant 2023年第1期16卷 43-63页

作者： Shuangqian Shen Chuansong Zhan Chenkun Yang Alisdair R.Fernie Jie Luo Sanya Nanfan Research Institute of Hainan University Hainan Yazhou Bay Seed LaboratorySanya 572025China College of Tropical Crops Hainan UniversityHaikou 570228China Max Planck Institute of Molecular Plant Physiology Potsdam-Golm 14476Germany

Plants are natural experts in organic synthesis,being able to generate large numbers of specific metabolites with widely varying structures that help them adapt to variable survival challenges.metabolomics is a research discipline that integrates the capabilities of several types of research including analytical chemistry,statistics,and biochemistry.Its ongoing development provides strategies for gaining a systematic understanding of quantitative changes in the levels of metabolites.metabolomics is usually performed by targeting either a specific cell,a specific tissue,or the entire organism.Considerable advances in science and technology over the last three decades have propelled us into the era of multi-omics,in which metabolomics,despite at an earlier developmental stage than genomics,transcriptomics,and proteomics,offers the distinct advantage of studying the cellular entities that have the greatest influence on end phenotype.Here,we summarize the state of the art of metabolite detection and identification,and illustrate these techniques with four case study applications:(i)comparing metabolite composition within and between species,(ii)assessing spatio-temporal metabolic changes during plant development,(iii)mining characteristic metabolites of plants in different ecological environments and upon exposure to various stresses,and(iv)assessing the performance of metabolomics as a means of functional gene identification,metabolic pathway elucidation,and metabolomics-assisted breeding through analyzing plant populations with diverse genetic variations.In addition,we highlight the prominent contributions of joint analyses of plant metabolomics and other omics datasets,including those from genomics,transcriptomics,proteomics,epigenomics,phenomics,microbiomes,and ion-omics studies.Finally,we discuss future directions and challenges exploiting metabolomics-centered approaches in understanding plant metabolic diversity.

关键词： metabolomics multi-omics high-throughput metabolic profiling bioactive markers

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metabolomics: A useful tool for ischemic stroke research

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Journal of Pharmaceutical Analysis 2023年第9期13卷 968-983页

作者： Wentao Li Chongyu Shao Chang Li Huifen Zhou Li Yu Jiehong Yang Haitong Wan Yu He School of Pharmaceutical Sciences Zhejiang Chinese Medical UniversityHangzhou310053China School of Basic Medicine Sciences Zhejiang Chinese Medical UniversityHangzhou310053China

Ischemic stroke(IS)is a multifactorial and heterogeneous disease.Despite years of studies,effective strategies for the diagnosis,management and treatment of stroke are still lacking in clinical practice.metabolomics is a growing field in systems biology.It is starting to show promise in the identification of biomarkers and in the use of pharmacometabolomics to help patients with certain disorders choose their course of treatment.The development of metabolomics has enabled further and more biological applications.Particularly,metabolomics is increasingly being used to diagnose diseases,discover new drug targets,elucidate mechanisms,and monitor therapeutic outcomes and its potential effect on precision medicine.In this review,we reviewed some recent advances in the study of metabolomics as well as how metabolomics might be used to identify novel biomarkers and understand the mechanisms of IS.Then,the use of metabolomics approaches to investigate the molecular processes and active ingredients of Chinese herbal formulations with anti-IS capabilities is summarized.We finally summarized recent developments in single cell metabolomics for exploring the metabolic profiles of single cells.Although the field is relatively young,the development of single cell metabolomics promises to provide a powerful tool for unraveling the pathogenesis of IS.

关键词： metabolomics Ischemic stroke Biomarker Precision medicine Single cell metabolomics

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metabolomics Combined with Network Pharmacology Uncovers Effective Targets of Tao-Hong-Si-Wu Decoction for Its Protection from Sepsis-Associated Acute Lung Injury

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Journal of Analysis and Testing 2023年第2期7卷 172-186页

作者： Jinzhi He Longfei Wang Yang Wang Zeng Li Feihu Chen Zhicheng Liu Anhui Provincial Laboratory of Infl ammatory and Immunity Disease Anhui Institute of Innovative Drugs School of PharmacyAnhui Medical UniversityHefei 230032China Shanxi Key Laboratory of Big Data for Clinical Decision Research School of ManagementShanxi Medical UniversityTaiyuan 030000China

Sepsis-induced acute lung injury(ALI)is a leading cause of death among septic complications.Tao-Hong-Si-Wu decoction(TSD),a classical recipe from traditional Chinese medicine used for treating ischemic stroke,has been recently reported to alleviate inflammation and inflammation-stimulated injuries related to the pathology of ALI.Here,we first observed the therapeutic effect of TSD on sepsis-induced ALI.Based on integrated metabolomics and network pharmacology analysis(NPA)techniques,we aim to understand the mechanism of TSD alleviating ALI.TSD’s effects were observed in rats modeled by cecal ligation and puncture(CLP)and rat macrophages stimulated by lipopolysaccharide(LPS).metabolomics analyses were applied to determine the ingredients in the medicine and key metabolites correlated to the NPA for the prediction of TSD targets.Gene and protein expressions of the key predicted targets were evaluated in the lung tissue and macrophages of septic model rat by quantitative polymerase chain reaction(PCR)and enzyme-linked immunosorbent assays,respectively.TSD improved survival rate and protected against lung injury in CLP rats.Eleven endogenous metabolites were related to TSD’s actions.TSD significantly suppressed IL-6 and TNF-αsecretions and their gene expressions both in the lung tissue of the model rats and in LPS-stimulated macrophages.TSD also restored decreased lung protein expression of VEGFA in septic model rats.Targeted proteins and their affecting metabolites were finally validated in an external test set of rats.This study shows that metabolomics coupled with NPA is a promising approach to explore potential targets of medicine with complex compositions.

关键词： metabolomics Drug eff ect analysis Sepsis Traditional Chinese medicine Cytokines Bioanalysis

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metabolomics analysis reveals the renal protective effect of Panax ginseng C. A. Mey in type 1 diabetic rats

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Chinese Journal of Natural Medicines 2022年第5期20卷 378-386页

作者： WANG Xin-Sen HU Ming-Xin GUAN Qing-Xiang MEN Li-Hui LIU Zhong-Ying School of Pharmaceutical Sciences Jilin UniversityChangchun 130021China College of Basic Medical Sciences Jilin UniversityChangchun 130021China

The dry root and rhizome of Panax ginseng C. A. Mey has garnered much interest owing to its medicinal properties against diabetes and cardiovascular diseases. In this study, an ultra-high performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UHPLC-Q-TOF-MS)-based metabolomics approach was used to illustrate the therapeutic mechanisms of ginseng extract on the serum and urinary metabolic profiles in streptozotocin-induced type 1 diabetes mellitus (T1DM) rats. Pharmacological and renal parameters in response to the administration of ginseng were also evaluated. In total, 16 serum endogenous metabolites and 14 urine endogenous metabolites, including pyruvic acid, indoleacetic acid, and phenylacetylglycine, were identified as potential biomarkers for diabetes. Pathway enrichment and network analysis revealed that the biomarkers modulated by ginseng were primarily involved in phenylalanine and pyruvate metabolism, as well as in arginine biosynthesis. Moreover, the levels of several renal injury-related biomarkers in T1DM rats were significantly restored following treatment with ginseng. The administration of the extract helped maintain tissue structure integrity and ameliorated renal injury. The findings suggest that the regulatory effect of ginseng extract on T1DM involves metabolic management of diabetic rats, which subsequently attenuates T1DM-induced early renal dysfunction.

关键词： Panax ginseng C.A.Mey Type 1 diabetes metabolomics

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metabolomics for the diagnosis of bladder cancer: A systematic review

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Asian Journal of Urology 2024年第2期11卷 221-241页

作者： Herney Andrés García-Perdomo Angélica María Dávila-Raigoza Fernando Korkes Division of Urology/Urooncology Department of SurgerySchool of MedicineUniversidad del ValleCaliColombia UROGIV Research Group School of MedicineUniversidad del ValleCaliColombia Urologic Oncology Division of UrologyABC Medical SchoolSao PauloBrazil

Objective: metabolomics has been extensively utilized in bladder cancer (BCa) research, employing mass spectrometry and nuclear magnetic resonance spectroscopy to compare various variables (tissues, serum, blood, and urine). This study aimed to identify potential biomarkers for early BCa diagnosis.Methods: A search strategy was designed to identify clinical trials, descriptive and analytical observational studies from databases such as Medline, Embase, Cochrane Central Register of Controlled Trials, and Latin American and Caribbean Literature in Health Sciences. Inclusion criteria comprised studies involving BCa tissue, serum, blood, or urine profiling using widely adopted metabolomics techniques like mass spectrometry and nuclear magnetic resonance. Primary outcomes included description of metabolites and metabolomics profiling in BCa patients and the association of metabolites and metabolomics profiling with BCa diagnosis compared to control patients. The risk of bias was assessed using the Quality Assessment of Studies of Diagnostic Accuracy.Results: The search strategy yielded 2832 studies, of which 30 case-control studies were included. Urine was predominantly used as the primary sample for metabolite identification. Risk of bias was often unclear inpatient selection, blinding of the index test, and reference standard assessment, but no applicability concerns were observed. Metabolites and metabolomics profiles associated with BCa diagnosis were identified in glucose, amino acids, nucleotides, lipids, and aldehydes metabolism.Conclusion: The identified metabolites in urine included citric acid, valine, tryptophan, taurine, aspartic acid, uridine, ribose, phosphocholine, and carnitine. Tissue samples exhibited elevated levels of lactic acid, amino acids, and lipids. Consistent findings across tissue, urine, and serum samples revealed downregulation of citric acid and upregulation of lactic acid, valine, tryptophan, taurine, glutamine, aspartic acid, uridine, ribose, and phosphocholine.

关键词： Metabolite metabolomics Bladder cancer metabolomicsprofile

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metabolomics provide insights into the endogenous mechanism of strobilation in the scyphozoan jellyfi sh Rhopilema esculentum

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Journal of Oceanology and Limnology 2022年第1期40卷 226-234页

作者： Jianlong GE Xiaohui CHEN Changlin LIU Jie TAN Li BIAN Lifei CHEN Siqing CHEN Yellow Sea Fisheries Research Institute Chinese Academy of Fishery SciencesLaboratory for Marine Fisheries Science and Food Production ProcessesPilot National Laboratory for Marine Science and Technology(Qingdao)Qingdao 266071China Yancheng Huayi Aquatic Products Co.Ltd. Yancheng 224300China

Strobilation is a well-organized metamorphosis process in scyphozoan jellyfi sh,through which the benthic polyp develops into the pelagic medusa.So far,knowledge on the molecular mechanisms behind the drastic morphological and physiological changes remains limited.In the present study,the metabolic profi les in polyp and strobila stages of jellyfi sh Rhopilema esculentum were examined using ultra-performance liquid chromatography coupled to a mass spectrometer.A total of 3071 metabolites with putative annotation were detected,of which 167 were identifi ed as diff erential metabolites between the polyp and strobila.Among the metabolites,31 signifi cantly decreased and 136 signifi cantly increased in abundance in the strobila.Thyroxin,one of the previously proposed strobilation inducer of Aurelia,was not detected in this study.The indole-containing compounds are known for triggering strobilation in Discomedusae.Two indole derivatives and an indole-isomer containing metabolite were detected among the most signifi cantly increased metabolites,which may be potential endogenous molecules for strobilation initiation.The membrane-associated phospholipids and the infl ammation and oxidative stress-related eicosanoids were found to have signifi cant changes.Although the functions of these metabolites in strobilation are not yet completely known,they provide some clues to the induction of the process of strobilation and metabolic responses that take place during strobilation.

关键词： Rhopilema esculentum scyphozoan jellyfi sh strobilation metabolomics

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metabolomics investigation on antiobesity effects of Corydalis bungeana on high-fat high-sugar diet-induced obese rats

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Chinese Herbal Medicines 2022年第3期14卷 414-421页

作者： Minghai Fu Terigele Bao Hongzhen Yu LiSha A. HuiFang Li Genna Ba Sungbo Cho Key Laboratory of Tropical Translational Medicine of Ministry of Education Hainan Key Laboratory for Research and Development of Tropical HerbsSchool of PharmacyHainan Medical UniversityHaikou 571199China NMPA Key Laboratory of Quality Control of Traditional Chinese Medicine(Mongolian Medicine) Inner Mongolia Minzu UniversityTongliao 028000China

Objective:Corydalis bungeana(CB)is a well-used medicinal herb in Mongolian folk medicine and has been traditionally applied as an antiobesity agent.However,the evidence-based pharmacological effects of CB and its specific metabolic alterations in the obese model are not entirely understood.This study aimed to utilize untargeted metabolomic techniques to identify biomarkers and gain mechanistic insight into the serum metabolite alterations associated with weight loss and lipid metabolism in obese rats.Methods:A high-fat high-sugar(HFHS)diet was used to induce obese models in rats.CB extract was orally gavaged at 0.18,0.9 and 1.8 g/kg doses for six weeks,and feed intake,body weight,fat pad weight,and blood indexes were measured.Blood serum metabolites were evaluated by gas chromatography/quadrupole time-of-fight tandem mass spectrometry(GC-TOF/MS).Results:The results showed that compared with the obese group,the administration of CB extract caused significant decreases in body weight(P<0.05),feed intake,Lee’s index,and perirenal,mesenteric,epididymal fat weight.CB extract also reduced blood triglyceride and total cholesterol levels(P<0.05)of obese rats.Metabolomic findings showed that nine differential metabolites,including pyruvic acid,D-glucuronic acid,malic acid,dimethylglycine,oxoglutaric acid,pantothenic acid,sorbitol acid,fumaric acid and glucose 6-phosphate were identified under CB treatment and altered metabolic pathways such as TCA cycle,pantothenate and CoA biosynthesis,and glycolysis/gluconeogenesis.Conclusion:This study demonstrated weight loss and lipid lowering effects of CB on HFHS diet-induced obese rats and identified nine metabolites as potential biomarkers for evaluating the favorable therapeutic mechanism of CB via regulation of lipid and glucose metabolism.

关键词： Corydalis bungeana Turcz. GC-TOF/MS metabolomics Mongolian medicine obesity

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metabolomics in drug discovery: Restoring antibiotic pipeline

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亚太热带生物医学杂志:英文版 2023年第9期13卷 378-383页

作者： Faiza Azhar Mariam Busharat Shah Rukh Arshad Chaudhary Zainab Waheed Muhammad Nauman Jamil Department of Pharmaceutical Chemistry Punjab University College of PharmacyUniversity of the PunjabLahorePakistan School of Medical Indigenous and Health SciencesUniversity of WollongongNew South WalesAustralia Department of General Surgery Lahore General HospitalLahorePakistan Department of Pharmaceutical Chemistry Hamza College of PharmacyLahorePakistan

metabolomics has emerged as a valuable tool in drug discovery and development,providing new insights into the mechanisms of action and toxicity of potential therapeutic agents.metabolomics focuses on the comprehensive analysis of primary as well as secondary metabolites,within biological systems.metabolomics provides a comprehensive understanding of the metabolic changes that occur within microbial pathogens when exposed to therapeutic agents,thus allowing for the identification of unique metabolic targets that can be exploited for therapeutic intervention.This approach can also uncover key metabolic pathways essential for survival,which can serve as potential targets for novel antibiotics.By analyzing the metabolites produced by diverse microbial communities,metabolomics can guide the discovery of previously unexplored sources of antibiotics.This review explores some examples that enable medicinal chemists to optimize drug structure,enhancing efficacy and minimizing toxicity via metabolomic approaches.

关键词： metabolomics Infectious diseases Drug discovery Antibiotics Biomarkers

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metabolomics mechanism of traditional soy sauce associated with fermentation time

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Food Science and Human Wellness 2022年第2期11卷 297-304页

作者： Li Zhu Siyu He Ying Lu Jianhong Gan Ningping Tao Xichang Wang Zaoli Jiang Yuanxiang Hong Changhua Xu College of Food Science and Technology Shanghai Ocean UniversityShanghai 201306China Shanghai Engineering Research Center of Aquatic-Product Processing&Preservation Shanghai 201306China Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation(Shanghai) Ministry of AgricultureShanghai 201306China Department of Pharmacology Yale UniversityNew HavenCT06520US Xiamen Gulong Food Co. Ltd.Xiamen 361000China National R&D Branch Center for Freshwater Aquatic Products Processing Technology(Shanghai) Shanghai 201306China

Given that fermentation time has significant impact on quality and flavor of soy sauce,a global understanding of the metabolic mechanism as fermentation time prolonged is essential for producing satisfactory and consistent quality of traditional soy sauce.Herein,the metabolic compounds changes of soy sauce associated with fermentation time up to 10 years were comprehensively investigated by using Chinese traditional fermented soy sauce(CTFSS)as a demonstration.Results showed that formaldehyde nitrogen,total soluble nitrogen(TSN),non-salt soluble solids,amino acids,free 5’-nucleotides and volatile compounds in CTFSS changed obviously during fermentation.Specifically,glutamic acid and aspartic acid were prominent in CTFSS.Continuous decrease in content of hypoxanthine(Hx)was found from 1 M(1-month soy sauce)to7 M(7-months soy sauce).Furthermore,a significant opposite tendency for changes between some volatile compounds and amino acids was indicated that there was a transformation between these two components.Therefore,a better understanding to the influence of fermentation time on soy sauce had been proposed.As the formation and conversion of amino acids and sugars might be mainly responsible for flavor formation in CTFSS,the ratio of these two reactions rate led the metabolism to be divided into three steps,degradation,conversion and balance.

关键词： Soy sauce Fermentation Amino acids Volatile compounds Flavor metabolomics

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metabolomics reveals the key role of oxygen metabolism in heat susceptibility of an alpine-dwelling ghost moth, Thitarodes xiaojinensis (Lepidoptera: Hepialidae)

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Insect Science 2019年第4期26卷 695-710页

作者： Wei Zhu Qian Meng Huan Zhang Meng-Long Wang Xumn Li Hong-Tuo Wang Gui-Ling Zhou Lin Miao Qi-Lian Qin Ji-Hong Zhang State Key Laboratory of Integrated Management of Pest Insects and Rodents Institute of Zoology Chinese Academy of Sciences Beijing China Department of Herpetology Chengdu Institute of Biology Chinese Academy of Sciences Chengdu China

Ghost moths inhabiting the alpine meadows of the Tibetan Plateau are cold? adapted stenothermal organisms that are susceptible to heat (dead within 7 days at 27 °C exposure). Exploring the metabolic basis of their heat susceptibility would extend our understanding of the thermal biology of alpine-dwelling invertebrates. Here, gas chromatography-mass spectrometry-based metabolomics was combined with physiological and transcriptional approaches to determine the metabolic mechanisms of heat susceptibility in Thitarodes xiaojinensis larvae. The metabolomics results showed that 27 °C heat stress impaired the Krebs cycle and lipolysis in T. xiaojinensis larvae, as demonstrated by the accumulation of intermediary metabolites. In addition, carbohydrate reserves were highly and exclusively consumed, and an anaerobic product, lactate, accumulated. This evidence suggested a strong reliance on glycolysis to anaerobically generate energy. The respiration rate and enzymatic activity test results indicated a deficiency in O2 metabolism;in addition, the Krebs cycle capacity was not decreased, and the metabolic flux through aerobic pathways was limited. These findings were further supported by the occurrence of hypoxia symptoms in midgut mitochondria (vacuolation and swelling) and increased transcription of hypoxia-induced factor 1-α.Overall, heat stress caused O2 limitation and depressed the overall intensity of aerobic metabolism in ghost moths, and less efficient anaerobic glycolysis was activated to sustain their energy supply. As carbohydrates were depleted, the energy supply became deficient. Our study presents a comprehensive metabolic explanation for the heat susceptibility of ghost moths and reveals the relationship between O2 metabolism and heat susceptibility in these larvae.

关键词： energy metabolism ghost moths metabolomics thermal intolerance oxygen limitation respiration rate

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