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Progress in NMR-based metabolomics of

Qifang PAN,Jingya ZHAO,Yuliang WANG,Kexuan TANG

《农业科学与工程前沿（英文）》 2015年第2卷第3期页码 195-204 doi: 10.15302/J-FASE-2015063

摘要： Metabolomics has been rapidly developed as an important field in plant sciences and natural products chemistry. As the only natural source for a diversity of monoterpenoid indole alkaloids (MIAs), especially the low-abundance antitumor agents vinblastine and vincristine, is highly valued and has been studied extensively as a model for medicinal plants improvement. Due to multistep enzymatic biosynthesis and complex regulation, genetic modification in the MIA pathway has resulted in complicated changes of both secondary and primary metabolism in , affecting not only the MIA pathway but also other pathways. Research at the metabolic level is necessary to increase knowledge on the genetic regulation of the whole metabolic network connected to MIA biosynthesis. Nuclear magnetic resonance (NMR) is a very suitable and powerful complementary technique for the identiﬁcation and quantiﬁcation of metabolites in the plant matrix. NMR-based metabolomics has been used in studies of for pathway elucidation, understanding stress responses, classification among different cultivars, safety and quality controls of transgenic plants, cross talk between pathways, and diversion of carbon fluxes, with the aim of fully unravelling MIA biosynthesis, its regulation and the function of the alkaloids in the plant from a systems biology point of view.

关键词： Catharanthus roseus monoterpenoid indole alkaloids NMR metabolomics

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Time-dependent metabolomics uncover dynamic metabolic adaptions in MCF-7 cells exposed to bisphenol A

《环境科学与工程前沿（英文）》 2023年第17卷第1期 doi: 10.1007/s11783-023-1604-5

摘要：

● Metabolomic temporal profiling of cells exposed to xenobiotics.

关键词： Metabolomics BPA MCF-7 Temporal profiling Metabolic adaption Dysregulation correlation

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Metabolomics in human type 2 diabetes research

null

《医学前沿（英文）》 2013年第7卷第1期页码 4-13 doi: 10.1007/s11684-013-0248-4

摘要：

The high prevalence of diabetes and diabetic complications has caused a huge burden on the modern society. Although scientific advances have led to effective strategies for preventing and treating diabetes over the past several decades, little progress has been made toward curing the disease or even getting it under control, from a public health and overall societal standpoint. There is still a lack of reliable biomarkers indicative of metabolic alterations associated with diabetes and different drug responses, highlighting the need for the development of early diagnostic and prognostic markers for diabetes and diabetic complications. The emergence of metabolomics has allowed researchers to systemically measure the small molecule metabolites, which are sensitive to the changes of both environmental and genetic factors and therefore, could be regarded as the link between genotypes and phenotypes. During the last decade, the progression made in metabolomics has provided insightful information on disease development and disease onset prediction. Recent studies using metabolomics approach coupled with statistical tools to predict incident diabetes revealed a number of metabolites that are significantly altered, including branched-chain and aromatic amino acids, such as isoleucine, leucine, valine, tyrosine and phenylalanine, as diagnostic or highly-significant predictors of future diabetes. This review summarizes the current findings of metabolomic studies in human investigations with the most common form of diabetes, type 2 diabetes.

关键词： metabolomics type 2 diabetes metabolic pathway mass spectrometry nuclear magnetic resonance (NMR)

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Sepsis biomarkers: an omics perspective

null

《医学前沿（英文）》 2014年第8卷第1期页码 58-67 doi: 10.1007/s11684-014-0318-2

摘要：

Sepsis is a common cause of death in hospitalized patients worldwide. The early detection of sepsis remains a great challenge for clinicians, and delayed diagnosis frequently undermines treatment efforts, thereby contributing to high mortality. Omics technologies allow high-throughput screening of sepsis biomarkers. This review describes currently available and novel sepsis biomarkers in the context of genomics, transcriptomics, proteomics, and metabolomics. The combination of these technologies can help refine the diagnosis of sepsis. This review paper serves as a reference for future studies that employ an integrated, multi-omics approach to disease identification.

关键词： sepsis biomarker genomics transcriptomics proteomics metabolomics

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High-throughput metabolomics reveals the perturbed metabolic pathways and biomarkers of Yang Huang syndrome

Heng Fang, Aihua Zhang, Xiaohang Zhou, Jingbo Yu, Qi Song, Xijun Wang

《医学前沿（英文）》 2020年第14卷第5期页码 651-663 doi: 10.1007/s11684-019-0709-5

摘要： High-throughput metabolomics can clarify the underlying molecular mechanism of diseases via the qualitative and quantitative analysis of metabolites. This study used the established Yang Huang syndrome (YHS) mouse model to evaluate the efficacy of geniposide (GEN). Urine metabolic data were quantified by ultra-performance liquid chromatography–tandem mass spectrometry. The non-target screening of the massive biological information dataset was performed, and a total of 33 metabolites, including tyramine glucuronide, aurine, and L-cysteine, were identified relating to YHS. These differential metabolites directly participated in the disturbance of phase I reaction and hydrophilic transformation of bilirubin. Interestingly, they were completely reversed by GEN. While, as the auxiliary technical means, we also focused on the molecular prediction and docking results in network pharmacological and integrated analysis part. We used integrated analysis to communicate the multiple results of metabolomics and network pharmacology. This study is the first to report that GEN indirectly regulates the metabolite “tyramine glucuronide” through its direct effect on the target heme oxygenase 1 . Meanwhile, heme oxygenase-1, a prediction of network pharmacology, was the confirmed metabolic enzyme of phase I reaction in hepatocytes. Our study indicated that the combination of high-throughput metabolomics and network pharmacology is a robust combination for deciphering the pathogenesis of the traditional Chinese medicine (TCM) syndrome.

关键词： metabolomics liquid chromatography-mass spectrometry metabolites metabolic pathways

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Genomic and metabolomic analysis of with enhanced poly--glutamic acid production through atmospheric and room temperature plasma mutagenesis

《化学科学与工程前沿（英文）》 2022年第16卷第12期页码 1751-1760 doi: 10.1007/s11705-022-2211-x

摘要： Poly-γ-glutamic acid is an extracellular polymeric substance with various applications owing to its valuable properties of biodegradability, flocculating activity, water solubility, and nontoxicity. However, the ability of natural strains to produce poly-γ-glutamic acid is low. Atmospheric and room temperature plasma was applied in this study to conduct mutation breeding of Bacillus licheniformis CGMCC 2876, and a mutant strain M32 with an 11% increase in poly-γ-glutamic acid was obtained. Genome resequencing analysis identified 7 nonsynonymous mutations of ppsC encoding lipopeptide synthetase associated with poly-γ-glutamic acid metabolic pathways. From molecular docking, more binding sites and higher binding energy were speculated between the mutated plipastatin synthase subunit C and glutamate, which might contribute to the higher poly-γ-glutamic acid production. Moreover, the metabolic mechanism analysis revealed that the upregulated amino acids of M32 provided substrates for glutamate and promoted the conversion between L- and D-glutamate acids. In addition, the glycolytic pathway is enhanced, leading to a better capacity for using glucose. The maximum poly-γ-glutamic acid yield of 14.08 g·L^–1 was finally reached with 30 g·L^–1 glutamate.

关键词： ARTP mutagenesis Bacillus licheniformis poly-γ-glutamic acid metabolomics

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中医方证代谢组学——中药效应评价的有效途径 Review

张爱华, 孙晖, 闫广利, 韩莹, 赵琦琦, 王喜军

《工程（英文）》 2019年第5卷第1期页码 60-68 doi: 10.1016/j.eng.2018.11.008

摘要：

有效性评价是发现中药药效物质基础、先导化合物和质量标志物的重要前提，因此急需建立一种生物学语言，将中药有效性科学地表达出来，进一步凸显中医药的实用价值。证候和方剂是中医药的重要组成部分，与中药有效性直接相关。我们以证候和方剂为研究对象，建立了科学评价中药有效性的创新方法学体系——中医方证代谢组学。它将中药血清药物化学理论与代谢组学技术有机整合，在解决证候生物标记物的基础上，建立方剂药效生物评价体系，发现并确认中药药效物质基础。该策略为提高中医理论和临床实践的科学价值提供了有力支持。本文概述了中医方证代谢组学的研究策略，利用该方法揭示临床常见中医证候生物标记物及开展相关方剂的有效性评价研究，着重阐述了中药药效物质基础及质量标记物的发现。

关键词：中医方证代谢组学中药血清药物化学有效性代谢组学证候生物标记物质量标记物

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功能代谢组学揭示黄芪多糖通过2-羟基丁酸改善肥胖小鼠的脂质代谢 Article

李冰冰, 洪颖, 顾彧, 叶圣洁, 胡凯莉, 姚建, 丁侃, 赵爱华, 贾伟, 李后开

《工程（英文）》 2022年第9卷第2期页码 111-122 doi: 10.1016/j.eng.2020.05.023

摘要：

多糖广泛存在于草本植物中，具有多种活性，特别是具有免疫调节作用和改善代谢紊乱的作用。然而，其潜在机制还没有被很好地诠释。功能代谢组学越来越多地被用于通过鉴定具有特定功能的代谢产物来研究多糖对宿主的系统性影响。本研究采用功能代谢组学策略，探讨黄芪多糖（Astragalus polysaccharide, APS）代谢获益的潜在机制。在为期8 周的高脂肪饮食（high-fat diet, HFD）喂养的肥胖小鼠中测定了APS的作用。然后，进行基于气相色谱-飞行时间质谱（gas chromatography-time-of-flight mass spectrometry, GC-TOFMS）的非靶向代谢组学分析血清和肝组织，并进行基于液相色谱- 串联质谱（liquid chromatography-tandem mass spectrometry, LC-MS/MS）的靶向代谢组学分析。使用体外和体内代谢紊乱模型测试了代谢产物的潜在功能。我们的结果首次证实了APS对肥胖小鼠的代谢益处。然后，代谢组学分析显示，补充APS 可逆转HFD 诱导的代谢变化，并确定2-羟基丁酸（2-hydroxybutyric acid, 2-HB）是APS活性的潜在功能性代谢产物，该代谢物被HFD显著降低，并被APS逆转。进一步研究表明，2-HB可抑制油酸（oleic acid, OA）诱导的甘油三酯（triglyceride, TG）累积。还发现其可刺激肝细胞中脂质降解蛋白的表达和3T3-L1 细胞中的TG脂解。此外，在高脂肪和高蔗糖（high-fat and high-sucrose, HFHS）喂养的小鼠中发现2-HB可降低血清TG并调节参与脂质降解的蛋白质。总之，我们的研究表明，APS的代谢
益处至少部分归因于2-HB 的产生，2-HB 在体外和体内均可调节脂质代谢。我们的结果同样证实，功能代谢组学在研究植物多糖系统益处的潜在机制方面是切实可行的。

关键词：黄芪多糖功能代谢组学 2-羟基丁酸肥胖

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Screening for main components associated with the idiosyncratic hepatotoxicity of a tonic herb, Polygonum multiflorum

null

《医学前沿（英文）》 2017年第11卷第2期页码 253-265 doi: 10.1007/s11684-017-0508-9

摘要：

The main constituents of a typical medicinal herb, Polygonum multiflorum (Heshouwu in Chinese), that induces idiosyncratic liver injury remain unclear. Our previous work has shown that cotreatment with a nontoxic dose of lipopolysaccharide (LPS) and therapeutic dose of Heshouwu can induce liver injury in rats, whereas the solo treatment cannot induce observable injury. In the present work, using the constituent “knock-out” and “knock-in” strategy, we found that the ethyl acetate (EA) extract of Heshouwu displayed comparable idiosyncratic hepatotoxicity to the whole extract in LPS-treated rats. Results indicated a significant elevation of plasma alanine aminotransferase, aspartate aminotransferase, and liver histologic changes, whereas other separated fractions failed to induce liver injury. The mixture of EA extract with other separated fractions induced comparable idiosyncratic hepatotoxicity to the whole extract in LPS-treated rats. Chemical analysis further revealed that 2,3,5,4'-tetrahydroxy trans-stilbene-2-O-β-glucoside (trans-SG) and its cis-isomer were the two major compounds in EA extract. Furthermore, the isolated cis-, and not its trans-isomer, displayed comparable idiosyncratic hepatotoxicity to EA extract in LPS-treated rats. Higher contents of cis-SG were detected in Heshouwu liquor or preparations from actual liver intoxication patients associated with Heshouwu compared with general collected samples. In addition, plasma metabolomics analysis showed that cis-SG-disturbing enriched pathways remarkably differed from trans-SG ones in LPS-treated rats. All these results suggested that cis-SG was closely associated with the idiosyncratic hepatotoxicity of Heshouwu. Considering that the cis-trans isomerization of trans-SG was mediated by ultraviolet light or sunlight, our findings serve as reference for controlling photoisomerization in drug discovery and for the clinical use of Heshouwu and stilbene-related medications.

关键词： Polygonum multiflorum idiosyncratic hepatotoxicity metabolomics stilbene cis-transisomerization

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METABOLIC AND TRANSCRIPTOME ANALYSIS REVEALS METABOLITE VARIATION AND FLAVONOID REGULATORY NETWORKS IN FRESH SHOOTS OF TEA (

Chen-Kai JIANG, De-Jiang NI, Ming-Zhe YAO, Jian-Qiang MA, Liang CHEN

《农业科学与工程前沿（英文）》页码 215-230 doi: 10.15302/J-FASE-2021382

摘要： Metabolites, especially secondary metabolites, are very important in the adaption of tea plants and the quality of tea products. Here, we focus on the seasonal variation in metabolites of fresh tea shoots and their regulatory mechanism at the transcriptional level. The metabolic profiles of fresh tea shoots of 10 tea accessions collected in spring, summer, and autumn were analyzed using ultra-performance liquid chromatography coupled with quadrupole-obitrap mass spectrometry. We focused on the metabolites and key genes in the phenylpropanoid/flavonoid pathway integrated with transcriptome analysis. Multivariate statistical analysis indicates that metabolites were distinctly different with seasonal alternation. Flavonoids, amino acids, organic acids and alkaloids were the predominant metabolites. Levels of most key genes and downstream compounds in the flavonoid pathway were lowest in spring but the catechin quality index was highest in spring. The regulatory pathway was explored by constructing a metabolite correlation network and a weighted gene co-expression network.

关键词： harvest season metabolites tea shoots transcriptomics untargeted metabolomics

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Evidence chain-based causality identification in herb-induced liver injury: exemplification of a well-known liver-restorative herb

null

《医学前沿（英文）》 2015年第9卷第4期页码 457-467 doi: 10.1007/s11684-015-0417-8

摘要：

Herbal medicines have recently been recognized as the second most common cause of drug-induced liver injury (DILI) in the United States. However, reliable methods to identify the DILI causality of some herbs, such as Heshouwu (dried root of Polygonum multiflorum), remain lacking. In this study, a total of 12 307 inpatients with liver dysfunction and 147 literature-reported cases of Heshouwu DILI were screened. A general algorithm indicated that only 22.5% (9/40) and 30.6% (45/147) of all hospitalization and literature case reports, respectively, demonstrate the high probability of DILI causality of Heshouwu. By contrast, 95% (19/20) of all cases prospectively investigated by pharmacognosy, phytochemistry, and metabolomic tests exhibited highly probable causality, including a patient who was previously incorrectly attributed and a case that was excluded from Heshouwu causality by pharmacognostic evidence. Toxin (heavy metals, pesticides, and mycotoxins) contamination was also excluded from Heshouwu DILI causality. The objectivity of these screening methods for Heshouwu DILI diagnosis addresses safety concerns regarding stilbene-containing herbal medicines and dietary supplements.

关键词： drug-induced liver injury pharmacognosy metabolomics stilbene Polygonum multiflorum Chinese herbal medicine

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Photosynthesis and related metabolic mechanism of promoted rice (Oryza sativa L.) growth by TiO₂ nanoparticles

Yingdan Zhang, Na Liu, Wei Wang, Jianteng Sun, Lizhong Zhu

《环境科学与工程前沿（英文）》 2020年第14卷第6期 doi: 10.1007/s11783-020-1282-5

摘要： Abstract • The rice growth was promoted by nano-TiO2 of 0.1–100 mg/L. • Nano-TiO2 enhanced the energy storage in photosynthesis. • Nano-TiO2 reduced energy consumption in carbohydrate metabolism and TCA cycle. Titanium dioxide nanoparticle (nano-TiO2), as an excellent UV absorbent and photo-catalyst, has been widely applied in modern industry, thus inevitably discharged into environment. We proposed that nano-TiO2 in soil can promote crop yield through photosynthetic and metabolic disturbance, therefore, we investigated the effects of nano-TiO2 exposure on related physiologic-biochemical properties of rice (Oryza sativa L.). Results showed that rice biomass was increased >30% at every applied dosage (0.1–100 mg/L) of nano-TiO2. The actual photosynthetic rate (Y(II)) significantly increased by 10.0% and 17.2% in the treatments of 10 and 100 mg/L respectively, indicating an increased energy production from photosynthesis. Besides, non-photochemical quenching (Y(NPQ)) significantly decreased by 19.8%–26.0% of the control in all treatments respectively, representing a decline in heat dissipation. Detailed metabolism fingerprinting further revealed that a fortified transformation of monosaccharides (D-fructose, D-galactose, and D-talose) to disaccharides (D-cellobiose, and D-lactose) was accompanied with a weakened citric acid cycle, confirming the decrease of energy consumption in metabolism. All these results elucidated that nano-TiO2 promoted rice growth through the upregulation of energy storage in photosynthesis and the downregulation of energy consumption in metabolism. This study provides a mechanistic understanding of the stress-response hormesis of rice after exposure to nano-TiO2, and provides worthy information on the potential application and risk of nanomaterials in agricultural production.

关键词： Nano-TiO₂ Rice Photosynthesis Metabolomics Energy storage

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血浆代谢组学结合超微弱发光表征早期2型糖尿病的中医证型 Article

何敏, 孙濛濛, Slavik Koval, Roeland Van Wijk, Thomas Hankemeier, Jan Van der Greef, Eduard P.A. Van Wijk, 王梅

《工程（英文）》 2019年第5卷第5期页码 916-923 doi: 10.1016/j.eng.2019.03.011

摘要：

2型糖尿病（T2DM）的患病率在全球范围内呈迅速上升趋势。因通用干预措施收效甚微，所以疾病研究的重点已经转向个性化策略，特别是疾病的早期阶段的个性化策略。中医基于系统观建立并结合了个性化策略，提高了我们对个性化诊断的认识。从系统生物学的角度，例如将代谢组学与其他系统性诊断方法（如超微弱发光）相结合，可提高对个性化诊断的理解，同时为此类个性化诊疗策略提供生化相关物质基础。在本研究中，我们研究了44名处于2型糖尿病前期的受试者的血浆代谢组学，探讨了基于以下中医亚型进行疾病早期分型的可行性：气阴两虚、气阴两虚挟痰湿、气阴两虚挟血瘀。此外，通过血浆代谢组学和超微弱发光在中医亚分型方面的关系，获得体内生化参数与体外表征参数的关联性信息，从而尝试对疾病亚型分类及判断有更深一步的阐释。结果表明，血浆代谢物的主成分分析揭示了从中医角度划分的2型糖尿病前期不同亚型之间的差异性。对于3种2型糖尿病前期亚型，相对含量较高的脂质（如胆固醇酯和甘油三酯）是鉴别其中之二的重要元素，并且可能与较高的心血管疾病风险相关。血浆代谢组学数据表明，血脂谱是超微弱发光在2型糖尿病亚型分型中收集的重要组成部分。结果表明，2型糖尿病前期的不同中医亚型之间存在代谢差异，可通过血浆代谢物分析来区分这些亚型，血浆代谢组学为系统性超微弱发光体表测量提供了生化参数相关依据。

关键词： 2型糖尿病血浆代谢物疾病亚型超微弱发光相关性网络

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基于整合临床和动物实验的小分子筛选平台揭示经典方剂茵陈蒿汤治疗黄疸证显效状态下的活性化合物及潜在作用靶点 Article

熊辉, 张爱华, 郭雅静, 周小航, 孙晖, 杨乐, 方衡, 闫广利, 王喜军

《工程（英文）》 2021年第7卷第9期页码 1293-1305 doi: 10.1016/j.eng.2020.12.016

摘要：

中药方剂化学组成高度复杂，其药理作用具有多成分、多靶点的特点，使得阐明其生物活性化合物极具挑战性。茵陈蒿汤被广泛用于治疗黄疸相关疾病。尽管近年来茵陈蒿汤的药效及活性成分被不断证实，但仍然缺乏对其效应成分、效应机制和功能靶点的深入系统分析，尤其是临床研究方面。本研究建立了一个整合临床和动物实验平台用于发现茵陈蒿汤的活性化合物和潜在靶点。首先采用基于超高效液相色谱-四极杆飞行时间质谱（UPLC-Q-ToF-MS）技术的代谢组学方法结合中药血清药物化学方法揭示茵陈蒿汤的血清代谢谱和化学成分谱。此外，通过网络药理学和智能途径分析平台构建化合物-靶标-通路关联网络。最终发现茵陈蒿汤中8 个活性小分子与5 个核心靶点极度相关，并通过酶联免疫吸附测定实验进行生物学验证。结果表明茵陈蒿汤通过靶向胆固醇7α-羟化酶（CYP7A1）、多药耐药相关蛋白2（ABCC2）、多药耐药相关蛋白3（ABCC3）、尿苷二磷酸葡萄糖醛酸基转移酶1A1（UGT1A1）和法尼醇X受体（FXR）来调节包括初级胆汁酸生物合成、卟啉和叶绿素代谢以及胆汁分泌在内的代谢通路，从而发挥利胆退黄的作用。该整合策略可以成功地用于中药方剂活性小分子及其作用靶点的发现。

关键词：有效性活性化合物小分子靶点中药代谢组学