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代谢组学 3

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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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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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Untargeted metabolomic analysis of pregnant women exposure to perfluorooctanoic acid at different degrees

《环境科学与工程前沿（英文）》 2023年 第17卷 第3期 doi: 10.1007/s11783-023-1628-x

摘要：

● Metabolome can distinguish pregnant women exposure to PFOA at different degrees.

关键词： Perfluorooctanoic acid     Exposure     Pregnant women     Metabolomic     GSH     Microbiota metabolism    

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Multi-omics joint analysis revealed the metabolic profile of retroperitoneal liposarcoma

《医学前沿（英文）》 doi: 10.1007/s11684-023-1020-z

摘要： Retroperitoneal liposarcoma (RLPS) is the main subtype of retroperitoneal soft sarcoma (RSTS) and has a poor prognosis and few treatment options, except for surgery. The proteomic and metabolic profiles of RLPS have remained unclear. The aim of our study was to reveal the metabolic profile of RLPS. Here, we performed proteomic analysis (n = 10), metabolomic analysis (n = 51), and lipidomic analysis (n = 50) of retroperitoneal dedifferentiated liposarcoma (RDDLPS) and retroperitoneal well-differentiated liposarcoma (RWDLPS) tissue and paired adjacent adipose tissue obtained during surgery. Data analysis mainly revealed that glycolysis, purine metabolism, pyrimidine metabolism and phospholipid formation were upregulated in both RDDLPS and RWDLPS tissue compared with the adjacent adipose tissue, whereas the tricarboxylic acid (TCA) cycle, lipid absorption and synthesis, fatty acid degradation and biosynthesis, as well as glycine, serine, and threonine metabolism were downregulated. Of particular importance, the glycolytic inhibitor 2-deoxy-D-glucose and pentose phosphate pathway (PPP) inhibitor RRX-001 significantly promoted the antitumor effects of the MDM2 inhibitor RG7112 and CDK4 inhibitor abemaciclib. Our study not only describes the metabolic profiles of RDDLPS and RWDLPS, but also offers potential therapeutic targets and strategies for RLPS.

关键词： RLPS     proteomics     metabolomics     lipidomics     metabolism    

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Cross-sectional network analysis of plasma proteins/metabolites correlated with pathogenesis and therapeutic response in acute promyelocytic leukemia

《医学前沿（英文）》 doi: 10.1007/s11684-023-1022-x

摘要： The treatment of PML/RARA+ acute promyelocytic leukemia (APL) with all-trans-retinoic acid and arsenic trioxide (ATRA/ATO) has been recognized as a model for translational medicine research. Though an altered microenvironment is a general cancer hallmark, how APL blasts shape their plasma composition is poorly understood. Here, we reported a cross-sectional correlation network to interpret multilayered datasets on clinical parameters, proteomes, and metabolomes of paired plasma samples from patients with APL before or after ATRA/ATO induction therapy. Our study revealed the two prominent features of the APL plasma, suggesting a possible involvement of APL blasts in modulating plasma composition. One was characterized by altered secretory protein and metabolite profiles correlating with heightened proliferation and energy consumption in APL blasts, and the other featured APL plasma-enriched proteins or enzymes catalyzing plasma-altered metabolites that were potential trans-regulatory targets of PML/RARA. Furthermore, results indicated heightened interferon-gamma signaling characterizing a tumor-suppressing function of the immune system at the first hematological complete remission stage, which likely resulted from therapy-induced cell death or senescence and ensuing supraphysiological levels of intracellular proteins. Overall, our work sheds new light on the pathophysiology and treatment of APL and provides an information-rich reference data cohort for the exploratory and translational study of leukemia microenvironment.

关键词： acute promyelocytic leukemia     plasma proteomics     plasma metabolomics     cross-sectional correlation network     pathogenesis     treatment    

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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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对良好中药标准的深层化学认知 Review

候晋军, 张建青, 姚长良, Rudolf Bauer, Ikhlas A. Khan, 吴婉莹, 果德安

《工程（英文）》 2019年 第5卷 第1期   页码 83-97 doi: 10.1016/j.eng.2018.12.005

摘要：

中药（TCM）是一种天然来源的复杂体系，具有多种多样的化学成分，在中国被广泛应用。中药的质量控制对政府和检测机构来说是一项巨大的挑战，涉及大量科学问题，包括：中药中有多少成分？如何全面地描述中药的诸多成分以及随后如何表征这些成分？为了推荐对照品的选择，这些（活性）代谢产物在多成分中药中的水平和范围是什么？以及选择的指标成分成分需要哪些质量要求，并且从实用的角度看，如何以低成本在短时间内对这些成分进行定量评价？所有这些因素均需要深思熟虑，才能理解中药独特的化学性质，从而提高中药质量标准，从而为患者提供更好的和更稳定的药物治疗。为了回应这些科学问题，本文汇总了有关中药化学分析技术和方法的最新探索性研究。这些方法的进展包括针对液相色谱- 高分辨质谱（LC-HARMS）联用技术的多维分离、LC-HRMS 联用技术的智能触发数据依赖型采集、利用液相色谱- 质谱联用技术（LC-MS）进行靶向分析、超临界流体色谱以及大的质谱（MS）数据集的数据挖掘。此外，为了节省对照品和中药质量标准的分析时间，本文提出了两种质量策略，分别是应用一标多测（SSDMC）和一法多用法。最后，本文介绍了一系列针对中药分析方法的改进。

关键词： 中药     液相色谱     质谱     数据依赖型采集     化学计量学     非靶向     数据挖掘     质量控制    

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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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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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标题 作者 时间 类型 操作

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

期刊论文

Progress in NMR-based metabolomics of

Qifang PAN,Jingya ZHAO,Yuliang WANG,Kexuan TANG

期刊论文

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

期刊论文

Metabolomics in human type 2 diabetes research

null

期刊论文

Sepsis biomarkers: an omics perspective

null

期刊论文

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

期刊论文

Untargeted metabolomic analysis of pregnant women exposure to perfluorooctanoic acid at different degrees

期刊论文

Multi-omics joint analysis revealed the metabolic profile of retroperitoneal liposarcoma

期刊论文

Cross-sectional network analysis of plasma proteins/metabolites correlated with pathogenesis and therapeutic response in acute promyelocytic leukemia

期刊论文

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

期刊论文

中医方证代谢组学——中药效应评价的有效途径

张爱华, 孙晖, 闫广利, 韩莹, 赵琦琦, 王喜军

期刊论文

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

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

期刊论文

对良好中药标准的深层化学认知

候晋军, 张建青, 姚长良, Rudolf Bauer, Ikhlas A. Khan, 吴婉莹, 果德安

期刊论文

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

期刊论文

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

null

期刊论文