State-of-the-Art Metabolomics and Lipidomics in Life Sciences: Methods and Applications

A special issue of Metabolites (ISSN 2218-1989). This special issue belongs to the section "Lipid Metabolism".

Deadline for manuscript submissions: closed (15 August 2023) | Viewed by 19103

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Special Issue Editors


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Guest Editor
Institute for Clinical Chemistry and Pathobiochemistry, Department for Diagnostic Laboratory Medicine, University Hospital Tübingen, 72076 Tübingen, Germany
Interests: exercise metabolism; skeletal muscle; liver; insulin resistance; mitochondrial respiration; myometabokines
Key Lab of Analytical Science for Separation, Metabonomics Research Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
Interests: metabolomics; LC-MS; GC-MS; metabolic reprogramming and markers

Special Issue Information

Dear Colleagues,

The understanding of mechanisms in disease development and treatment has been the center of life science research for decades or even centuries. Over the past twenty years, substantial progress has been made by the establishment regarding the application of metabolomics and lipidomics approaches, which has allowed researchers, for the first time, to study a plethora of metabolites and metabolic pathways simultaneously.

From microbes to plants, to animals, to humans—all kinds of samples have been investigated by these techniques, thereby making a considerable contribution to the increase in knowledge in all facets of life sciences. Additionally, novel analytical methods and strategies, along with new bioinformatic tools for the evaluation of these very complex metabolomics, lipidomics or multi-omics data, have been developed.

Profs. Guowang Xu and Rainer Lehmann have been closely cooperating for 25 years in this field of research. In 2023 Metabolites is pleased to announce this Special Issue dedicated to Profs. Guowang Xu and Rainer Lehmann about state-of-the-art metabolomics and lipidomics research in life science to celebrate this fruitful Sino-German scientific cooperation and their close friendship.

This Special Issue welcomes, especially from colleagues and friends, the submission of high-quality reviews, original research articles or other types of papers addressing all aspects of life science research from microbes, plants, animals to humans applying metabolomics or lipidomics, as well as reports on new biomarkers, protocols, strategies or bioinformatic tools.

Prof. Dr. Cora Weigert
Dr. Xinyu Liu
Guest Editors

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Keywords

  • metabolomics
  • lipidomics
  • life science
  • biomedical
  • human
  • blood
  • urine
  • cell culture
  • tissue
  • microbiome
  • plants

Published Papers (15 papers)

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Editorial

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6 pages, 163 KiB  
Editorial
State-of-the-Art Metabolomics and Lipidomics in Life Sciences: Methods and Applications
by Xinyu Liu and Cora Weigert
Metabolites 2024, 14(1), 8; https://doi.org/10.3390/metabo14010008 - 21 Dec 2023
Viewed by 925
Abstract
This Special Issue was initiated to celebrate and congratulate Prof [...] Full article

Research

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22 pages, 3281 KiB  
Article
Transcriptome and Lipidomic Analysis Suggests Lipid Metabolism Reprogramming and Upregulating SPHK1 Promotes Stemness in Pancreatic Ductal Adenocarcinoma Stem-like Cells
by Jinzhi Xu, Lina Zhou, Xiaojing Du, Zhuoran Qi, Sinuo Chen, Jian Zhang, Xin Cao and Jinglin Xia
Metabolites 2023, 13(11), 1132; https://doi.org/10.3390/metabo13111132 - 04 Nov 2023
Viewed by 1377
Abstract
Cancer stem cells (CSCs) are considered to play a key role in the development and progression of pancreatic ductal adenocarcinoma (PDAC). However, little is known about lipid metabolism reprogramming in PDAC CSCs. Here, we assigned stemness indices, which were used to describe and [...] Read more.
Cancer stem cells (CSCs) are considered to play a key role in the development and progression of pancreatic ductal adenocarcinoma (PDAC). However, little is known about lipid metabolism reprogramming in PDAC CSCs. Here, we assigned stemness indices, which were used to describe and quantify CSCs, to every patient from the Cancer Genome Atlas (TCGA-PAAD) database and observed differences in lipid metabolism between patients with high and low stemness indices. Then, tumor-repopulating cells (TRCs) cultured in soft 3D (three-dimensional) fibrin gels were demonstrated to be an available PDAC cancer stem-like cell (CSLCs) model. Comprehensive transcriptome and lipidomic analysis results suggested that fatty acid metabolism, glycerophospholipid metabolism, and, especially, the sphingolipid metabolism pathway were mostly associated with CSLCs properties. SPHK1 (sphingosine kinases 1), one of the genes involved in sphingolipid metabolism and encoding the key enzyme to catalyze sphingosine to generate S1P (sphingosine-1-phosphate), was identified to be the key gene in promoting the stemness of PDAC. In summary, we explored the characteristics of lipid metabolism both in patients with high stemness indices and in novel CSLCs models, and unraveled a molecular mechanism via which sphingolipid metabolism maintained tumor stemness. These findings may contribute to the development of a strategy for targeting lipid metabolism to inhibit CSCs in PDAC treatment. Full article
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15 pages, 27086 KiB  
Article
Study on the Common Molecular Mechanism of Metabolic Acidosis and Myocardial Damage Complicated by Neonatal Pneumonia
by Yifei Zhan, Huaiyan Wang, Zeying Wu and Zhongda Zeng
Metabolites 2023, 13(11), 1118; https://doi.org/10.3390/metabo13111118 - 30 Oct 2023
Viewed by 1040
Abstract
Pneumonia is a common clinical disease in the neonatal period and poses a serious risk to infant health. Therefore, the understanding of molecular mechanisms is of great importance for the development of methods for the rapid and accurate identification, classification and staging, and [...] Read more.
Pneumonia is a common clinical disease in the neonatal period and poses a serious risk to infant health. Therefore, the understanding of molecular mechanisms is of great importance for the development of methods for the rapid and accurate identification, classification and staging, and even disease diagnosis and therapy of pneumonia. In this study, a nontargeted metabonomic method was developed and applied for the analysis of serum samples collected from 20 cases in the pneumonia control group (PN) and 20 and 10 cases of pneumonia patients with metabolic acidosis (MA) and myocardial damage (MD), respectively, with the help of ultrahigh-performance liquid chromatography–high-resolution mass spectrometry (UPLC–HRMS). The results showed that compared with the pneumonia group, 23 and 21 differential metabolites were identified in pneumonia with two complications. They showed high sensitivity and specificity, with the area under the curve (ROC) of the receiver operating characteristic curve (ROC) larger than 0.7 for each differential molecule. There were 14 metabolites and three metabolic pathways of sphingolipid metabolism, porphyrin and chlorophyll metabolism, and glycerophospholipid metabolism existing in both groups of PN and MA, and PN and MD, all involving significant changes in pathways closely related to amino acid metabolism disorders, abnormal cell apoptosis, and inflammatory responses. These findings of molecular mechanisms should help a lot to fully understand and even treat the complications of pneumonia in infants. Full article
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18 pages, 8937 KiB  
Article
A Nucleotide Metabolism-Related Gene Signature for Risk Stratification and Prognosis Prediction in Hepatocellular Carcinoma Based on an Integrated Transcriptomics and Metabolomics Approach
by Tianfu Wei, Jifeng Liu, Shurong Ma, Mimi Wang, Qihang Yuan, Anliang Huang, Zeming Wu, Dong Shang and Peiyuan Yin
Metabolites 2023, 13(11), 1116; https://doi.org/10.3390/metabo13111116 - 30 Oct 2023
Cited by 1 | Viewed by 1204
Abstract
Hepatocellular carcinoma (HCC) is a leading cause of cancer-related mortality worldwide. The in-depth study of genes and metabolites related to nucleotide metabolism will provide new ideas for predicting the prognosis of HCC patients. This study integrated the transcriptome data of different cancer types [...] Read more.
Hepatocellular carcinoma (HCC) is a leading cause of cancer-related mortality worldwide. The in-depth study of genes and metabolites related to nucleotide metabolism will provide new ideas for predicting the prognosis of HCC patients. This study integrated the transcriptome data of different cancer types to explore the characteristics and significance of nucleotide metabolism-related genes (NMGRs) in different cancer types. Then, we constructed a new HCC classifier and prognosis model based on HCC samples from TCGA and GEO, and detected the gene expression level in the model through molecular biology experiments. Finally, nucleotide metabolism-related products in serum of HCC patients were examined using untargeted metabolomics. A total of 97 NMRGs were obtained based on bioinformatics techniques. In addition, a clinical model that could accurately predict the prognostic outcome of HCC was constructed, which contained 11 NMRGs. The results of PCR experiments showed that the expression levels of these genes were basically consistent with the predicted trends. Meanwhile, the results of untargeted metabolomics also proved that there was a significant nucleotide metabolism disorder in the development of HCC. Our results provide a promising insight into nucleotide metabolism in HCC, as well as a tailored prognostic and chemotherapy sensitivity prediction tool for patients. Full article
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12 pages, 1482 KiB  
Article
A New Biomarker Profiling Strategy for Gut Microbiome Research: Valid Association of Metabolites to Metabolism of Microbiota Detected by Non-Targeted Metabolomics in Human Urine
by Sijia Zheng, Lina Zhou, Miriam Hoene, Andreas Peter, Andreas L. Birkenfeld, Cora Weigert, Xinyu Liu, Xinjie Zhao, Guowang Xu and Rainer Lehmann
Metabolites 2023, 13(10), 1061; https://doi.org/10.3390/metabo13101061 - 09 Oct 2023
Viewed by 1269
Abstract
The gut microbiome is of tremendous relevance to human health and disease, so it is a hot topic of omics-driven biomedical research. However, a valid identification of gut microbiota-associated molecules in human blood or urine is difficult to achieve. We hypothesize that bowel [...] Read more.
The gut microbiome is of tremendous relevance to human health and disease, so it is a hot topic of omics-driven biomedical research. However, a valid identification of gut microbiota-associated molecules in human blood or urine is difficult to achieve. We hypothesize that bowel evacuation is an easy-to-use approach to reveal such metabolites. A non-targeted and modifying group-assisted metabolomics approach (covering 40 types of modifications) was applied to investigate urine samples collected in two independent experiments at various time points before and after laxative use. Fasting over the same time period served as the control condition. As a result, depletion of the fecal microbiome significantly affected the levels of 331 metabolite ions in urine, including 100 modified metabolites. Dominating modifications were glucuronidations, carboxylations, sulfations, adenine conjugations, butyrylations, malonylations, and acetylations. A total of 32 compounds, including common, but also unexpected fecal microbiota-associated metabolites, were annotated. The applied strategy has potential to generate a microbiome-associated metabolite map (M3) of urine from healthy humans, and presumably also other body fluids. Comparative analyses of M3 vs. disease-related metabolite profiles, or therapy-dependent changes may open promising perspectives for human gut microbiome research and diagnostics beyond analyzing feces. Full article
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13 pages, 1960 KiB  
Article
Gas Chromatography–Mass Spectrometry Reveals Stage-Specific Metabolic Signatures of Ankylosing Spondylitis
by Yixuan Guo, Shuangshuang Wei, Mengdi Yin, Dandan Cao, Yiling Li, Chengping Wen and Jia Zhou
Metabolites 2023, 13(10), 1058; https://doi.org/10.3390/metabo13101058 - 07 Oct 2023
Cited by 1 | Viewed by 978
Abstract
Ankylosing spondylitis (AS) is a type of chronic rheumatic immune disease, and the crucial point of AS treatment is identifying the correct stage of the disease. However, there is a lack of effective diagnostic methods for AS staging. The primary objective of this [...] Read more.
Ankylosing spondylitis (AS) is a type of chronic rheumatic immune disease, and the crucial point of AS treatment is identifying the correct stage of the disease. However, there is a lack of effective diagnostic methods for AS staging. The primary objective of this study was to perform an untargeted metabolomic approach in AS patients in an effort to reveal metabolic differences between patients in remission and acute stages. Serum samples from 40 controls and 57 AS patients were analyzed via gas chromatography–mass spectrometry (GC–MS). Twenty-four kinds of differential metabolites were identified between the healthy controls and AS patients, mainly involving valine/leucine/isoleucine biosynthesis and degradation, phenylalanine/tyrosine/tryptophan biosynthesis, glutathione metabolism, etc. Furthermore, the levels of fatty acids (linoleate, dodecanoate, hexadecanoate, and octadecanoate), amino acids (serine and pyroglutamate), 2-hydroxybutanoate, glucose, etc., were lower in patients in the acute stage than those in the remission stage, which may be associated with the aggravated inflammatory response and elevated oxidative stress in the acute stage. Multiple stage-specific metabolites were significantly correlated with inflammatory indicators (CRP and ESR). In addition, the combination of serum 2-hydroxybutanoate and hexadecanoate plays a significant role in the diagnosis of AS stages. These metabolomics-based findings provide new perspectives for AS staging, treatment, and pathogenesis studies. Full article
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16 pages, 4279 KiB  
Article
Evaluating the Effects of Omega-3 Polyunsaturated Fatty Acids on Inflammatory Bowel Disease via Circulating Metabolites: A Mediation Mendelian Randomization Study
by Xiaojing Jia, Chunyan Hu, Xueyan Wu, Hongyan Qi, Lin Lin, Min Xu, Yu Xu, Tiange Wang, Zhiyun Zhao, Yuhong Chen, Mian Li, Ruizhi Zheng, Hong Lin, Shuangyuan Wang, Weiqing Wang, Yufang Bi, Jie Zheng and Jieli Lu
Metabolites 2023, 13(10), 1041; https://doi.org/10.3390/metabo13101041 - 28 Sep 2023
Cited by 1 | Viewed by 1383
Abstract
Epidemiological evidence regarding the effect of omega-3 polyunsaturated fatty acid (PUFA) supplementation on inflammatory bowel disease (IBD) is conflicting. Additionally, little evidence exists regarding the effects of specific omega-3 components on IBD risk. We applied two-sample Mendelian randomization (MR) to disentangle the effects [...] Read more.
Epidemiological evidence regarding the effect of omega-3 polyunsaturated fatty acid (PUFA) supplementation on inflammatory bowel disease (IBD) is conflicting. Additionally, little evidence exists regarding the effects of specific omega-3 components on IBD risk. We applied two-sample Mendelian randomization (MR) to disentangle the effects of omega-3 PUFAs (including total omega-3, α-linolenic acid, eicosapentaenoic acid (EPA), or docosahexaenoic acid (DHA)) on the risk of IBD, Crohn’s disease (CD) and ulcerative colitis (UC). Our findings indicated that genetically predicted increased EPA concentrations were associated with decreased risk of IBD (odds ratio 0.78 (95% CI 0.63–0.98)). This effect was found to be mediated through lower levels of linoleic acid and histidine metabolites. However, we found limited evidence to support the effects of total omega-3, α-linolenic acid, and DHA on the risks of IBD. In the fatty acid desaturase 2 (FADS2) region, robust colocalization evidence was observed, suggesting the primary role of the FADS2 gene in mediating the effects of omega-3 PUFAs on IBD. Therefore, the present MR study highlights EPA as the predominant active component of omega-3 fatty acids in relation to decreased risk of IBD, potentially via its interaction with linoleic acid and histidine metabolites. Additionally, the FADS2 gene likely mediates the effects of omega-3 PUFAs on IBD risk. Full article
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17 pages, 6286 KiB  
Article
Metabolomic Signatures Associated with Radiation-Induced Lung Injury by Correlating Lung Tissue to Plasma in a Rat Model
by Liming Gu, Wenli Wang, Yifeng Gu, Jianping Cao and Chang Wang
Metabolites 2023, 13(9), 1020; https://doi.org/10.3390/metabo13091020 - 17 Sep 2023
Viewed by 1055
Abstract
The lung has raised significant concerns because of its radiosensitivity. Radiation-induced lung injury (RILI) has a serious impact on the quality of patients’ lives and limits the effect of radiotherapy on chest tumors. In clinical practice, effective drug intervention for RILI remains to [...] Read more.
The lung has raised significant concerns because of its radiosensitivity. Radiation-induced lung injury (RILI) has a serious impact on the quality of patients’ lives and limits the effect of radiotherapy on chest tumors. In clinical practice, effective drug intervention for RILI remains to be fully elucidated. Therefore, an in-depth understanding of the biological characteristics is essential to reveal the mechanisms underlying the complex biological processes and discover novel therapeutic targets in RILI. In this study, Wistar rats received 0, 10, 20 or 35 Gy whole-thorax irradiation (WTI). Lung and plasma samples were collected within 5 days post-irradiation. Then, these samples were processed using liquid chromatography–mass spectrometry (LC-MS). A panel of potential plasma metabolic markers was selected by correlation analysis between the lung tissue and plasma metabolic features, followed by the evaluation of radiation injury levels within 5 days following whole-thorax irradiation (WTI). In addition, the multiple metabolic dysregulations primarily involved amino acids, bile acids and lipid and fatty acid β-oxidation-related metabolites, implying disturbances in the urea cycle, intestinal flora metabolism and mitochondrial dysfunction. In particular, the accumulation of long-chain acylcarnitines (ACs) was observed as early as 2 d post-WTI by dynamic plasma metabolic data analysis. Our findings indicate that plasma metabolic markers have the potential for RILI assessment. These results reveal metabolic characteristics following WTI and provide new insights into therapeutic interventions for RILI. Full article
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13 pages, 1868 KiB  
Article
Rapid Detection of Volatile Organic Metabolites in Urine by High-Pressure Photoionization Mass Spectrometry for Breast Cancer Screening: A Pilot Study
by Ming Yang, Jichun Jiang, Lei Hua, Dandan Jiang, Yadong Wang, Depeng Li, Ruoyu Wang, Xiaohui Zhang and Haiyang Li
Metabolites 2023, 13(7), 870; https://doi.org/10.3390/metabo13070870 - 21 Jul 2023
Cited by 1 | Viewed by 984
Abstract
Despite surpassing lung cancer as the most frequently diagnosed cancer, female breast cancer (BC) still lacks rapid detection methods for screening that can be implemented on a large scale in practical clinical settings. However, urine is a readily available biofluid obtained non-invasively and [...] Read more.
Despite surpassing lung cancer as the most frequently diagnosed cancer, female breast cancer (BC) still lacks rapid detection methods for screening that can be implemented on a large scale in practical clinical settings. However, urine is a readily available biofluid obtained non-invasively and contains numerous volatile organic metabolites (VOMs) that offer valuable metabolic information concerning the onset and progression of diseases. In this work, a rapid method for analysis of VOMs in urine by using high-pressure photon ionization time-of-flight mass spectrometry (HPPI-TOFMS) coupled with dynamic purge injection. A simple pretreatment process of urine samples by adding acid and salt was employed for efficient VOM sampling, and the numbers of metabolites increased and the detection sensitivity was improved after the acid (HCl) and salt (NaCl) addition. The established mass spectrometry detection method was applied to analyze a set of training samples collected from a local hospital, including 24 breast cancer patients and 27 healthy controls. Statistical analysis techniques such as principal component analysis, partial least squares discriminant analysis, and the Mann–Whitney U test were used, and nine VOMs were identified as differential metabolites. Finally, acrolein, 2-pentanone, and methyl allyl sulfide were selected to build a metabolite combination model for distinguishing breast cancer patients from the healthy group, and the achieved sensitivity and specificity were 92.6% and 91.7%, respectively, according to the receiver operating characteristic curve analysis. The results demonstrate that this technology has potential to become a rapid screening tool for breast cancer, with significant room for further development. Full article
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17 pages, 3331 KiB  
Article
The Integration of Metabolomics, Electronic Tongue, and Chromatic Difference Reveals the Correlations between the Critical Compounds and Flavor Characteristics of Two Grades of High-Quality Dianhong Congou Black Tea
by Shan Zhang, Xujiang Shan, Linchi Niu, Le Chen, Jinjin Wang, Qinghua Zhou, Haibo Yuan, Jia Li and Tian Wu
Metabolites 2023, 13(7), 864; https://doi.org/10.3390/metabo13070864 - 20 Jul 2023
Cited by 3 | Viewed by 992
Abstract
Tea’s biochemical compounds and flavor quality vary depending on its grade ranking. Dianhong Congou black tea (DCT) is a unique tea category produced using the large-leaf tea varieties from Yunnan, China. To date, the flavor characteristics and critical components of two grades of [...] Read more.
Tea’s biochemical compounds and flavor quality vary depending on its grade ranking. Dianhong Congou black tea (DCT) is a unique tea category produced using the large-leaf tea varieties from Yunnan, China. To date, the flavor characteristics and critical components of two grades of high-quality DCT, single-bud-grade DCT (BDCT), and special-grade DCT (SDCT) manufactured mainly with single buds and buds with one leaf, respectively, are far from clear. Herein, comparisons of two grades were performed by the integration of human sensory evaluation, an electronic tongue, chromatic differences, the quantification of major components, and metabolomics. The BDCT possessed a brisk, umami taste and a brighter infusion color, while the SDCT presented a comprehensive taste and redder liquor color. Quantification analysis showed that the levels of total polyphenols, catechins, and theaflavins (TFs) were significantly higher in the BDCT. Fifty-six different key compounds were screened by metabolomics, including catechins, flavone/flavonol glycosides, amino acids, phenolic acids, etc. Correlation analysis revealed that the sensory features of the BDCT and SDCT were attributed to their higher contents of catechins, TFs, theogallin, digalloylglucose, and accumulations of thearubigins (TRs), flavone/flavonol glycosides, and soluble sugars, respectively. This report is the first to focus on the comprehensive evaluation of the biochemical compositions and sensory characteristics of two grades of high-quality DCT, advancing the understanding of DCT from a multi-dimensional perspective. Full article
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18 pages, 1903 KiB  
Article
Crosstalk between Breast Milk N-Acetylneuraminic Acid and Infant Growth in a Gut Microbiota-Dependent Manner
by Runze Ouyang, Sijia Zheng, Xiaolin Wang, Qi Li, Juan Ding, Xiao Ma, Zhihong Zhuo, Zhen Li, Qi Xin, Xin Lu, Lina Zhou, Zhigang Ren, Surong Mei, Xinyu Liu and Guowang Xu
Metabolites 2023, 13(7), 846; https://doi.org/10.3390/metabo13070846 - 13 Jul 2023
Cited by 3 | Viewed by 1498
Abstract
The healthy growth of infants during early life is associated with lifelong consequences. Breastfeeding has positive impacts on reducing obesity risk, which is likely due to the varied components of breast milk, such as N-acetylneuraminic acid (Neu5Ac). However, the effect of breast milk [...] Read more.
The healthy growth of infants during early life is associated with lifelong consequences. Breastfeeding has positive impacts on reducing obesity risk, which is likely due to the varied components of breast milk, such as N-acetylneuraminic acid (Neu5Ac). However, the effect of breast milk Neu5Ac on infant growth has not been well studied. In this study, targeted metabolomic and metagenomic analyses were performed to illustrate the association between breast milk Neu5Ac and infant growth. Results demonstrated that Neu5Ac was significantly abundant in breast milk from infants with low obesity risk in two independent Chinese cohorts. Neu5Ac from breast milk altered infant gut microbiota and bile acid metabolism, resulting in a distinct fecal bile acid profile in the high-Neu5Ac group, which was characterized by reduced levels of primary bile acids and elevated levels of secondary bile acids. Taurodeoxycholic acid 3-sulfate and taurochenodeoxycholic acid 3-sulfate were correlated with high breast milk Neu5Ac and low obesity risk in infants, and their associations with healthy growth were reproduced in mice colonized with infant-derived microbiota. Parabacteroides might be linked to bile acid metabolism and act as a mediator between Neu5Ac and infant growth. These results showed the gut microbiota-dependent crosstalk between breast milk Neu5Ac and infant growth. Full article
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18 pages, 2790 KiB  
Article
Anti-Allergic Effect of Dietary Polyphenols Curcumin and Epigallocatechin Gallate via Anti-Degranulation in IgE/Antigen-Stimulated Mast Cell Model: A Lipidomics Perspective
by Jun Zeng, Jingwen Hao, Zhiqiang Yang, Chunyu Ma, Longhua Gao, Yue Chen, Guiling Li and Jia Li
Metabolites 2023, 13(5), 628; https://doi.org/10.3390/metabo13050628 - 05 May 2023
Cited by 3 | Viewed by 1990
Abstract
Polyphenol-rich foods exhibit anti-allergic/-inflammatory properties. As major effector cells of allergies, mast cells undergo degranulation after activation and then initiate inflammatory responses. Key immune phenomena could be regulated by the production and metabolism of lipid mediators by mast cells. Here, we analyzed the [...] Read more.
Polyphenol-rich foods exhibit anti-allergic/-inflammatory properties. As major effector cells of allergies, mast cells undergo degranulation after activation and then initiate inflammatory responses. Key immune phenomena could be regulated by the production and metabolism of lipid mediators by mast cells. Here, we analyzed the antiallergic activities of two representative dietary polyphenols, curcumin and epigallocatechin gallate (EGCG), and traced their effects on cellular lipidome rewiring in the progression of degranulation. Both curcumin and EGCG significantly inhibited degranulation as they suppressed the release of β-hexosaminidase, interleukin-4, and tumor necrosis factor-α from the IgE/antigen-stimulated mast cell model. A comprehensive lipidomics study involving 957 identified lipid species revealed that although the lipidome remodeling patterns (lipid response and composition) of curcumin intervention were considerably similar to those of EGCG, lipid metabolism was more potently disturbed by curcumin. Seventy-eight percent of significant differential lipids upon IgE/antigen stimulation could be regulated by curcumin/EGCG. LPC-O 22:0 was defined as a potential biomarker for its sensitivity to IgE/antigen stimulation and curcumin/EGCG intervention. The key changes in diacylglycerols, fatty acids, and bismonoacylglycerophosphates provided clues that cell signaling disturbances could be associated with curcumin/EGCG intervention. Our work supplies a novel perspective for understanding curcumin/EGCG involvement in antianaphylaxis and helps guide future attempts to use dietary polyphenols. Full article
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13 pages, 2634 KiB  
Article
A Strategy for Uncovering the Serum Metabolome by Direct-Infusion High-Resolution Mass Spectrometry
by Xiaoshan Sun, Zhen Jia, Yuqing Zhang, Xinjie Zhao, Chunxia Zhao, Xin Lu and Guowang Xu
Metabolites 2023, 13(3), 460; https://doi.org/10.3390/metabo13030460 - 22 Mar 2023
Cited by 2 | Viewed by 1332
Abstract
Direct infusion nanoelectrospray high-resolution mass spectrometry (DI-nESI-HRMS) is a promising tool for high-throughput metabolomics analysis. However, metabolite assignment is limited by the inadequate mass accuracy and chemical space of the metabolome database. Here, a serum metabolome characterization method was proposed to make full [...] Read more.
Direct infusion nanoelectrospray high-resolution mass spectrometry (DI-nESI-HRMS) is a promising tool for high-throughput metabolomics analysis. However, metabolite assignment is limited by the inadequate mass accuracy and chemical space of the metabolome database. Here, a serum metabolome characterization method was proposed to make full use of the potential of DI-nESI-HRMS. Different from the widely used database search approach, unambiguous formula assignments were achieved by a reaction network combined with mass accuracy and isotopic patterns filter. To provide enough initial known nodes, an initial network was directly constructed by known metabolite formulas. Then experimental formula candidates were screened by the predefined reaction with the network. The effects of sources and scales of networks on assignment performance were investigated. Further, a scoring rule for filtering unambiguous formula candidates was proposed. The developed approach was validated by a pooled serum sample spiked with reference standards. The coverage and accuracy rates for the spiked standards were 98.9% and 93.6%, respectively. A total of 1958 monoisotopic features were assigned with unique formula candidates for the pooled serum, which is twice more than the database search. Finally, a case study of serum metabolomics in diabetes was carried out using the developed method. Full article
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Review

Jump to: Editorial, Research

21 pages, 1198 KiB  
Review
Unlocking the Potential: Amino Acids’ Role in Predicting and Exploring Therapeutic Avenues for Type 2 Diabetes Mellitus
by Yilan Ding, Shuangyuan Wang and Jieli Lu
Metabolites 2023, 13(9), 1017; https://doi.org/10.3390/metabo13091017 - 15 Sep 2023
Cited by 1 | Viewed by 1133
Abstract
Diabetes mellitus, particularly type 2 diabetes mellitus (T2DM), imposes a significant global burden with adverse clinical outcomes and escalating healthcare expenditures. Early identification of biomarkers can facilitate better screening, earlier diagnosis, and the prevention of diabetes. However, current clinical predictors often fail to [...] Read more.
Diabetes mellitus, particularly type 2 diabetes mellitus (T2DM), imposes a significant global burden with adverse clinical outcomes and escalating healthcare expenditures. Early identification of biomarkers can facilitate better screening, earlier diagnosis, and the prevention of diabetes. However, current clinical predictors often fail to detect abnormalities during the prediabetic state. Emerging studies have identified specific amino acids as potential biomarkers for predicting the onset and progression of diabetes. Understanding the underlying pathophysiological mechanisms can offer valuable insights into disease prevention and therapeutic interventions. This review provides a comprehensive summary of evidence supporting the use of amino acids and metabolites as clinical biomarkers for insulin resistance and diabetes. We discuss promising combinations of amino acids, including branched-chain amino acids, aromatic amino acids, glycine, asparagine and aspartate, in the prediction of T2DM. Furthermore, we delve into the mechanisms involving various signaling pathways and the metabolism underlying the role of amino acids in disease development. Finally, we highlight the potential of targeting predictive amino acids for preventive and therapeutic interventions, aiming to inspire further clinical investigations and mitigate the progression of T2DM, particularly in the prediabetic stage. Full article
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19 pages, 787 KiB  
Review
Recent Advances and Perspectives in Relation to the Metabolomics-Based Study of Diabetic Retinopathy
by Shuling He, Lvyun Sun, Jiali Chen and Yang Ouyang
Metabolites 2023, 13(9), 1007; https://doi.org/10.3390/metabo13091007 - 12 Sep 2023
Cited by 1 | Viewed by 951
Abstract
Diabetic retinopathy (DR), a prevalent microvascular complication of diabetes, is a major cause of acquired blindness in adults. Currently, a clinical diagnosis of DR primarily relies on fundus fluorescein angiography, with a limited availability of effective biomarkers. Metabolomics, a discipline dedicated to scrutinizing [...] Read more.
Diabetic retinopathy (DR), a prevalent microvascular complication of diabetes, is a major cause of acquired blindness in adults. Currently, a clinical diagnosis of DR primarily relies on fundus fluorescein angiography, with a limited availability of effective biomarkers. Metabolomics, a discipline dedicated to scrutinizing the response of various metabolites within living organisms, has shown noteworthy advancements in uncovering metabolic disorders and identifying key metabolites associated with DR in recent years. Consequently, this review aims to present the latest advancements in metabolomics techniques and comprehensively discuss the principal metabolic outcomes derived from analyzing blood, vitreous humor, aqueous humor, urine, and fecal samples. Full article
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