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Sun B, Fang Y, Yang H, Meng F, He C, Zhao Y, Zhao K, Zhang H. The combination of deep learning and pseudo-MS image improves the applicability of metabolomics to congenital heart defect prenatal screening. Talanta 2024; 275:126109. [PMID: 38648686 DOI: 10.1016/j.talanta.2024.126109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 04/09/2024] [Accepted: 04/12/2024] [Indexed: 04/25/2024]
Abstract
To investigate the metabolic alterations in maternal individuals with fetal congenital heart disease (FCHD), establish the FCHD diagnostic models, and assess the performance of these models, we recruited two batches of pregnant women. By metabolomics analysis using Ultra High-performance Liquid Chromatography-Mass/Mass (UPLC-MS/MS), a total of 36 significantly altered metabolites (VIP >1.0) were identified between FCHD and non-FCHD groups. Two logistic regression models and four support vector machine (SVM) models exhibited strong performance and clinical utility in the training set (area under the curve (AUC) = 1.00). The convolutional neural network (CNN) model also demonstrated commendable performance and clinical utility (AUC = 0.89 in the training set). Notably, in the validation set, the performance of the CNN model (AUC = 0.66, precision = 0.714) exhibited better robustness than the six models above (AUC≤0.50). In conclusion, the CNN model based on pseudo-MS images holds promise for real-world and clinical applications due to its better repeatability.
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Affiliation(s)
- Borui Sun
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Yiwei Fang
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China; Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49, North Garden Road, Haidian district, Beijing, 100191, China; National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing, 100191, China; State Key Laboratory of Female Fertility Promotion, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, 100191, China; Key Laboratory of Assisted Reproduction, Ministry of Education, Peking University, Beijing, 100191, China; Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China.
| | - Hui Yang
- Department of Obstetrics, Maternal and Child Health Hospital of Hubei Province, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430070, China
| | - Fan Meng
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Chao He
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Yun Zhao
- Department of Obstetrics, Maternal and Child Health Hospital of Hubei Province, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430070, China.
| | - Kai Zhao
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
| | - Huiping Zhang
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
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Chai X, Zhang Y, Zhang W, Feng K, Jiang Y, Zhu A, Chen X, Di L, Wang R. Tumor Metabolism: A New Field for the Treatment of Glioma. Bioconjug Chem 2024. [PMID: 39013195 DOI: 10.1021/acs.bioconjchem.4c00287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Abstract
The clinical treatment of glioma remains relatively immature. Commonly used clinical treatments for gliomas are surgery combined with chemotherapy and radiotherapy, but there is a problem of drug resistance. In addition, immunotherapy and targeted therapies also suffer from the problem of immune evasion. The advent of metabolic therapy holds immense potential for advancing more efficacious and tolerable therapies against this aggressive disease. Metabolic therapy alters the metabolic processes of tumor cells at the molecular level to inhibit tumor growth and spread, and lead to better outcomes for patients with glioma that are insensitive to conventional treatments. Moreover, compared with conventional therapy, it has less impact on normal cells, less toxicity and side effects, and higher safety. The objective of this review is to examine the changes in metabolic characteristics throughout the development of glioma, enumerate the current methodologies employed for studying tumor metabolism, and highlight the metabolic reprogramming pathways of glioma along with their potential molecular mechanisms. Importantly, it seeks to elucidate potential metabolic targets for glioblastoma (GBM) therapy and summarize effective combination treatment strategies based on various studies.
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Affiliation(s)
- Xiaoqian Chai
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China
- Jiangsu Provincial TCM Engineering Technology Research Center of High Efficient Drug Delivery System, Nanjing 210023, China
| | - Yingjie Zhang
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China
- Jiangsu Provincial TCM Engineering Technology Research Center of High Efficient Drug Delivery System, Nanjing 210023, China
| | - Wen Zhang
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China
- Jiangsu Provincial TCM Engineering Technology Research Center of High Efficient Drug Delivery System, Nanjing 210023, China
| | - Kuanhan Feng
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China
- Jiangsu Provincial TCM Engineering Technology Research Center of High Efficient Drug Delivery System, Nanjing 210023, China
| | - Yingyu Jiang
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China
- Jiangsu Provincial TCM Engineering Technology Research Center of High Efficient Drug Delivery System, Nanjing 210023, China
| | - Anran Zhu
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China
- Jiangsu Provincial TCM Engineering Technology Research Center of High Efficient Drug Delivery System, Nanjing 210023, China
| | - Xiaojin Chen
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China
- Jiangsu Provincial TCM Engineering Technology Research Center of High Efficient Drug Delivery System, Nanjing 210023, China
| | - Liuqing Di
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China
- Jiangsu Provincial TCM Engineering Technology Research Center of High Efficient Drug Delivery System, Nanjing 210023, China
| | - Ruoning Wang
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China
- Jiangsu Provincial TCM Engineering Technology Research Center of High Efficient Drug Delivery System, Nanjing 210023, China
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Gao C, Wu X, Yang Z, Qin L, Wu D, Fan Q, Zhao Y, Tan D, Li J, Zhang J, He Y. Quantitative analysis of six sesquiterpene glycosides from Dendrobium nobile Lindl. under different growth conditions by high-performance liquid chromatography coupled with triple quadrupole tandem mass spectrometry in MRM mode. PHYTOCHEMICAL ANALYSIS : PCA 2024; 35:1249-1260. [PMID: 38659238 DOI: 10.1002/pca.3356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 03/13/2024] [Accepted: 03/20/2024] [Indexed: 04/26/2024]
Abstract
INTRODUCTION The sesquiterpene glycosides (SGs) from Dendrobium nobile Lindl. have immunomodulatory effects. However, there are no studies on the growth conditions affecting its contents and quantitative analysis methods. OBJECTIVE In the present study, a quantitative analysis method for six SGs from D. nobile was established. We explored which growth conditions could affect the contents of SGs, providing a basis for the cultivation and clinical application of D. nobile. METHODS Firstly, based on the optimization of mass spectrometry parameters and extraction conditions for six SGs in D. nobile, a method for the determination of the contents of six SGs was established using high-performance liquid chromatography coupled with triple quadrupole tandem mass spectrometry (HPLC-QqQ-MS/MS) in multiple reaction monitoring (MRM) mode. Then, the methodology of the established method was validated. Secondly, the established method was applied to determine the contents of six SGs from 78 samples of D. nobile grown under different growth conditions. Finally, chemometrics analysis was employed to analyze the results and select optimal growth conditions for D. nobile. RESULTS The results indicated significant variations in the contents of SGs from D. nobile grown under different growth conditions. The primary factors influencing SG contents included age, geographical origin, altitude, and epiphytic pattern. CONCLUSION Therefore, the established method for determining SG contents from D. nobile is stable. In particular, the SG contents were relatively high in samples of 3-year-old D. nobile grown at an altitude of approximately 500 m on Danxia rocks in Chishui, Guizhou.
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Affiliation(s)
- Chunxue Gao
- Guizhou Engineering Research Center of Industrial Key-technology for Dendrobium Nobile, School of Pharmacy, Zunyi Medical University, Zunyi, China
| | - Xingdong Wu
- Guizhou Engineering Research Center of Industrial Key-technology for Dendrobium Nobile, School of Pharmacy, Zunyi Medical University, Zunyi, China
| | - Zhou Yang
- Guizhou Engineering Research Center of Industrial Key-technology for Dendrobium Nobile, School of Pharmacy, Zunyi Medical University, Zunyi, China
- Guizhou Standard Pharmaceutical Health Co., Ltd., Zunyi, China
- Key Laboratory of Natural Bioactive Substances of Fujian Province, Fuzhou, China
| | - Lin Qin
- Guizhou Engineering Research Center of Industrial Key-technology for Dendrobium Nobile, School of Pharmacy, Zunyi Medical University, Zunyi, China
| | - Di Wu
- Guizhou Engineering Research Center of Industrial Key-technology for Dendrobium Nobile, School of Pharmacy, Zunyi Medical University, Zunyi, China
| | - Qingjie Fan
- Guizhou Engineering Research Center of Industrial Key-technology for Dendrobium Nobile, School of Pharmacy, Zunyi Medical University, Zunyi, China
| | - Yongxia Zhao
- Guizhou Engineering Research Center of Industrial Key-technology for Dendrobium Nobile, School of Pharmacy, Zunyi Medical University, Zunyi, China
| | - Daopeng Tan
- Guizhou Engineering Research Center of Industrial Key-technology for Dendrobium Nobile, School of Pharmacy, Zunyi Medical University, Zunyi, China
| | - Jiaying Li
- Guizhou Engineering Research Center of Industrial Key-technology for Dendrobium Nobile, School of Pharmacy, Zunyi Medical University, Zunyi, China
| | - Jianyong Zhang
- Guizhou Engineering Research Center of Industrial Key-technology for Dendrobium Nobile, School of Pharmacy, Zunyi Medical University, Zunyi, China
| | - Yuqi He
- Guizhou Engineering Research Center of Industrial Key-technology for Dendrobium Nobile, School of Pharmacy, Zunyi Medical University, Zunyi, China
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Vanden Broecke E, Van Mulders L, De Paepe E, Daminet S, Vanhaecke L. Optimization and validation of metabolomics methods for feline urine and serum towards application in veterinary medicine. Anal Chim Acta 2024; 1310:342694. [PMID: 38811133 DOI: 10.1016/j.aca.2024.342694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 05/02/2024] [Accepted: 05/05/2024] [Indexed: 05/31/2024]
Abstract
BACKGROUND Metabolomics is an emerging and powerful technology that offers a comprehensive view of an organism's physiological status. Although widely applied in human medicine, it is only recently making its introduction in veterinary medicine. As a result, validated metabolomics protocols in feline medicine are lacking at the moment. Since biological interpretation of metabolomics data can be misled by the extraction method used, species and matrix-specific optimized and validated metabolomic protocols are sorely needed. RESULTS Systematic optimization was performed using fractional factorial experiments for both serum (n = 57) and urine (n = 24), evaluating dilution for both matrices, and aliquot and solvent volume, protein precipitation time and temperature for serum. For the targeted (n = 76) and untargeted (n = 1949) validation of serum respectively, excellent instrumental, intra-assay and inter-day precision were observed (CV ≤ 15% or 30%, respectively). Linearity deemed sufficient both targeted and untargeted (R2 ≥ 0.99 or 0.90, respectively). An appropriate targeted recovery between 70 and 130% was achieved. For the targeted (n = 69) and untargeted (n = 2348) validation of the urinary protocol, excellent instrumental and intra-assay precision were obtained (CV ≤ 15% or 30%, respectively). Subsequently, the discriminative ability of our metabolomics methods was confirmed for feline chronic kidney disease (CKD) by univariate statistics (n = 41 significant metabolites for serum, and n = 55 for urine, p-value<0.05) and validated OPLS-DA models (R2(Y) > 0.95, Q2(Y) > 0.65, p-value<0.001 for both matrices). SIGNIFICANCE This study is the first to present an optimized and validated wholistic metabolomics methods for feline serum and urine using ultra-high performance liquid chromatography coupled to quadrupole-Orbitrap high-resolution mass spectrometry. This robust methodology opens avenues for biomarker panel selection and a deeper understanding of feline CKD pathophysiology and other feline applications.
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Affiliation(s)
- Ellen Vanden Broecke
- Ghent University, Faculty of Veterinary Medicine, Department of Translational Physiology, Infectiology and Public Health, Laboratory of Integrative Metabolomics (LIMET), Salisburylaan 133, B-9820, Merelbeke, Belgium; Ghent University, Faculty of Veterinary Medicine, Department of Small Animals, Salisburylaan 133, B-9820, Merelbeke, Belgium
| | - Laurens Van Mulders
- Ghent University, Faculty of Veterinary Medicine, Department of Translational Physiology, Infectiology and Public Health, Laboratory of Integrative Metabolomics (LIMET), Salisburylaan 133, B-9820, Merelbeke, Belgium; Ghent University, Faculty of Veterinary Medicine, Department of Small Animals, Salisburylaan 133, B-9820, Merelbeke, Belgium
| | - Ellen De Paepe
- Ghent University, Faculty of Veterinary Medicine, Department of Translational Physiology, Infectiology and Public Health, Laboratory of Integrative Metabolomics (LIMET), Salisburylaan 133, B-9820, Merelbeke, Belgium
| | - Sylvie Daminet
- Ghent University, Faculty of Veterinary Medicine, Department of Small Animals, Salisburylaan 133, B-9820, Merelbeke, Belgium
| | - Lynn Vanhaecke
- Ghent University, Faculty of Veterinary Medicine, Department of Translational Physiology, Infectiology and Public Health, Laboratory of Integrative Metabolomics (LIMET), Salisburylaan 133, B-9820, Merelbeke, Belgium; Queen's University Belfast, School of Biological Sciences, Institute for Global Food Security, Chlorine Gardens 19, BT9-5DL, Belfast, Northern Ireland, United Kingdom.
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Wei L, Chen S, Deng X, Liu Y, Wang H, Gao X, Huang Y. Metabolomic discoveries for early diagnosis and traditional Chinese medicine efficacy in ischemic stroke. Biomark Res 2024; 12:63. [PMID: 38902829 PMCID: PMC11188286 DOI: 10.1186/s40364-024-00608-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Accepted: 06/11/2024] [Indexed: 06/22/2024] Open
Abstract
Ischemic stroke (IS), a devastating cerebrovascular accident, presents with high mortality and morbidity. Following IS onset, a cascade of pathological changes, including excitotoxicity, inflammatory damage, and blood-brain barrier disruption, significantly impacts prognosis. However, current clinical practices struggle with early diagnosis and identifying these alterations. Metabolomics, a powerful tool in systems biology, offers a promising avenue for uncovering early diagnostic biomarkers for IS. By analyzing dynamic metabolic profiles, metabolomics can not only aid in identifying early IS biomarkers but also evaluate Traditional Chinese Medicine (TCM) efficacy and explore its mechanisms of action in IS treatment. Animal studies demonstrate that TCM interventions modulate specific metabolite levels, potentially reflecting their therapeutic effects. Identifying relevant metabolites in cerebral ischemia patients holds immense potential for early diagnosis and improved outcomes. This review focuses on recent metabolomic discoveries of potential early diagnostic biomarkers for IS. We explore variations in metabolites observed across different ages, genders, disease severity, and stages. Additionally, the review examines how specific TCM extracts influence IS development through metabolic changes, potentially revealing their mechanisms of action. Finally, we emphasize the importance of integrating metabolomics with other omics approaches for a comprehensive understanding of IS pathophysiology and TCM efficacy, paving the way for precision medicine in IS management.
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Affiliation(s)
- Liangzhe Wei
- Department of Neurosurgery, Ningbo Hospital, Zhejiang University School of Medicine, Ningbo, 315010, China
- Ningbo Key Laboratory of Neurological Diseases and Brain Function, Department of Neurosurgery, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, 315010, China
| | - Siqi Chen
- Ningbo Key Laboratory of Neurological Diseases and Brain Function, Department of Neurosurgery, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, 315010, China
- Key Laboratory of Precision Medicine for Atherosclerotic Diseases of Zhejiang Province, Ningbo, Zhejiang, 315010, China
| | - Xinpeng Deng
- Department of Neurosurgery, Ningbo Hospital, Zhejiang University School of Medicine, Ningbo, 315010, China
- Ningbo Key Laboratory of Neurological Diseases and Brain Function, Department of Neurosurgery, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, 315010, China
| | - Yuchun Liu
- Department of Neurosurgery, Ningbo Hospital, Zhejiang University School of Medicine, Ningbo, 315010, China
- Ningbo Key Laboratory of Neurological Diseases and Brain Function, Department of Neurosurgery, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, 315010, China
| | - Haifeng Wang
- Department of Neurosurgery, Ningbo Hospital, Zhejiang University School of Medicine, Ningbo, 315010, China
- Ningbo Key Laboratory of Neurological Diseases and Brain Function, Department of Neurosurgery, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, 315010, China
| | - Xiang Gao
- Department of Neurosurgery, Ningbo Hospital, Zhejiang University School of Medicine, Ningbo, 315010, China.
- Ningbo Key Laboratory of Neurological Diseases and Brain Function, Department of Neurosurgery, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, 315010, China.
- Key Laboratory of Precision Medicine for Atherosclerotic Diseases of Zhejiang Province, Ningbo, Zhejiang, 315010, China.
| | - Yi Huang
- Department of Neurosurgery, Ningbo Hospital, Zhejiang University School of Medicine, Ningbo, 315010, China.
- Ningbo Key Laboratory of Neurological Diseases and Brain Function, Department of Neurosurgery, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, 315010, China.
- Key Laboratory of Precision Medicine for Atherosclerotic Diseases of Zhejiang Province, Ningbo, Zhejiang, 315010, China.
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Peng Q, Jiang L, Shen Y, Xu Y, Shen X, Zou L, Zhu Y, Shen Y. LC-MS metabolomics analysis of serum metabolites during neoadjuvant chemoradiotherapy in locally advanced rectal cancer. Clin Transl Oncol 2024:10.1007/s12094-024-03537-x. [PMID: 38831193 DOI: 10.1007/s12094-024-03537-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Accepted: 05/18/2024] [Indexed: 06/05/2024]
Abstract
BACKGROUND This study aimed to investigate the serum metabolite profiles during neoadjuvant chemoradiotherapy (NCRT) in locally advanced rectal cancer (LARC) using liquid chromatography-mass spectrometry (LC-MS) metabolomics analysis. METHODS 60 serum samples were collected from 20 patients with LARC before, during, and after radiotherapy. LC-MS metabolomics analysis was performed to identify the metabolite variations. Functional annotation was applied to discover altered metabolic pathways. The key metabolites were screened and their ability to predict sensitivity to radiotherapy was calculated using random forests and ROC curves. RESULTS The results showed that NCRT led to significant changes in the serum metabolite profiles. The serum metabolic profiles showed an apparent separation between different time points and different sensitivity groups. Moreover, the functional annotation showed that the differential metabolites were associated with a series of important metabolic pathways. Pre-radiotherapy (3Z,6Z)-3,6-Nonadiena and pro-radiotherapy 1-Hydroxyibuprofen showed good predictive performance in discriminating the sensitive and non-sensitive group to NCRT, with an AUC of 0.812 and 0.75, respectively. Importantly, the combination of different metabolites significantly increased the predictive ability. CONCLUSION This study demonstrated the potential of LC-MS metabolomics for revealing the serum metabolite profiles during NCRT in LARC. The identified metabolites may serve as potential biomarkers and therapeutic targets for the management of this disease. Furthermore, the understanding of the affected metabolic pathways may help design more personalized therapeutic strategies for LARC patients.
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Affiliation(s)
- Qiliang Peng
- Department of Radiotherapy and Oncology, The Second Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Radiotherapy & Oncology, Soochow University, Suzhou, China
- State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou, China
| | - Lili Jiang
- Department of Oncology, Nantong Haimen District People's Hospital, Jiangsu, China
| | - Yi Shen
- Department of Radiation Oncology, Suzhou Hospital, Affiliated Hospital of Medical School, Nanjing University, Suzhou, China
| | - Yao Xu
- Department of Radiology, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Xinan Shen
- Department of Radiotherapy and Oncology, The Second Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Radiotherapy & Oncology, Soochow University, Suzhou, China
| | - Li Zou
- Department of Radiotherapy and Oncology, The Second Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Radiotherapy & Oncology, Soochow University, Suzhou, China
| | - Yaqun Zhu
- Department of Radiotherapy and Oncology, The Second Affiliated Hospital of Soochow University, Suzhou, China.
- Institute of Radiotherapy & Oncology, Soochow University, Suzhou, China.
| | - Yuntian Shen
- Department of Radiotherapy and Oncology, The Second Affiliated Hospital of Soochow University, Suzhou, China.
- Institute of Radiotherapy & Oncology, Soochow University, Suzhou, China.
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Sirocchi C, Biancucci F, Donati M, Bogliolo A, Magnani M, Menotta M, Montagna S. Exploring machine learning for untargeted metabolomics using molecular fingerprints. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2024; 250:108163. [PMID: 38626559 DOI: 10.1016/j.cmpb.2024.108163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 03/15/2024] [Accepted: 04/03/2024] [Indexed: 04/18/2024]
Abstract
BACKGROUND Metabolomics, the study of substrates and products of cellular metabolism, offers valuable insights into an organism's state under specific conditions and has the potential to revolutionise preventive healthcare and pharmaceutical research. However, analysing large metabolomics datasets remains challenging, with available methods relying on limited and incompletely annotated metabolic pathways. METHODS This study, inspired by well-established methods in drug discovery, employs machine learning on metabolite fingerprints to explore the relationship of their structure with responses in experimental conditions beyond known pathways, shedding light on metabolic processes. It evaluates fingerprinting effectiveness in representing metabolites, addressing challenges like class imbalance, data sparsity, high dimensionality, duplicate structural encoding, and interpretable features. Feature importance analysis is then applied to reveal key chemical configurations affecting classification, identifying related metabolite groups. RESULTS The approach is tested on two datasets: one on Ataxia Telangiectasia and another on endothelial cells under low oxygen. Machine learning on molecular fingerprints predicts metabolite responses effectively, and feature importance analysis aligns with known metabolic pathways, unveiling new affected metabolite groups for further study. CONCLUSION In conclusion, the presented approach leverages the strengths of drug discovery to address critical issues in metabolomics research and aims to bridge the gap between these two disciplines. This work lays the foundation for future research in this direction, possibly exploring alternative structural encodings and machine learning models.
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Affiliation(s)
- Christel Sirocchi
- Department of Pure and Applied Sciences, University of Urbino, Piazza della Repubblica, 13, Urbino, 61029, Italy.
| | - Federica Biancucci
- Department of Biomolecular Sciences, University of Urbino, Via Saffi 2, Urbino, 61029, Italy
| | - Matteo Donati
- Department of Pure and Applied Sciences, University of Urbino, Piazza della Repubblica, 13, Urbino, 61029, Italy
| | - Alessandro Bogliolo
- Department of Pure and Applied Sciences, University of Urbino, Piazza della Repubblica, 13, Urbino, 61029, Italy
| | - Mauro Magnani
- Department of Biomolecular Sciences, University of Urbino, Via Saffi 2, Urbino, 61029, Italy
| | - Michele Menotta
- Department of Biomolecular Sciences, University of Urbino, Via Saffi 2, Urbino, 61029, Italy
| | - Sara Montagna
- Department of Pure and Applied Sciences, University of Urbino, Piazza della Repubblica, 13, Urbino, 61029, Italy
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Yang S, Zheng L, Li L, Zhang J, Wang J, Zhao H, Chen Y, Liu X, Gan H, Chen J, Yan M, He C, Li K, Ding C, Li Y. Integrative multiomics analysis identifies molecular subtypes and potential targets of hepatocellular carcinoma. Clin Transl Med 2024; 14:e1727. [PMID: 38804617 PMCID: PMC11131356 DOI: 10.1002/ctm2.1727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 05/10/2024] [Accepted: 05/15/2024] [Indexed: 05/29/2024] Open
Abstract
BACKGROUND The liver is anatomically divided into eight segments based on the distribution of Glisson's triad. However, the molecular mechanisms underlying each segment and its association with hepatocellular carcinoma (HCC) heterogeneity are not well understood. In this study, our objective is to conduct a comprehensive multiomics profiling of the segmentation atlas in order to investigate potential subtypes and therapeutic approaches for HCC. METHODS A high throughput liquid chromatography-tandem mass spectrometer strategy was employed to comprehensively analyse proteome, lipidome and metabolome data, with a focus on segment-resolved multiomics profiling. To classify HCC subtypes, the obtained data with normal reference profiling were integrated. Additionally, potential therapeutic targets for HCC were identified using immunohistochemistry assays. The effectiveness of these targets were further validated through patient-derived organoid (PDO) assays. RESULTS A multiomics profiling of 8536 high-confidence proteins, 1029 polar metabolites and 3381 nonredundant lipids was performed to analyse the segmentation atlas of HCC. The analysis of the data revealed that in normal adjacent tissues, the left lobe was primarily involved in energy metabolism, while the right lobe was associated with small molecule metabolism. Based on the normal reference atlas, HCC patients with segment-resolved classification were divided into three subtypes. The C1 subtype showed enrichment in ribosome biogenesis, the C2 subtype exhibited an intermediate phenotype, while the C3 subtype was closely associated with neutrophil degranulation. Furthermore, using the PDO assay, exportin 1 (XPO1) and 5-lipoxygenase (ALOX5) were identified as potential targets for the C1 and C3 subtypes, respectively. CONCLUSION Our extensive analysis of the segmentation atlas in multiomics profiling defines molecular subtypes of HCC and uncovers potential therapeutic strategies that have the potential to enhance the prognosis of HCC.
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Affiliation(s)
- Shuai Yang
- Department of Hematology & OncologyJiangbei CampusThe First Affiliated Hospital of Army Medical UniversityChongqingChina
| | - Lu Zheng
- Department of Hepatobiliary SurgeryXinqiao HospitalArmy Medical UniversityChongqingChina
| | - Lingling Li
- State Key Laboratory of Genetic EngineeringInstitutes of Biomedical SciencesHuman Phenome InstituteSchool of Life SciencesZhongshan HospitalFudan UniversityShanghaiChina
| | - Jiangang Zhang
- Department of Medical OncologyChongqing University Cancer HospitalChongqingChina
| | - Jingchun Wang
- Department of GastroenterologyXinqiao Hospital, Army Medical UniversityChongqingChina
| | - Huakan Zhao
- Department of Medical OncologyChongqing University Cancer HospitalChongqingChina
| | - Yu Chen
- Department of Medical OncologyChongqing University Cancer HospitalChongqingChina
| | - Xudong Liu
- Department of Medical OncologyChongqing University Cancer HospitalChongqingChina
| | - Hui Gan
- Department of RadiologyXinqiao HospitalArmy Medical UniversityChongqingChina
| | - Junying Chen
- Department of PathologyJiangbei CampusThe First Affiliated Hospital of Army Medical UniversityChongqingChina
| | - Mei Yan
- Department of PathologyJiangbei CampusThe First Affiliated Hospital of Army Medical UniversityChongqingChina
| | - Chuanyin He
- Department of PathologyJiangbei CampusThe First Affiliated Hospital of Army Medical UniversityChongqingChina
| | - Kai Li
- State Key Laboratory of Genetic EngineeringInstitutes of Biomedical SciencesHuman Phenome InstituteSchool of Life SciencesZhongshan HospitalFudan UniversityShanghaiChina
| | - Chen Ding
- State Key Laboratory of Genetic EngineeringInstitutes of Biomedical SciencesHuman Phenome InstituteSchool of Life SciencesZhongshan HospitalFudan UniversityShanghaiChina
| | - Yongsheng Li
- Department of Medical OncologyChongqing University Cancer HospitalChongqingChina
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Ovbude ST, Sharmeen S, Kyei I, Olupathage H, Jones J, Bell RJ, Powers R, Hage DS. Applications of chromatographic methods in metabolomics: A review. J Chromatogr B Analyt Technol Biomed Life Sci 2024; 1239:124124. [PMID: 38640794 DOI: 10.1016/j.jchromb.2024.124124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 03/11/2024] [Accepted: 04/10/2024] [Indexed: 04/21/2024]
Abstract
Chromatography is a robust and reliable separation method that can use various stationary phases to separate complex mixtures commonly seen in metabolomics. This review examines the types of chromatography and stationary phases that have been used in targeted or untargeted metabolomics with methods such as mass spectrometry (MS) and nuclear magnetic resonance (NMR) spectroscopy. General considerations for sample pretreatment and separations in metabolomics are considered, along with the various supports and separation formats for chromatography that have been used in such work. The types of liquid chromatography (LC) that have been most extensively used in metabolomics will be examined, such as reversed-phase liquid chromatography and hydrophilic liquid interaction chromatography. In addition, other forms of LC that have been used in more limited applications for metabolomics (e.g., ion-exchange, size-exclusion, and affinity methods) will be discussed to illustrate how these techniques may be utilized for new and future research in this field. Multidimensional LC methods are also discussed, as well as the use of gas chromatography and supercritical fluid chromatography in metabolomics. In addition, the roles of chromatography in NMR- vs. MS-based metabolomics are considered. Applications are given within the field of metabolomics for each type of chromatography, along with potential advantages or limitations of these separation methods.
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Affiliation(s)
- Susan T Ovbude
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA
| | - Sadia Sharmeen
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA
| | - Isaac Kyei
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA
| | - Harshana Olupathage
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA
| | - Jacob Jones
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA
| | - Richard J Bell
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA
| | - Robert Powers
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA; Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA
| | - David S Hage
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA.
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10
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Wu Y, Fan H, Feng Y, Yang J, Cen X, Li W. Unveiling the gut microbiota and metabolite profiles in guinea pigs with form deprivation myopia through 16S rRNA gene sequencing and untargeted metabolomics. Heliyon 2024; 10:e30491. [PMID: 38756593 PMCID: PMC11096930 DOI: 10.1016/j.heliyon.2024.e30491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 04/26/2024] [Accepted: 04/28/2024] [Indexed: 05/18/2024] Open
Abstract
Aim The aim of this study was to confirm the presence of the form deprivation myopia (FDM) guinea pig eye-gut axis and investigate the relationship between serum vasoactive intestinal peptide (VIP), lipopolysaccharides (LPS), specific gut microbiota and their metabolites. Method 20 specific-pathogen-free (SPF) guinea pigs were divided into the FDM and the control(Con) group. Following model induction, serum levels of VIP and LPS were quantified. A combination of 16S ribosomal ribosomal Ribonucleic Acid (rRNA) gene sequencing, non-targeted metabolomics and bioinformatics analysis were employed to identify disparities in gut microbiota and metabolites between the two groups of guinea pigs. Result Compared to the control group, FDM guinea pigs exhibited a significant trend towards myopia, along with significantly elevated concentrations of LPS and VIP (p < 0.0001). Furthermore, Ruminococcus_albus emerged as the predominant bacterial community enriched in FDM (p < 0.05), and demonstrated positive correlations with 10 metabolites, including l-Glutamic acid, Additionally, Ruminococcus_albus exhibited positive correlations with VIP and LPS levels (p < 0.05). Conclusion The findings suggest that the Ruminococcus_Albus and glutamate metabolic pathways play a significant role in myopia development, leading to concurrent alterations in serum VIP and LPS levels in FDM guinea pigs. This underscores the potential of specific gut microbiota and their metabolites as pivotal biomarkers involved in the pathogenesis of myopia.
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Affiliation(s)
- Yajun Wu
- Aier Academy of Ophthalmology, Central South University, Changsha, Hunan, 410000, China
- Department of Ophthalmology, Shanghai Aier Eye Hospital, Shanghai, 200235, China
- Shanghai Aier Eye Institute, Shanghai, 200235, China
| | - Hua Fan
- Shanxi Aier Eye Hospital, Taiyuan, Shanxi, 030000, China
| | - Yuliang Feng
- Aier Academy of Ophthalmology, Central South University, Changsha, Hunan, 410000, China
- Department of Ophthalmology, Shanghai Aier Eye Hospital, Shanghai, 200235, China
- Shanghai Aier Eye Institute, Shanghai, 200235, China
| | - Jiasong Yang
- Aier Academy of Ophthalmology, Central South University, Changsha, Hunan, 410000, China
- Department of Ophthalmology, Shanghai Aier Eye Hospital, Shanghai, 200235, China
- Shanghai Aier Eye Institute, Shanghai, 200235, China
| | - Xiaobo Cen
- WestChina-Frontier PharmaTech Co., Ltd, Chengdu, Sichuan, 610000, China
| | - Wensheng Li
- Aier Academy of Ophthalmology, Central South University, Changsha, Hunan, 410000, China
- Department of Ophthalmology, Shanghai Aier Eye Hospital, Shanghai, 200235, China
- Shanghai Aier Eye Institute, Shanghai, 200235, China
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11
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Kalinski JCJ, Noundou XS, Petras D, Matcher GF, Polyzois A, Aron AT, Gentry EC, Bornman TG, Adams JB, Dorrington RA. Urban and agricultural influences on the coastal dissolved organic matter pool in the Algoa Bay estuaries. CHEMOSPHERE 2024; 355:141782. [PMID: 38548083 DOI: 10.1016/j.chemosphere.2024.141782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 02/28/2024] [Accepted: 03/22/2024] [Indexed: 04/08/2024]
Abstract
While anthropogenic pollution is a major threat to aquatic ecosystem health, our knowledge of the presence of xenobiotics in coastal Dissolved Organic Matter (DOM) is still relatively poor. This is especially true for water bodies in the Global South with limited information gained mostly from targeted studies that rely on comparison with authentic standards. In recent years, non-targeted tandem mass spectrometry has emerged as a powerful tool to collectively detect and identify pollutants and biogenic DOM components in the environment, but this approach has yet to be widely utilized for monitoring ecologically important aquatic systems. In this study we compared the DOM composition of Algoa Bay, Eastern Cape, South Africa, and its two estuaries. The Swartkops Estuary is highly urbanized and severely impacted by anthropogenic pollution, while the Sundays Estuary is impacted by commercial agriculture in its catchment. We employed solid-phase extraction followed by liquid chromatography tandem mass spectrometry to annotate more than 200 pharmaceuticals, pesticides, urban xenobiotics, and natural products based on spectral matching. The identification with authentic standards confirmed the presence of methamphetamine, carbamazepine, sulfamethoxazole, N-acetylsulfamethoxazole, imazapyr, caffeine and hexa(methoxymethyl)melamine, and allowed semi-quantitative estimations for annotated xenobiotics. The Swartkops Estuary DOM composition was strongly impacted by features annotated as urban pollutants including pharmaceuticals such as melamines and antiretrovirals. By contrast, the Sundays Estuary exhibited significant enrichment of molecules annotated as agrochemicals widely used in the citrus farming industry, with predicted concentrations for some of them exceeding predicted no-effect concentrations. This study provides new insight into anthropogenic impact on the Algoa Bay system and demonstrates the utility of non-targeted tandem mass spectrometry as a sensitive tool for assessing the health of ecologically important coastal ecosystems and will serve as a valuable foundation for strategizing long-term monitoring efforts.
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Affiliation(s)
| | - Xavier Siwe Noundou
- Department of Biochemistry and Microbiology, Rhodes University, Makhanda, South Africa; Department of Pharmaceutical Sciences, Sefako Makgatho Health Sciences University, Pretoria, South Africa
| | - Daniel Petras
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, USA; Department of Biochemistry, University of California Riverside, Riverside, USA; CMFI Cluster of Excellence, Interfaculty Institute of Microbiology and Medicine, University of Tuebingen, Tuebingen, Germany
| | - Gwynneth F Matcher
- Department of Biochemistry and Microbiology, Rhodes University, Makhanda, South Africa; South African Institute for Aquatic Biodiversity, 6139, Makhanda, South Africa
| | - Alexandros Polyzois
- Department of Biochemistry and Microbiology, Rhodes University, Makhanda, South Africa; Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, United States
| | - Allegra T Aron
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, USA; Department of Chemistry and Biochemistry, University of Denver, Denver, CO, 80210, United States
| | - Emily C Gentry
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, USA; Department of Chemistry, Virginia Tech, Blacksburg, VA, 24061, United States
| | - Thomas G Bornman
- Department of Biochemistry and Microbiology, Rhodes University, Makhanda, South Africa; South African Environmental Observation Network SAEON, Elwandle Coastal Node, Gqeberha, South Africa; Institute for Coastal and Marine Research, Nelson Mandela University, Gqeberha, South Africa
| | - Janine B Adams
- DSI/NRF Research Chair, Shallow Water Ecosystems, Department of Botany and Institute for Coastal and Marine Research, Nelson Mandela University, Gqeberha, South Africa; Department of Botany, Institute for Coastal and Marine Research CMR, Nelson Mandela University, Gqeberha, South Africa
| | - Rosemary A Dorrington
- Department of Biochemistry and Microbiology, Rhodes University, Makhanda, South Africa; South African Institute for Aquatic Biodiversity, 6139, Makhanda, South Africa.
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12
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Zhang Y, Ni M, Tao Y, Shen M, Xu W, Fan M, Shan J, Cheng H. Multiple-matrix metabolomics analysis for the distinct detection of colorectal cancer and adenoma. Metabolomics 2024; 20:47. [PMID: 38642214 DOI: 10.1007/s11306-024-02114-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 03/31/2024] [Indexed: 04/22/2024]
Abstract
OBJECTIVES Although colorectal cancer (CRC) is the leading cause of cancer-related morbidity and mortality, current diagnostic tests for early-stage CRC and colorectal adenoma (CRA) are suboptimal. Therefore, there is an urgent need to explore less invasive screening procedures for CRC and CRA diagnosis. METHODS Untargeted gas chromatography-mass spectrometry (GC-MS) metabolic profiling approach was applied to identify candidate metabolites. We performed metabolomics profiling on plasma samples from 412 subjects including 200 CRC patients, 160 CRA patients and 52 normal controls (NC). Among these patients, 45 CRC patients, 152 CRA patients and 50 normal controls had their fecal samples tested simultaneously. RESULTS Differential metabolites were screened in the adenoma-carcinoma sequence. Three diagnostic models were further developed to identify cancer group, cancer stage, and cancer microsatellite status using those significant metabolites. The three-metabolite-only classifiers used to distinguish the cancer group always keeps the area under the receiver operating characteristic curve (AUC) greater than 0.7. The AUC performance of the classifiers applied to discriminate CRC stage is generally greater than 0.8, and the classifiers used to distinguish microsatellite status of CRC is greater than 0.9. CONCLUSION This finding highlights potential early-driver metabolites in CRA and early-stage CRC. We also find potential metabolic markers for discriminating the microsatellite state of CRC. Our study and diagnostic model have potential applications for non-invasive CRC and CRA detection.
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Affiliation(s)
- Ye Zhang
- Department of Oncology, Jiangsu Province Hospital of Chinese Medicine, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
- The First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, China
- Jiangsu Collaborative Innovation Center of Traditional Chinese Medicine in Prevention and Treatment of Tumor, Nanjing University of Chinese Medicine, Nanjing, China
| | - Mingxin Ni
- The First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, China
- Jiangsu Collaborative Innovation Center of Traditional Chinese Medicine in Prevention and Treatment of Tumor, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yuquan Tao
- The First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, China
- Jiangsu Collaborative Innovation Center of Traditional Chinese Medicine in Prevention and Treatment of Tumor, Nanjing University of Chinese Medicine, Nanjing, China
| | - Meng Shen
- The First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, China
- Jiangsu Collaborative Innovation Center of Traditional Chinese Medicine in Prevention and Treatment of Tumor, Nanjing University of Chinese Medicine, Nanjing, China
| | - Weichen Xu
- Jiangsu Key Laboratory of Pediatric Respiratory Disease, Institute of Pediatrics, Medical Metabolomics Center, Nanjing University of Chinese Medicine, Nanjing, China
| | - Minmin Fan
- The First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, China.
- Jiangsu Collaborative Innovation Center of Traditional Chinese Medicine in Prevention and Treatment of Tumor, Nanjing University of Chinese Medicine, Nanjing, China.
| | - Jinjun Shan
- Jiangsu Key Laboratory of Pediatric Respiratory Disease, Institute of Pediatrics, Medical Metabolomics Center, Nanjing University of Chinese Medicine, Nanjing, China.
| | - Haibo Cheng
- Department of Oncology, Jiangsu Province Hospital of Chinese Medicine, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China.
- The First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, China.
- Jiangsu Collaborative Innovation Center of Traditional Chinese Medicine in Prevention and Treatment of Tumor, Nanjing University of Chinese Medicine, Nanjing, China.
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Sabi EM, AlMogren M, Sebaa R, Sumaily KM, AlMalki R, Mujamammi AH, Abdel Rahman AM. Comprehensive metabolomics analysis reveals novel biomarkers and pathways in falsely suspected glutaric aciduria Type-1 newborns. Clin Chim Acta 2024; 557:117861. [PMID: 38490341 DOI: 10.1016/j.cca.2024.117861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 02/04/2024] [Accepted: 03/05/2024] [Indexed: 03/17/2024]
Abstract
BACKGROUND Glutaric aciduria type-1 (GA-1) is a rare metabolic disorder due to glutaryl coenzyme A dehydrogenase deficiency, causing elevated levels of glutaryl-CoA and its derivatives. GA-1 exhibits symptoms like macrocephaly, developmental delays, and movement disorders. Timely diagnosis through genetic testing and newborn screening is crucial. However, in some cases, transiently elevated level of glutarylcarnitine (C5DC) challenges accurate diagnosis, highlighting the need for alternative diagnostic methods, like mass spectrometry-based untargeted metabolomics, to identify additional biomarkers for distinguishing falsely suspected GA-1 from healthy newborns. METHODOLOGY DBS samples from falsely suspected GA-1 newborns (n = 47) and matched control were collected through the NBS program. Untargeted metabolomics using liquid chromatography-high-resolution mass spectrometry (LC-HRMS) was performed to enable biomarker and pathway investigations for significantly altered metabolites. RESULTS 582 and 546 were up- and down-regulated metabolites in transient GA-1. 155 endogenous metabolites displayed significant variations compared to the control group. Furthermore, our data identified novel altered metabolic biomarkers, such as N-palmitoylcysteine, heptacarboxyporphyrin, 3-hydroxylinoleoylcarnitine, and monoacylglyceride (MG) (0:0/20:1/0:0), along with perturbed metabolic pathways like sphingolipid and thiamine metabolism associated with the transient elevated C5DC levels in DBS samples. CONCLUSIONS A distinct metabolic pattern linked to the transient C5DC elevation in newborns was reported to enhance the prediction of the falsely positive cases, which could help avoiding unnecessary medical treatments and minimizing the financial burdens in the health sector.
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Affiliation(s)
- Essa M Sabi
- Clinical Biochemistry Unit, Pathology Department, College of Medicine, King Saud University, Riyadh 11461, Saudi Arabia
| | - Maha AlMogren
- Metabolomics Section, Department of Clinical Genomics, Center for Genomics Medicine, King Faisal Specialist Hospital and Research Centre (KFSHRC), Riyadh 11211, KSA, Saudi Arabia
| | - Rajaa Sebaa
- Department of Medical Laboratories, College of Applied Medical Sciences, Shaqra University, Shaqra 11961, Saudi Arabia
| | - Khalid M Sumaily
- Clinical Biochemistry Unit, Pathology Department, College of Medicine, King Saud University, Riyadh 11461, Saudi Arabia
| | - Reem AlMalki
- Metabolomics Section, Department of Clinical Genomics, Center for Genomics Medicine, King Faisal Specialist Hospital and Research Centre (KFSHRC), Riyadh 11211, KSA, Saudi Arabia
| | - Ahmed H Mujamammi
- Clinical Biochemistry Unit, Pathology Department, College of Medicine, King Saud University, Riyadh 11461, Saudi Arabia
| | - Anas M Abdel Rahman
- Metabolomics Section, Department of Clinical Genomics, Center for Genomics Medicine, King Faisal Specialist Hospital and Research Centre (KFSHRC), Riyadh 11211, KSA, Saudi Arabia; The Department of Biochemistry and Molecular Medicine, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia.
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14
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Li S, Looby N, Chandran V, Kulasingam V. Challenges in the Metabolomics-Based Biomarker Validation Pipeline. Metabolites 2024; 14:200. [PMID: 38668328 PMCID: PMC11051909 DOI: 10.3390/metabo14040200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 03/27/2024] [Accepted: 03/31/2024] [Indexed: 04/28/2024] Open
Abstract
As end-products of the intersection between the genome and environmental influences, metabolites represent a promising approach to the discovery of novel biomarkers for diseases. However, many potential biomarker candidates identified by metabolomics studies fail to progress beyond analytical validation for routine implementation in clinics. Awareness of the challenges present can facilitate the development and advancement of innovative strategies that allow improved and more efficient applications of metabolite-based markers in clinical settings. This minireview provides a comprehensive summary of the pre-analytical factors, required analytical validation studies, and kit development challenges that must be resolved before the successful translation of novel metabolite biomarkers originating from research. We discuss the necessity for strict protocols for sample collection, storage, and the regulatory requirements to be fulfilled for a bioanalytical method to be considered as analytically validated. We focus especially on the blood as a biological matrix and liquid chromatography coupled with tandem mass spectrometry as the analytical platform for biomarker validation. Furthermore, we examine the challenges of developing a commercially viable metabolomics kit for distribution. To bridge the gap between the research lab and clinical implementation and utility of relevant metabolites, the understanding of the translational challenges for a biomarker panel is crucial for more efficient development of metabolomics-based precision medicine.
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Affiliation(s)
- Shenghan Li
- Division of Rheumatology, Psoriatic Arthritis Program, Schroeder Arthritis Program, University Health Network, Toronto, ON M5T 0S8, Canada; (S.L.); (N.L.)
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A1, Canada
- Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada
| | - Nikita Looby
- Division of Rheumatology, Psoriatic Arthritis Program, Schroeder Arthritis Program, University Health Network, Toronto, ON M5T 0S8, Canada; (S.L.); (N.L.)
- Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada
- Division of Orthopaedic Surgery, Osteoarthritis Research Program, Schroeder Arthritis Institute, University Health Network, Toronto, ON M5T 0S8, Canada
| | - Vinod Chandran
- Division of Rheumatology, Psoriatic Arthritis Program, Schroeder Arthritis Program, University Health Network, Toronto, ON M5T 0S8, Canada; (S.L.); (N.L.)
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A1, Canada
- Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada
- Division of Rheumatology, Department of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Vathany Kulasingam
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A1, Canada
- Division of Clinical Biochemistry, Laboratory Medicine Program, University Health Network, Toronto, ON M5G 2C4, Canada
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Alves MF, Katchborian-Neto A, Bueno PCP, Carnevale-Neto F, Casoti R, Ferreira MS, Murgu M, de Paula ACC, Dias DF, Soares MG, Chagas-Paula DA. LC-MS/DIA-based strategy for comprehensive flavonoid profiling: an Ocotea spp. applicability case. RSC Adv 2024; 14:10481-10498. [PMID: 38567345 PMCID: PMC10985591 DOI: 10.1039/d4ra01384k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 03/22/2024] [Indexed: 04/04/2024] Open
Abstract
We introduce a liquid chromatography - mass spectrometry with data-independent acquisition (LC-MS/DIA)-based strategy, specifically tailored to achieve comprehensive and reliable glycosylated flavonoid profiling. This approach facilitates in-depth and simultaneous exploration of all detected precursors and fragments during data processing, employing the widely-used open-source MZmine 3 software. It was applied to a dataset of six Ocotea plant species. This framework suggested 49 flavonoids potentially newly described for these plant species, alongside 45 known features within the genus. Flavonols kaempferol and quercetin, both exhibiting O-glycosylation patterns, were particularly prevalent. Gas-phase fragmentation reactions further supported these findings. For the first time, the apigenin flavone backbone was also annotated in most of the examined Ocotea species. Apigenin derivatives were found mainly in the C-glycoside form, with O. porosa displaying the highest flavone : flavonol ratio. The approach also allowed an unprecedented detection of kaempferol and quercetin in O. porosa species, and it has underscored the untapped potential of LC-MS/DIA data for broad and reliable flavonoid profiling. Our study annotated more than 50 flavonoid backbones in each species, surpassing the current literature.
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Affiliation(s)
- Matheus Fernandes Alves
- Institute of Chemistry, Federal University of Alfenas-MG 37130-001 Alfenas Minas Gerais Brazil
| | - Albert Katchborian-Neto
- Institute of Chemistry, Federal University of Alfenas-MG 37130-001 Alfenas Minas Gerais Brazil
| | - Paula Carolina Pires Bueno
- Leibniz Institute of Vegetable and Ornamental Crops (IGZ) Theodor-Echtermeyer-Weg 1 14979 Großbeeren Germany
| | - Fausto Carnevale-Neto
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington 850 Republican Street Seattle Washington 98109 USA
| | - Rosana Casoti
- Antibiotics Department, Federal University of Pernambuco 50670-901 Recife Pernambuco Brazil
| | - Miller Santos Ferreira
- Institute of Chemistry, Federal University of Alfenas-MG 37130-001 Alfenas Minas Gerais Brazil
| | - Michael Murgu
- Waters Corporation Alameda Tocantins 125, Alphaville 06455-020 São Paulo Brazil
| | | | - Danielle Ferreira Dias
- Institute of Chemistry, Federal University of Alfenas-MG 37130-001 Alfenas Minas Gerais Brazil
| | - Marisi Gomes Soares
- Institute of Chemistry, Federal University of Alfenas-MG 37130-001 Alfenas Minas Gerais Brazil
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16
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Wu J, Cao M, Jia Z, Zhu X, Zhou Y, Dong Y, Yu L, Hu C, Huang Y, Chen Z. Synergistic mechanism of stir-baked curcumae radix with vinegar in dysmenorrhea rats based on UPLC-Q-TOF/MS metabolomics. J Pharm Biomed Anal 2024; 240:115944. [PMID: 38183732 DOI: 10.1016/j.jpba.2023.115944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 12/11/2023] [Accepted: 12/25/2023] [Indexed: 01/08/2024]
Abstract
Curcumae Radix (i.e. Huangsiyujin: HSYJ), a well-known traditional Chinese medicine (TCM), has been widely used in clinical practice for many years to treat depression and primary dysmenorrhea. Modern pharmacological researches have demonstrated its anti-inflammatory, antidepressant, and dysmenorrhea relief effects. According to the processing theory of TCM, it is believed that stir-baked HSYJ with vinegar may enhance the ability to disperse stagnant hepatoqi and alleviate pain. However, whether the vinegar concoction of HSYJ can enhance the therapeutic effect on the Qi stagnation due to liver depression (LDQS) type of dysmenorrhea and what its mechanism has not been well explained. Based on the processing drugs theory of "stir-baked with vinegar into liver", a metabolomic approach was used to investigate the therapeutic effect and mechanism of stir-baked HSYJ with vinegar to enhance the treatment of dysmenorrhea in rats. By establishing a rat model of dysmenorrhea of the "LDQS" type, observation of hemorheology, uterine pathological sections, COX-2 and OTR protein expression and other indicators; analysis of urinary metabolic changes in rats by UPLC-Q-TOF-MS technique, to compare the differential biomarkers and metabolic pathways in the treatment of dysmenorrhea due to "liver stagnation and qi stagnation" before and after stir-baked HSYJ with vinegar. Stir-baked HSYJ with vinegar significantly inhibited the writhing response of rats, improved hemorheology, repaired damaged diseased uterus and inhibited high expression of COX-2 and OTR proteins in uterus; 68 differential metabolites were screened from the urine of rats, compared with the raw HSYJ, the levels of 14 metabolites were significantly changed in stir-baked HSYJ with vinegar, involving the pathways of phenylalanine, tyrosine and tryptophan metabolism, cysteine and methionine metabolism, aspartate and glutamate metabolism. The potentiating effect of stir-baked HSYJ with vinegar may be related to the regulation of multiple amino acid metabolic pathways.
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Affiliation(s)
- Jie Wu
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Mayijie Cao
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Zhuolin Jia
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Xiaoli Zhu
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Ye Zhou
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yidian Dong
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Lingying Yu
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Changjiang Hu
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China; Key Laboratory for Quality and Efficiency Evaluation of TCM Formula Granules, Sichuan Neo-Green Pharmaceutical Technology Development Co., Ltd, Chengdu, China
| | - Yu Huang
- Key Laboratory for Quality and Efficiency Evaluation of TCM Formula Granules, Sichuan Neo-Green Pharmaceutical Technology Development Co., Ltd, Chengdu, China
| | - Zhimin Chen
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
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17
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Chen Z, Liu S, Zhou H, Wang M, Pei S, Wang R, Liu Z. UPLC-Q-TOF/MS based serum and urine metabolomics strategy to analyze the mechanism of nervonic acid in treating Alzheimer's disease. J Pharm Biomed Anal 2024; 240:115930. [PMID: 38157740 DOI: 10.1016/j.jpba.2023.115930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 12/07/2023] [Accepted: 12/17/2023] [Indexed: 01/03/2024]
Abstract
Nervonic acid is a natural component of breast milk and is frequently used as a food additive due to its excellent neuroprotective effects. Although it has been reported that nervonic acid may play a role in the recovery of human cognitive impairment, its specific mechanism of action is still unclear. In this study, the results of serum biochemical indexes showed that nervonic acid improved inflammation and reduced amyloid β peptide (Aβ) deposition and tau protein phosphorylation in Alzheimer's disease (AD) rats. Subsequently, we further used a metabolomics approach to investigate the potential mechanism of action of nervonic acid in the treatment of AD. The results of serum and urine metabolomics study showed that the intervention of nervonic acid significantly reversed the metabolic profile disorder in AD rats. A total of 52 metabolites were identified. They mainly involved linoleic acid metabolism, alpha-linolenic acid metabolism, phenylalanine metabolism and arachidonic acid metabolism, and all these metabolic pathways were associated with the emergence of inflammation in vivo. It suggests that the therapeutic effect of nervonic acid on AD is likely to be produced by ameliorating inflammation. The results obtained in this study provide new insights into the mechanism of nervonic acid treatment of AD and lay a foundation for the clinical application of nervonic acid in the treatment of Alzheimer's disease.
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Affiliation(s)
- Ziyi Chen
- School of Pharmaceutical Sciences, Jilin University, Changchun 130021, China
| | - Shu Liu
- National Center of Mass Spectrometry in Changchun & Jilin Provincial Key Laboratory of Chinese Medicine Chemistry and Mass Spectrometry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Hui Zhou
- Key Laboratory of Biotechnology and Bioresources Utilization, Ministry of Education, Institute of Plant Resources, Dalian Minzu University, Dalian 116029, China
| | - Meiyuan Wang
- School of Pharmaceutical Sciences, Jilin University, Changchun 130021, China
| | - Shuhua Pei
- School of Pharmaceutical Sciences, Jilin University, Changchun 130021, China
| | - Rongjin Wang
- School of Pharmaceutical Sciences, Jilin University, Changchun 130021, China.
| | - Zhongying Liu
- School of Pharmaceutical Sciences, Jilin University, Changchun 130021, China.
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Li W, Chen X, Yao M, Sun B, Zhu K, Wang W, Zhang A. LC-MS based untargeted metabolomics studies of the metabolic response of Ginkgo biloba extract on arsenism patients. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 274:116183. [PMID: 38471343 DOI: 10.1016/j.ecoenv.2024.116183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/14/2024] [Accepted: 03/05/2024] [Indexed: 03/14/2024]
Abstract
Arsenic is an environmentally ubiquitous toxic metalloid. Chronic exposure to arsenic may lead to arsenicosis, while no specific therapeutic strategies are available for the arsenism patients. And Ginkgo biloba extract (GBE) exhibited protective effect in our previous study. However, the mechanisms by which GBE protects the arsenism patients remain poorly understood. A liquid chromatography-mass spectrometry (LC-MS) based untargeted metabolomics analysis was used to study metabolic response in arsenism patients upon GBE intervention. In total, 39 coal-burning type of arsenism patients and 50 healthy residents were enrolled from Guizhou province of China. The intervention group (n = 39) were arsenism patients orally administered with GBE (three times per day) for continuous 90 days. Plasma samples from 50 healthy controls (HC) and 39 arsenism patients before and after GBE intervention were collected and analyzed by established LC-MS method. Statistical analysis was performed by MetaboAnalyst 5.0 to identify differential metabolites. Multivariate analysis revealed a separation in arsenism patients between before (BG) and after GBE intervention (AG) group. It was observed that 35 differential metabolites were identified between BG and AG group, and 30 of them were completely or partially reversed by GBE intervention, with 14 differential metabolites significantly up-regulated and 16 differential metabolites considerably down-regulated. These metabolites were involved in promoting immune response and anti-inflammatory functions, and alleviating oxidative stress. Taken together, these findings indicate that the GBE intervention could probably exert its protective effects by reversing disordered metabolites modulating these functions in arsenism patients, and provide insights into further exploration of mechanistic studies.
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Affiliation(s)
- Weiwei Li
- Key Laboratory of Environmental Pollution, Monitoring and Disease Control, Ministry of Education, Department of Toxicology, School of Public Health, Guizhou Medical University, Guiyang 550025, PR China
| | - Xiong Chen
- Key Laboratory of Environmental Pollution, Monitoring and Disease Control, Ministry of Education, Department of Toxicology, School of Public Health, Guizhou Medical University, Guiyang 550025, PR China
| | - Maolin Yao
- Key Laboratory of Environmental Pollution, Monitoring and Disease Control, Ministry of Education, Department of Toxicology, School of Public Health, Guizhou Medical University, Guiyang 550025, PR China
| | - Baofei Sun
- Key Laboratory of Environmental Pollution, Monitoring and Disease Control, Ministry of Education, Department of Toxicology, School of Public Health, Guizhou Medical University, Guiyang 550025, PR China
| | - Kai Zhu
- Key Laboratory of Environmental Pollution, Monitoring and Disease Control, Ministry of Education, Department of Toxicology, School of Public Health, Guizhou Medical University, Guiyang 550025, PR China
| | - Wenjuan Wang
- Key Laboratory of Environmental Pollution, Monitoring and Disease Control, Ministry of Education, Department of Toxicology, School of Public Health, Guizhou Medical University, Guiyang 550025, PR China
| | - Aihua Zhang
- Key Laboratory of Environmental Pollution, Monitoring and Disease Control, Ministry of Education, Department of Toxicology, School of Public Health, Guizhou Medical University, Guiyang 550025, PR China.
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Xu C, Shao J. High-throughput omics technologies in inflammatory bowel disease. Clin Chim Acta 2024; 555:117828. [PMID: 38355001 DOI: 10.1016/j.cca.2024.117828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 02/06/2024] [Accepted: 02/10/2024] [Indexed: 02/16/2024]
Abstract
Inflammatory bowel disease (IBD) is a chronic, relapsing intestinal disease. Elucidation of the pathogenic mechanisms of IBD requires high-throughput technologies (HTTs) to effectively obtain and analyze large amounts of data. Recently, HTTs have been widely used in IBD, including genomics, transcriptomics, proteomics, microbiomics, metabolomics and single-cell sequencing. When combined with endoscopy, the application of these technologies can provide an in-depth understanding on the alterations of intestinal microbe diversity and abundance, the abnormalities of signaling pathway-mediated immune responses and functionality, and the evaluation of therapeutic effects, improving the accuracy of early diagnosis and treatment of IBD. This review comprehensively summarizes the development and advancement of HTTs, and also highlights the challenges and future directions of these technologies in IBD research. Although HTTs have made striking breakthrough in IBD, more standardized methods and large-scale dataset processing are still needed to achieve the goal of personalized medicine.
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Affiliation(s)
- Chen Xu
- Laboratory of Anti-infection and Immunity, College of Integrated Chinese and Western Medicine (College of Life Science), Anhui University of Chinese Medicine, Zhijing Building, 350 Longzihu Road, Xinzhan District, Hefei 230012, Anhui, PR China
| | - Jing Shao
- Laboratory of Anti-infection and Immunity, College of Integrated Chinese and Western Medicine (College of Life Science), Anhui University of Chinese Medicine, Zhijing Building, 350 Longzihu Road, Xinzhan District, Hefei 230012, Anhui, PR China; Institute of Integrated Traditional Chinese and Western Medicine, Anhui Academy of Chinese Medicine, Zhijing Building, 350 Longzihu Road, Xinzhan District, Hefei 230012, Anhui, PR China.
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20
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Wang Y, Tong L, Yang L, Ren B, Guo D. Metabolite profiling and antioxidant capacity of natural Ophiocordyceps gracilis and its cultures using LC-MS/MS-based metabolomics: Comparison with Ophiocordyceps sinensis. PHYTOCHEMICAL ANALYSIS : PCA 2024; 35:308-320. [PMID: 37779226 DOI: 10.1002/pca.3289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 09/11/2023] [Accepted: 09/12/2023] [Indexed: 10/03/2023]
Abstract
INTRODUCTION Ophiocordyceps gracilis is an entomopathogenic fungus and a precious traditional Chinese medicine with similar medicinal properties to Ophiocordyceps sinensis. However, information on the metabolite profiles of natural O. gracilis and its cultures is lacking, which limits their utilization. OBJECTIVE The metabolic variations and antioxidant activities of O. gracilis cultures and natural O. gracilis were analyzed to evaluate the nutritional and medicinal value of O. gracilis and its cultures. METHOD The metabolite profiles of O. gracilis cultures (fruiting bodies and aerial mycelia), natural O. gracilis, and natural O. sinensis were compared by LC-MS/MS coupled with multivariate data analysis. Furthermore, their antioxidant activities were evaluated based on their DPPH• , ABTS•+ , and • OH scavenging abilities. RESULTS A total of 612 metabolites were identified, and the metabolic compositions of the four Cordyceps samples were similar, with differences observed in the levels of some metabolites. There were 126 differential metabolites between natural O. gracilis and natural O. sinensis, among which fatty acids, carbohydrates, and secondary metabolites are predominant in natural O. gracilis. Furthermore, 116 differential metabolites between O. gracilis cultures and natural Cordyceps were identified, with generally higher levels in O. gracilis cultures than in natural Cordyceps. O. gracilis cultivated fruiting bodies exhibited the strongest antioxidant capacity among Cordyceps samples. Additionally, 46 primary and 24 secondary differential metabolites contribute to antioxidant activities. CONCLUSION This study provides a reference for the application of natural O. gracilis and its cultures in functional food and medicine from the perspective of metabolites and antioxidant capacity.
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Affiliation(s)
- Yue Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Lingling Tong
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Linhui Yang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Bo Ren
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Dongsheng Guo
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
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21
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Long Q, Luo F, Li B, Li Z, Guo Z, Chen Z, Wu W, Hu M. Gut microbiota and metabolic biomarkers in metabolic dysfunction-associated steatotic liver disease. Hepatol Commun 2024; 8:e0310. [PMID: 38407327 PMCID: PMC10898672 DOI: 10.1097/hc9.0000000000000310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 08/05/2023] [Indexed: 02/27/2024] Open
Abstract
Metabolic dysfunction-associated steatotic liver disease (MASLD), a replacement of the nomenclature employed for NAFLD, is the most prevalent chronic liver disease worldwide. Despite its high global prevalence, NAFLD is often under-recognized due to the absence of reliable noninvasive biomarkers for diagnosis and staging. Growing evidence suggests that the gut microbiome plays a significant role in the occurrence and progression of NAFLD by causing immune dysregulation and metabolic alterations due to gut dysbiosis. The rapid advancement of sequencing tools and metabolomics has enabled the identification of alterations in microbiome signatures and gut microbiota-derived metabolite profiles in numerous clinical studies related to NAFLD. Overall, these studies have shown a decrease in α-diversity and changes in gut microbiota abundance, characterized by increased levels of Escherichia and Prevotella, and decreased levels of Akkermansia muciniphila and Faecalibacterium in patients with NAFLD. Furthermore, bile acids, short-chain fatty acids, trimethylamine N-oxide, and tryptophan metabolites are believed to be closely associated with the onset and progression of NAFLD. In this review, we provide novel insights into the vital role of gut microbiome in the pathogenesis of NAFLD. Specifically, we summarize the major classes of gut microbiota and metabolic biomarkers in NAFLD, thereby highlighting the links between specific bacterial species and certain gut microbiota-derived metabolites in patients with NAFLD.
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22
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Zhou J, Wang J, Li D, Zhang Z, Wang C, Zhang X, Xu X, Gao J. An inulin-type fructan CP-A from Codonopsis pilosula alleviates TNBS-induced ulcerative colitis based on serum-untargeted metabolomics. Am J Physiol Gastrointest Liver Physiol 2024; 326:G216-G227. [PMID: 38193197 DOI: 10.1152/ajpgi.00214.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 12/12/2023] [Accepted: 12/21/2023] [Indexed: 01/10/2024]
Abstract
Ulcerative colitis (UC) is an inflammatory disease with abdominal pain, diarrhea, and bloody stool as the main symptoms. Several studies have confirmed that polysaccharides are effective against UC. It is commonly accepted that the traditional benefits of Radix Codonopsis can be attributed to its polysaccharide contents, and inulin-type fructan CP-A is the main active monomer in the polysaccharide components. Herein, we established a 2,4,6-trinitrobenzene sulfonic acid (TNBS)-induced UC rat model and lipopolysaccharide (LPS)-induced colonic epithelial cell model (NCM460) to investigate the effect of CP-A on UC. Untargeted metabolomics studies were conducted to identify differential metabolites using ultra-high performance liquid chromatography quadrupole time-of-flight tandem mass spectrometry (UHPLC-Q-TOF/MS) and enrich metabolic pathways in rat serum. The in vivo assays demonstrated that CP-A reduces colonic macroscopic injury, disease activity index (DAI), histopathological score, interleukin (IL)-8, and tumor necrosis factor-α (TNF-α) levels, as well as the expression of intercellular adhesion molecules. On the other hand, CP-A increases IL-10 and transforming growth factor-β (TGF-β) levels. The in vitro experiments indicated that CP-A treatment could reduce nitric oxide (NO) and IL-1β after LPS stimulation. The metabolomics results suggested that CP-A therapy for UC may be related to the mammalian target of rapamycin (mTOR) signaling pathway. The in vitro and in vivo validation of the pathway showed similar results, indicating that CP-A alleviates UC by preventing the activation of mTOR/p70S6K signaling pathway. These findings offer a fresh approach to treating UC and a theoretical foundation for the future advancement of CP-A.NEW & NOTEWORTHY We report that an inulin-type fructan from Codonopsis pilosula CP-A exhibits a therapeutic effect on experimental colitis. Its mechanism may be to alleviate intestinal inflammation by preventing the activation of mammalian target of rapamycin (mTOR)/p70S6K signaling pathway. These findings offer a fresh approach to treating ulcerative colitis (UC) and a theoretical foundation for the future advancement of CP-A.
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Affiliation(s)
- Jiangtao Zhou
- School of Pharmacy, Shanxi Medical University, Taiyuan, People's Republic of China
- Medicinal Basic Research Innovation Center of Chronic Kidney Disease, Ministry of Education, Shanxi Medical University, Taiyuan, People's Republic of China
- Shanxi Provincial Key Laboratory of Drug Synthesis and Novel Pharmaceutical Preparation Technology, Shanxi Medical University, Taiyuan, People's Republic of China
| | - Jiajing Wang
- School of Pharmacy, Shanxi Medical University, Taiyuan, People's Republic of China
| | - Deyun Li
- School of Pharmacy, Shanxi Medical University, Taiyuan, People's Republic of China
| | - Zhijia Zhang
- Urology Surgery, Shanxi Provincial People's Hospital, Taiyuan, People's Republic of China
| | - Changjian Wang
- School of Pharmacy, Shanxi Medical University, Taiyuan, People's Republic of China
| | - Xuepeng Zhang
- School of Pharmacy, Shanxi Medical University, Taiyuan, People's Republic of China
| | - Xiexin Xu
- School of Pharmacy, Shanxi Medical University, Taiyuan, People's Republic of China
| | - Jianping Gao
- School of Pharmacy, Shanxi Medical University, Taiyuan, People's Republic of China
- Medicinal Basic Research Innovation Center of Chronic Kidney Disease, Ministry of Education, Shanxi Medical University, Taiyuan, People's Republic of China
- Shanxi Provincial Key Laboratory of Drug Synthesis and Novel Pharmaceutical Preparation Technology, Shanxi Medical University, Taiyuan, People's Republic of China
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Pan S, Yu W, Zhang J, Guo Y, Qiao X, Xu P, Zhai Y. Environmental chemical TCPOBOP exposure alters milk liposomes and offspring growth trajectories in mice. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 272:116061. [PMID: 38340598 DOI: 10.1016/j.ecoenv.2024.116061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 01/24/2024] [Accepted: 01/29/2024] [Indexed: 02/12/2024]
Abstract
Exposure to environmental endocrine disruptors (EEDs) has become a global health concern, and EEDs are known to be potent inducers of constitutive androstane receptor (CAR). 1,4-bis [2-(3,5-dichloropyridyloxy)] benzene (TCPOBOP, hereafter abbreviated as TC), a specific ligand for CAR, has been considered as a potential EED. Here, we analyzed the effect of TC exposure to female mice on the histological morphology of their alveoli in the basic unit of lactation. We quantified differences in the milk metabolome of the control and TC-exposed group while assessing the correlations between metabolites and neonatal growth. Mammary histological results showed that TC exposure inhibited alveolar development. Based on the milk metabolomic data, we identified a total of 1505 differential metabolites in both the positive and negative ion mode, which indicated that TC exposure affected milk composition. As expected, the differential metabolites were significantly enriched in the drug metabolism pathway. Further analyses revealed that differential metabolites were significantly enriched in multiple lipid metabolic pathways, such as fatty acid biosynthesis, suggesting that most differential metabolites were concentrated in lipids. Simultaneously, a quantitative analysis showed that TC exposure led to a decrease in the relative abundance of total milk lipids, affecting the proportion of some lipid subclasses. Notably, a portion of lipid metabolites were associated with neonatal growth. Taken together, these findings suggest that TC exposure may affect milk lipidomes, resulting in the inability of mothers to provide adequate nutrients, ultimately affecting the growth and health of their offspring.
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Affiliation(s)
- Shijia Pan
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China; Key Laboratory for Cell Proliferation and Regulation Biology of State Education Ministry, College of Life Sciences, Beijing Normal University, Beijing 100875, China.
| | - Wen Yu
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China; Key Laboratory for Cell Proliferation and Regulation Biology of State Education Ministry, College of Life Sciences, Beijing Normal University, Beijing 100875, China.
| | - Jia Zhang
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China; Key Laboratory for Cell Proliferation and Regulation Biology of State Education Ministry, College of Life Sciences, Beijing Normal University, Beijing 100875, China.
| | - Yuan Guo
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China; Key Laboratory for Cell Proliferation and Regulation Biology of State Education Ministry, College of Life Sciences, Beijing Normal University, Beijing 100875, China.
| | - Xiaoxiao Qiao
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China; Key Laboratory for Cell Proliferation and Regulation Biology of State Education Ministry, College of Life Sciences, Beijing Normal University, Beijing 100875, China.
| | - Pengfei Xu
- Department of Hepatobiliary and Pancreatic Surgery, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China; Center for Pharmacogenetics and Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261, USA.
| | - Yonggong Zhai
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China; Key Laboratory for Cell Proliferation and Regulation Biology of State Education Ministry, College of Life Sciences, Beijing Normal University, Beijing 100875, China.
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Kameni M, Musaigwa F, Kamguia LM, Kamdem SD, Mbanya G, Lamberton PHL, Komguep Nono J. Harnessing Schistosoma-associated metabolite changes in the human host to identify biomarkers of infection and morbidity: Where are we and what should we do next? PLoS Negl Trop Dis 2024; 18:e0012009. [PMID: 38512811 PMCID: PMC10956858 DOI: 10.1371/journal.pntd.0012009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2024] Open
Abstract
Schistosomiasis is the second most widespread parasitic disease affecting humans. A key component of today's infection control measures is the diagnosis and monitoring of infection, informing individual- and community-level treatment. However, newly acquired infections and/or low parasite burden are still difficult to diagnose reliably. Furthermore, even though the pathological consequence of schistosome egg sequestration in host tissues is well described, the evidence linking egg burden to morbidity is increasingly challenged, making it inadequate for pathology monitoring. In the last decades, omics-based instruments and methods have been developed, adjusted, and applied in parasitic research. In particular, the profiling of the most reliable determinants of phenotypes, metabolites by metabolomics, emerged as a powerful boost in the understanding of basic interactions within the human host during infection. As such, the fine detection of host metabolites produced upon exposure to parasites such as Schistosoma spp. and the ensuing progression of the disease are believed to enable the identification of Schistosoma spp. potential biomarkers of infection and associated pathology. However, attempts to provide such a comprehensive understanding of the alterations of the human metabolome during schistosomiasis are rare, limited in their design when performed, and mostly inconclusive. In this review, we aimed to briefly summarize the most robust advances in knowledge on the changes in host metabolic profile during Schistosoma infections and provide recommendations for approaches to optimize the identification of metabolomic signatures of human schistosomiasis.
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Affiliation(s)
- Mireille Kameni
- Unit of Immunobiology and Helminth Infections, Laboratory of Molecular Biology and Biotechnology, Institute of Medical Research and Medicinal Plant Studies (IMPM), Ministry of Scientific Research and Innovation, Yaoundé, Cameroon
- Department of Microbiology and Parasitology, University of Bamenda, Bambili, North-West Region, Cameroon
| | - Fungai Musaigwa
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Leonel Meyo Kamguia
- Unit of Immunobiology and Helminth Infections, Laboratory of Molecular Biology and Biotechnology, Institute of Medical Research and Medicinal Plant Studies (IMPM), Ministry of Scientific Research and Innovation, Yaoundé, Cameroon
| | - Severin Donald Kamdem
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Gladice Mbanya
- Unit of Immunobiology and Helminth Infections, Laboratory of Molecular Biology and Biotechnology, Institute of Medical Research and Medicinal Plant Studies (IMPM), Ministry of Scientific Research and Innovation, Yaoundé, Cameroon
| | - Poppy H. L. Lamberton
- School of Biodiversity, One Health & Veterinary Medicine, University of Glasgow, Glasgow, United Kingdom
- Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, United Kingdom
| | - Justin Komguep Nono
- Unit of Immunobiology and Helminth Infections, Laboratory of Molecular Biology and Biotechnology, Institute of Medical Research and Medicinal Plant Studies (IMPM), Ministry of Scientific Research and Innovation, Yaoundé, Cameroon
- Division of Immunology, Health Science Faculty, University of Cape Town, Cape Town, South Africa
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Nishiumi S, Yokoyama T, Ojima N. User-friendly relative quantification procedure for gas chromatography/mass spectrometry-based plasma metabolome analysis. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2024; 38:e9683. [PMID: 38212648 DOI: 10.1002/rcm.9683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 11/20/2023] [Accepted: 11/27/2023] [Indexed: 01/13/2024]
Abstract
RATIONALE Recently, metabolome analysis has been applied to a variety of research fields, but differences between batches or facilities can cause discrepancies in the results of such analyses. To resolve these issues using comprehensive metabolome analysis, in which it is difficult to perform quantitative analyses of all detected metabolites, internal standard compounds are used to obtain relative metabolite levels. This study investigated gas chromatography/mass spectrometry-based plasma metabolome analysis methods that are superior to relative quantification using internal standard compounds. METHODS In experiment I, four analyses were performed under different analytical conditions at one facility, and then the data from the four analyses were compared. In experiment II, the same samples were analyzed at three facilities, and then the data from the three facilities were compared. RESULTS Regarding the relative values obtained through comparisons with the internal standard compound, differences in the analytical results were observed among the four analytical conditions in experiment I and among the three facilities in experiment II, and the differences observed among the three facilities (experiment II) were larger. When correction was performed using plasma as a quality control, which is the procedure suggested in this study, these differences were markedly ameliorated. CONCLUSION The suggested procedure involves the analysis of a plasma standard as a quality control for each batch and the calculation of relative target plasma to quality-control plasma values for each metabolite. This is an easy and low-cost method and could be readily employed by researchers during comprehensive plasma metabolome analysis.
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Affiliation(s)
- Shin Nishiumi
- Department of Omics Medicine, Hyogo Medical University, Nishinomiya, Japan
- Department of Biosphere Sciences, School of Human Sciences, Kobe College, Nishinomiya, Japan
| | - Tomonori Yokoyama
- Department of Omics Medicine, Hyogo Medical University, Nishinomiya, Japan
- Analytical and Measuring Instruments Division, Shimadzu Corporation, Kyoto, Japan
| | - Noriyuki Ojima
- Department of Omics Medicine, Hyogo Medical University, Nishinomiya, Japan
- Analytical and Measuring Instruments Division, Shimadzu Corporation, Kyoto, Japan
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26
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Chernonosov AA, Mednova IA, Levchuk LA, Mazurenko EO, Roschina OV, Simutkin GG, Bokhan NA, Koval VV, Ivanova SA. Untargeted Plasma Metabolomic Profiling in Patients with Depressive Disorders: A Preliminary Study. Metabolites 2024; 14:110. [PMID: 38393002 PMCID: PMC10890195 DOI: 10.3390/metabo14020110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 02/02/2024] [Accepted: 02/04/2024] [Indexed: 02/25/2024] Open
Abstract
Depressive disorder is a multifactorial disease that is based on dysfunctions in mental and biological processes. The search for biomarkers can improve its diagnosis, personalize therapy, and lead to a deep understanding of the biochemical processes underlying depression. The purpose of this work was a metabolomic analysis of blood serum to classify patients with depressive disorders and healthy individuals using Compound Discoverer software. Using high-resolution mass spectrometry, blood plasma samples from 60 people were analyzed, of which 30 were included in a comparison group (healthy donors), and 30 were patients with a depressive episode (F32.11) and recurrent depressive disorder (F33.11). Differences between patient and control groups were identified using the built-in utilities in Compound Discoverer software. Compounds were identified by their accurate mass and fragment patterns using the mzCloud database and tentatively identified by their exact mass using the ChemSpider search engine and the KEGG, ChEBI, FDA UNII-NLM, Human Metabolome and LipidMAPS databases. We identified 18 metabolites that could divide patients with depressive disorders from healthy donors. Of these, only two compounds were tentatively identified using the mzCloud database (betaine and piperine) based on their fragmentation spectra. For three compounds ((4S,5S,8S,10R)-4,5,8-trihydroxy-10-methyl-3,4,5,8,9,10-hexahydro-2H-oxecin-2-one, (2E,4E)-N-(2-hydroxy-2-methylpropyl)-2,4-tetradecadienamide and 17α-methyl-androstan-3-hydroxyimine-17β-ol), matches were found in the mzCloud database but with low score, which could not serve as reliable evidence of their structure. Another 13 compounds were identified by their exact mass in the ChemSpider database, 9 (g-butyrobetaine, 6-diazonio-5-oxo-L-norleucine, 11-aminoundecanoic acid, methyl N-acetyl-2-diazonionorleucinate, glycyl-glycyl-argininal, dilaurylmethylamine, 12-ketodeoxycholic acid, dicetylamine, 1-linoleoyl-2-hydroxy-sn-glycero-3-PC) had only molecular formulas proposed, and 4 were unidentified. Thus, the use of Compound Discoverer software alone was not sufficient to identify all revealed metabolites. Nevertheless, the combination of the found metabolites made it possible to divide patients with depressive disorders from healthy donors.
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Affiliation(s)
- Alexander A Chernonosov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Lavrentyev Avenue 8, Novosibirsk 630090, Russia
| | - Irina A Mednova
- Mental Health Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Aleutskaya Str. 4, Tomsk 634014, Russia
| | - Lyudmila A Levchuk
- Mental Health Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Aleutskaya Str. 4, Tomsk 634014, Russia
| | - Ekaterina O Mazurenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Lavrentyev Avenue 8, Novosibirsk 630090, Russia
| | - Olga V Roschina
- Mental Health Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Aleutskaya Str. 4, Tomsk 634014, Russia
| | - German G Simutkin
- Mental Health Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Aleutskaya Str. 4, Tomsk 634014, Russia
| | - Nikolay A Bokhan
- Mental Health Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Aleutskaya Str. 4, Tomsk 634014, Russia
- Department of Psychiatry, Addictology and Psychotherapy, Siberian State Medical University, Moskovsky Trakt 2, Tomsk 634050, Russia
| | - Vladimir V Koval
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Lavrentyev Avenue 8, Novosibirsk 630090, Russia
| | - Svetlana A Ivanova
- Mental Health Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Aleutskaya Str. 4, Tomsk 634014, Russia
- Department of Psychiatry, Addictology and Psychotherapy, Siberian State Medical University, Moskovsky Trakt 2, Tomsk 634050, Russia
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Olkowicz M, Ramadan K, Rosales-Solano H, Yu M, Wang A, Cypel M, Pawliszyn J. Mapping the metabolic responses to oxaliplatin-based chemotherapy with in vivo spatiotemporal metabolomics. J Pharm Anal 2024; 14:196-210. [PMID: 38464782 PMCID: PMC10921245 DOI: 10.1016/j.jpha.2023.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 07/14/2023] [Accepted: 08/07/2023] [Indexed: 03/12/2024] Open
Abstract
Adjuvant chemotherapy improves the survival outlook for patients undergoing operations for lung metastases caused by colorectal cancer (CRC). However, a multidisciplinary approach that evaluates several factors related to patient and tumor characteristics is necessary for managing chemotherapy treatment in metastatic CRC patients with lung disease, as such factors dictate the timing and drug regimen, which may affect treatment response and prognosis. In this study, we explore the potential of spatial metabolomics for evaluating metabolic phenotypes and therapy outcomes during the local delivery of the anticancer drug, oxaliplatin, to the lung. 12 male Yorkshire pigs underwent a 3 h left lung in vivo lung perfusion (IVLP) with various doses of oxaliplatin (7.5, 10, 20, 40, and 80 mg/L), which were administered to the perfusion circuit reservoir as a bolus. Biocompatible solid-phase microextraction (SPME) microprobes were combined with global metabolite profiling to obtain spatiotemporal information about the activity of the drug, determine toxic doses that exceed therapeutic efficacy, and conduct a mechanistic exploration of associated lung injury. Mild and subclinical lung injury was observed at 40 mg/L of oxaliplatin, and significant compromise of the hemodynamic lung function was found at 80 mg/L. This result was associated with massive alterations in metabolic patterns of lung tissue and perfusate, resulting in a total of 139 discriminant compounds. Uncontrolled inflammatory response, abnormalities in energy metabolism, and mitochondrial dysfunction next to accelerated kynurenine and aldosterone production were recognized as distinct features of dysregulated metabolipidome. Spatial pharmacometabolomics may be a promising tool for identifying pathological responses to chemotherapy.
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Affiliation(s)
- Mariola Olkowicz
- Department of Chemistry, University of Waterloo, Waterloo, ON, Canada
- Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, Krakow, Poland
| | - Khaled Ramadan
- Latner Thoracic Surgery Research Laboratories, Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
| | | | - Miao Yu
- The Jackson Laboratory, JAX Genomic Medicine, Farmington, CT, USA
| | - Aizhou Wang
- Latner Thoracic Surgery Research Laboratories, Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
| | - Marcelo Cypel
- Latner Thoracic Surgery Research Laboratories, Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
- Division of Thoracic Surgery, Department of Surgery, University Health Network, University of Toronto, Toronto Lung Transplant Program, Toronto, ON, Canada
| | - Janusz Pawliszyn
- Department of Chemistry, University of Waterloo, Waterloo, ON, Canada
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Chen Q, Lu Q, Zhang L, Zhang C, Zhang J, Gu Y, Huang Q, Tang H. A novel endogenous retention-index for minimizing retention-time variations in metabolomic analysis with reversed-phase ultrahigh-performance liquid-chromatography and mass spectrometry. Talanta 2024; 268:125318. [PMID: 37875029 DOI: 10.1016/j.talanta.2023.125318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 10/07/2023] [Accepted: 10/14/2023] [Indexed: 10/26/2023]
Abstract
Consistent retention time (tR) of metabolites is vital for identification in metabolomic analysis with ultrahigh-performance liquid-chromatography (UPLC). To minimize inter-experimental tR variations from the reversed-phase UPLC-MS, we developed an endogenous retention-index (endoRI) using in-sample straight-chain acylcarnitines with different chain-length (LC, C0-C26) without additives. The endoRI-corrections reduced the tR variations caused by the combined changes of mobile phases, gradients, flow-rates, elution time, columns and temperature from up to 5.1 min-0.2 min for most metabolites in a model metabolome consisting of 91 metabolites and multiple biological matrices including human serum, plasma, fecal, urine, A549 cells and rabbit liver extracts. The endoRI-corrections also reduced the inter-batch and inter-platform tR variations from 1.5 min to 0.15 min for 95 % of detected features in the above biological samples. We further established a quantitative model between tR and LC for predicting tR values of acylcarnitines when absent in samples. This makes it possible to compare metabolites' tR from different tR databases and the UPLC-based metabolomic data from different batches.
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Affiliation(s)
- Qinsheng Chen
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Metabonomics and Systems Biology Laboratory at Shanghai International Centre for Molecular Phenomics, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Qinwei Lu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Metabonomics and Systems Biology Laboratory at Shanghai International Centre for Molecular Phenomics, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Lianglong Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Metabonomics and Systems Biology Laboratory at Shanghai International Centre for Molecular Phenomics, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Chenhan Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Metabonomics and Systems Biology Laboratory at Shanghai International Centre for Molecular Phenomics, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Jingxian Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Metabonomics and Systems Biology Laboratory at Shanghai International Centre for Molecular Phenomics, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Yu Gu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Metabonomics and Systems Biology Laboratory at Shanghai International Centre for Molecular Phenomics, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Qingxia Huang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Metabonomics and Systems Biology Laboratory at Shanghai International Centre for Molecular Phenomics, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.
| | - Huiru Tang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Metabonomics and Systems Biology Laboratory at Shanghai International Centre for Molecular Phenomics, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.
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Daramola O, Gutierrez Reyes CD, Chávez-Reyes J, Marichal-Cancino BA, Nwaiwu J, Onigbinde S, Adeniyi M, Solomon J, Bhuiyan MMAA, Mechref Y. Metabolomic Changes in Rat Serum after Chronic Exposure to Glyphosate-Based Herbicide. Metabolites 2024; 14:50. [PMID: 38248853 PMCID: PMC10819816 DOI: 10.3390/metabo14010050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/09/2024] [Accepted: 01/11/2024] [Indexed: 01/23/2024] Open
Abstract
Glyphosate-based herbicides (GBHs) have gained extensive popularity in recent decades. For many years, glyphosate has been regarded as harmless or minimally toxic to mammals due to the absence of its primary target, the shikimic acid pathway in humans. Nonetheless, mounting evidence suggests that glyphosate may cause adverse health effects in humans via other mechanisms. In this study, we described the metabolomic changes in the serum of experimental rats exposed to chronic GBH using the highly sensitive LC-MS/MS technique. We investigated the possible relationship between chronic exposure to GBH and neurological disorders. Our findings suggest that chronic exposure to GBH can alter spatial learning memory and the expression of some important metabolites that are linked to neurophysiological disorders in young rats, with the female rats showing higher susceptibility compared to the males. This indicates that female rats are more likely to show early symptoms of the disorder on exposure to chronic GBH compared to male rats. We observed that four important metabolites (paraxanthine, epinephrine, L-(+)-arginine, and D-arginine) showed significant changes and involvement in neurological changes as suggested by ingenuity pathway analysis. In conclusion, our results indicate that chronic exposure to GBH can increase the risk of developing neurological disorders.
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Affiliation(s)
- Oluwatosin Daramola
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA; (O.D.); (C.D.G.R.); (J.N.); (S.O.); (M.A.); (J.S.); (M.M.A.A.B.)
| | - Cristian D. Gutierrez Reyes
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA; (O.D.); (C.D.G.R.); (J.N.); (S.O.); (M.A.); (J.S.); (M.M.A.A.B.)
| | - Jesús Chávez-Reyes
- Center of Basic Sciences, Department of Physiology and Pharmacology, Universidad Autónoma de Aguascalientes, Ags, CP 20131, Mexico; (J.C.-R.); (B.A.M.-C.)
| | - Bruno A. Marichal-Cancino
- Center of Basic Sciences, Department of Physiology and Pharmacology, Universidad Autónoma de Aguascalientes, Ags, CP 20131, Mexico; (J.C.-R.); (B.A.M.-C.)
| | - Judith Nwaiwu
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA; (O.D.); (C.D.G.R.); (J.N.); (S.O.); (M.A.); (J.S.); (M.M.A.A.B.)
| | - Sherifdeen Onigbinde
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA; (O.D.); (C.D.G.R.); (J.N.); (S.O.); (M.A.); (J.S.); (M.M.A.A.B.)
| | - Moyinoluwa Adeniyi
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA; (O.D.); (C.D.G.R.); (J.N.); (S.O.); (M.A.); (J.S.); (M.M.A.A.B.)
| | - Joy Solomon
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA; (O.D.); (C.D.G.R.); (J.N.); (S.O.); (M.A.); (J.S.); (M.M.A.A.B.)
| | - Md Mostofa Al Amin Bhuiyan
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA; (O.D.); (C.D.G.R.); (J.N.); (S.O.); (M.A.); (J.S.); (M.M.A.A.B.)
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA; (O.D.); (C.D.G.R.); (J.N.); (S.O.); (M.A.); (J.S.); (M.M.A.A.B.)
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Gao W, Gao S, Zhang Y, Wang M, Liu Y, Li T, Gao C, Zhou Y, Bian B, Wang H, Wei X, Sato T, Si N, Zhao W, Zhao H. Altered metabolic profiles and targets relevant to the protective effect of acteoside on diabetic nephropathy in db/db mice based on metabolomics and network pharmacology studies. JOURNAL OF ETHNOPHARMACOLOGY 2024; 318:117073. [PMID: 37619856 DOI: 10.1016/j.jep.2023.117073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 07/26/2023] [Accepted: 08/21/2023] [Indexed: 08/26/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Diabetic nephropathy (DN) was a major cause of end-stage renal failure and a common microvascular complication in patients with diabetes mellitus (DM). Acteoside (ACT) was the main ingredient extracted from the leaves of Rehmannia glutinosa, which had the functions of entering the lung, moisturizing the skin and relieving itching, nourishing yin and tonifying the kidney, cooling blood, and stopping bleeding. ACT had attracted worldwide interest because of its therapeutic effects on DM and its complications. AIM OF THE STUDY To clarify the metabolic profiles and targets of ACT in db/db mice based on metabolomics and network pharmacology studies. MATERIALS AND METHODS Db/db mice were used to observe the biochemical indices and histopathological changes in the kidney to evaluate the pharmacological effects of ACT on DN. Untargeted metabolomics studies were performed to investigate by UHPLC-LTQ-Orbitrap MS on urine, serum, and kidney samples. The key targets and pathways were analyzed by network pharmacology. For the pathways enriched by untargeted metabolomics, targeted metabolomics by UHPLC-QQQ-MS/MS was performed in kidney samples for validation. Sensitive biomarkers in kidney samples were evaluated. The effect of ACT on the improvement of DN from the perspective of metabolism of small molecules in vivo was described. RESULTS ACT could delay the progression of DN and improve the degree of histopathological damage to the kidney. The pathways were focused on amino acid metabolism by untargeted metabolomics. Through network pharmacology analysis, the effect pathways were related to signal transduction, carbohydrate, lipid, amino acid metabolism and mainly affected the endocrine and immune systems. Amino acid metabolism was disturbed in the kidney of db/db mice, which could be callback by ACT, such as tryptophan, glutamine, cysteine, leucine, threonine, proline, phenylalanine, histidine, serine, arginine, asparagine by targeted metabolomics. CONCLUSIONS In conclusion, this study provided strong support for ACT on DN treatment in clinics. Meanwhile, the Rehmannia glutinosa was used fully to raise the income level of farmers economically, while achieving the social benefit of empowering rural revitalization.
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Affiliation(s)
- Wenya Gao
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Shuangrong Gao
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Yan Zhang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Mengxiao Wang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Yuyang Liu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Tao Li
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China; Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Chang Gao
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Yanyan Zhou
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Baolin Bian
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Hongjie Wang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Xiaolu Wei
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Takashi Sato
- Department of Biochemistry, Tokyo University of Pharmacy and Life Sciences, Tokyo 192-0392, Japan
| | - Nan Si
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Wei Zhao
- Center for Drug Evaluation, National Medical Products Administration, Beijing, 100022, China.
| | - Haiyu Zhao
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
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31
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Wang X, Cai W, Liu Y, Lu Y, Liu M, Cao X, Guo D. Exploring biomarkers associated with severity of knee osteoarthritis in Southern China using widely targeted metabolomics. BMC Musculoskelet Disord 2023; 24:953. [PMID: 38066443 PMCID: PMC10704822 DOI: 10.1186/s12891-023-07084-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Accepted: 11/30/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Metabolomics is a tool to study the pathogenesis of diseases and their associated metabolites, but there are still insufficient metabolomic studies on severe knee osteoarthritis.To investigate the differences in serum metabolites between healthy populations and knee osteoarthritis (KOA) patients in Southern China using widely targeted metabolomics, and to explore biomarkers and their metabolic pathways that could be associated with the severity of KOA. METHODS There were 10 healthy individuals in the control group and 32 patients with KOA. According to the Kellgren-Lawrence (KL) grading system, KOA was further divided into mild (n = 13, KL grade 1 and 2) and severe (n = 19, KL grade 3 and 4). Serum samples from all participants were collected and analyzed metabolomics based on ultra-performance liquid chromatography/electrospray ionization/tandem mass spectrometry. We screened for differential metabolites between patients and controls, and between mild and severe KOA. We explored the metabolic pathways involved in differential metabolism using the Kyoto Encyclopedia of Genes and Genomes database. RESULTS Sixty-one metabolites were differentially expressed in the sera of the patient group compared with the control group (45 upregulated and 16 downregulated). Analysis of the mild and severe KOA groups showed a total of 12 differential metabolites. Receiver operating characteristic curve analysis showed N-alpha-acetyl-L-asparagine was a good predictor of advanced osteoarthritis(OA).Differential metabolites are enriched in multiple pathways such as arachidonic acid metabolism. CONCLUSION Widely targeted metabolomics found that upregulation of the amino acid metabolite N-α-acetyl-L-asparagine was significantly associated with severe KOA and could be a biomarker for predicting severity of KOA. Arachidonic acid metabolism may play an important role in patients with severe KOA.
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Affiliation(s)
- Xiaochao Wang
- Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Wanling Cai
- Shuguang Hospital Affiliated to Shanghai University of Chinese Traditional Medicine, Shanghai, China
| | - Yihan Liu
- Department of Neurological Rehabilitation, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yaoming Lu
- Department of Orthopaedic Surgery, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, Guangdong, China
| | - Mange Liu
- Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Xuewei Cao
- Department of Orthopaedic Surgery, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, Guangdong, China
| | - Da Guo
- Department of Orthopaedic Surgery, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, Guangdong, China.
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Wu W, Song Y, Sun M, Li Y, Xu Y, Xu M, Yang Y, Li S, Zhang F. Corneal metabolic biomarkers for moderate and high myopia in human. Exp Eye Res 2023; 237:109689. [PMID: 37871883 DOI: 10.1016/j.exer.2023.109689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 10/13/2023] [Accepted: 10/20/2023] [Indexed: 10/25/2023]
Abstract
This study aimed to identify the corneal metabolic biomarkers for moderate and high myopia in human. We enrolled 221 eyes from 221 subjects with myopia to perform the femtosecond laser small incision lenticule extraction (SMILE) surgery. Among these, 71 eyes of 71 subjects were enrolled in the low myopic group, 75 eyes of 75 subjects in the moderate myopic group and 75 eyes of 75 subjects in the high myopic group. The untargeted metabolomics analysis was performed to analyze the corneal tissues extracted during the SMILE surgery using an ultra-high-performance liquid chromatography (UHPLC) coupled to a quadrupole time-of-flight (Q-TOF) mass spectrometry (MS). The one-way analysis of variance (ANOVA) was used to identify the different metabolites among the three myopic groups, the orthogonal partial least-squares discriminant analysis (OPLS-DA) model was used to reveal the different metabolites between moderate myopia and low myopia, and between high myopia and low myopia. The Venn gram was used to find the overlapped metabolites of the three datasets of the different metabolites. The stepwise multiple linear regression analysis was used to determine the metabolic molecules associated with manifest refractive spherical equivalents (MRSE). The Receiver Operating Characteristics (ROC) analysis was performed to reveal the corneal biomarkers for moderate and high myopia. The hub biomarker was further selected by the networks among different metabolites created by the Cytoscape software. A total of 1594 metabolites were identified in myopic corneas. 321 metabolites were different among the three myopic groups, 106 metabolites were different between high myopic corneas and low myopic corneas, 104 metabolites were different between moderate myopic corneas and low myopic corneas, and 30 metabolic molecules overlapped among the three datasets. The multivariate linear regression analysis revealed the myopic degree was significantly influenced by the corneal levels of azelaic acid, arginine-proline (Arg-Pro), 1-stearoyl-2-myristoyl-sn-glycero-3-phosphocholine, and hypoxanthine. The ROC curve analysis showed that azelaic acid, Arg-Pro and hypoxanthine were effective in discriminating low myopia from moderate to high myopia with the area under the curve (AUC) values as 0.982, 0.991 and 0.982 for azelaic acid, Arg-Pro and hypoxanthine respectively. The network analysis suggested that Arg-Pro had the maximum connections among these three biomarkers. Thus, this study identified azelaic acid, Arg-Pro and hypoxanthine as corneal biomarkers to discriminate low myopia from moderate to high myopia, with Arg-Pro serving as the hub biomarker for moderate and high myopia.
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Affiliation(s)
- Wenjing Wu
- Beijing Tongren Eye Center, Beijing Tongren Hospital of Capital Medical University, No. 1, Dongjiaomin Lane, Dongcheng District, Beijing, 100730, China
| | - Yanzheng Song
- Beijing Tongren Eye Center, Beijing Tongren Hospital of Capital Medical University, No. 1, Dongjiaomin Lane, Dongcheng District, Beijing, 100730, China
| | - Mingshen Sun
- Beijing Tongren Eye Center, Beijing Tongren Hospital of Capital Medical University, No. 1, Dongjiaomin Lane, Dongcheng District, Beijing, 100730, China
| | - Yu Li
- Beijing Tongren Eye Center, Beijing Tongren Hospital of Capital Medical University, No. 1, Dongjiaomin Lane, Dongcheng District, Beijing, 100730, China
| | - Yushan Xu
- Beijing Tongren Eye Center, Beijing Tongren Hospital of Capital Medical University, No. 1, Dongjiaomin Lane, Dongcheng District, Beijing, 100730, China
| | - Mengyao Xu
- Beijing Tongren Eye Center, Beijing Tongren Hospital of Capital Medical University, No. 1, Dongjiaomin Lane, Dongcheng District, Beijing, 100730, China
| | - Yuxin Yang
- Beijing Tongren Eye Center, Beijing Tongren Hospital of Capital Medical University, No. 1, Dongjiaomin Lane, Dongcheng District, Beijing, 100730, China
| | - Shiming Li
- Beijing Tongren Eye Center, Beijing Tongren Hospital of Capital Medical University, No. 1, Dongjiaomin Lane, Dongcheng District, Beijing, 100730, China
| | - Fengju Zhang
- Beijing Tongren Eye Center, Beijing Tongren Hospital of Capital Medical University, No. 1, Dongjiaomin Lane, Dongcheng District, Beijing, 100730, China.
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Wevers D, Ramautar R, Clark C, Hankemeier T, Ali A. Opportunities and challenges for sample preparation and enrichment in mass spectrometry for single-cell metabolomics. Electrophoresis 2023; 44:2000-2024. [PMID: 37667867 DOI: 10.1002/elps.202300105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 08/08/2023] [Accepted: 08/19/2023] [Indexed: 09/06/2023]
Abstract
Single-cell heterogeneity in metabolism, drug resistance and disease type poses the need for analytical techniques for single-cell analysis. As the metabolome provides the closest view of the status quo in the cell, studying the metabolome at single-cell resolution may unravel said heterogeneity. A challenge in single-cell metabolome analysis is that metabolites cannot be amplified, so one needs to deal with picolitre volumes and a wide range of analyte concentrations. Due to high sensitivity and resolution, MS is preferred in single-cell metabolomics. Large numbers of cells need to be analysed for proper statistics; this requires high-throughput analysis, and hence automation of the analytical workflow. Significant advances in (micro)sampling methods, CE and ion mobility spectrometry have been made, some of which have been applied in high-throughput analyses. Microfluidics has enabled an automation of cell picking and metabolite extraction; image recognition has enabled automated cell identification. Many techniques have been used for data analysis, varying from conventional techniques to novel combinations of advanced chemometric approaches. Steps have been set in making data more findable, accessible, interoperable and reusable, but significant opportunities for improvement remain. Herein, advances in single-cell analysis workflows and data analysis are discussed, and recommendations are made based on the experimental goal.
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Affiliation(s)
- Dirk Wevers
- Wageningen University and Research, Wageningen, The Netherlands
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden, The Netherlands
| | - Rawi Ramautar
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden, The Netherlands
| | - Charlie Clark
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden, The Netherlands
| | - Thomas Hankemeier
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden, The Netherlands
| | - Ahmed Ali
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden, The Netherlands
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Fadhilah F, Indrati AR, Dewi S, Santoso P. The Kynurenine/Tryptophan Ratio as a Promising Metabolomic Biomarker for Diagnosing the Spectrum of Tuberculosis Infection and Disease. Int J Gen Med 2023; 16:5587-5595. [PMID: 38045904 PMCID: PMC10693202 DOI: 10.2147/ijgm.s438364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Accepted: 11/11/2023] [Indexed: 12/05/2023] Open
Abstract
The metabolic system and immunology used to be seen as distinct fields of study. Recent developments in our understanding of how the immune system operates in health and disease have connected these fields to complex systems. An effective technique for identifying probable abnormalities of metabolic homeostasis brought on by disease is metabolomics, which is defined as the thorough study of small molecule metabolic intermediates within a biological system that collectively make up the metabolome. A prognostic metabolic biomarker with adequate prognostic accuracy for tuberculosis progression has recently been created. The rate-limiting host enzyme for the conversion of tryptophan to kynurenine, indoleamine 2,3-dioxygenase (IDO), is greatly elevated in the lungs of tuberculosis disease patients. Targeted study on tryptophan in tuberculosis disease indicates that such decreases may also resembled this upregulation. Although tuberculosis diagnosis has improved with the use of interferon release assay and tuberculosis nucleic acid amplification, tuberculosis control is made difficult by the lack of a biomarker to diagnose active tuberculosis disease. We hope that the reader of this work can develop an understanding of the advantages of metabolomics testing, particularly as a sort of testing that can be used for both diagnosing and monitoring a patient's response to treatment for tuberculosis.
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Affiliation(s)
- Fitri Fadhilah
- Doctorate in Medicine Program, Faculty of Medicine, Universitas Padjadjaran, Bandung, West Java, Indonesia
| | - Agnes Rengga Indrati
- Clinical Pathology Department, Hasan Sadikin General Hospital, Faculty of Medicine, Universitas Padjadjaran, Bandung, West Java, Indonesia
| | - Sumartini Dewi
- Internal Medicine Department, Hasan Sadikin General Hospital, Faculty of Medicine, Universitas Padjadjaran, Bandung, West Java, Indonesia
| | - Prayudi Santoso
- Internal Medicine Department, Hasan Sadikin General Hospital, Faculty of Medicine, Universitas Padjadjaran, Bandung, West Java, Indonesia
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Lekka P, Fragopoulou E, Terpou A, Dasenaki M. Exploring Human Metabolome after Wine Intake-A Review. Molecules 2023; 28:7616. [PMID: 38005338 PMCID: PMC10673339 DOI: 10.3390/molecules28227616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 10/21/2023] [Accepted: 10/24/2023] [Indexed: 11/26/2023] Open
Abstract
Wine has a rich history dating back to 2200 BC, originally recognized for its medicinal properties. Today, with the aid of advanced technologies like metabolomics and sophisticated analytical techniques, we have gained remarkable insights into the molecular-level changes induced by wine consumption in the human organism. This review embarks on a comprehensive exploration of the alterations in human metabolome associated with wine consumption. A great number of 51 studies from the last 25 years were reviewed; these studies systematically investigated shifts in metabolic profiles within blood, urine, and feces samples, encompassing both short-term and long-term studies of the consumption of wine and wine derivatives. Significant metabolic alterations were observed in a wide variety of metabolites belonging to different compound classes, such as phenolic compounds, lipids, organic acids, and amino acids, among others. Within these classes, both endogenous metabolites as well as diet-related metabolites that exhibited up-regulation or down-regulation following wine consumption were included. The up-regulation of short-chain fatty acids and the down-regulation of sphingomyelins after wine intake, as well as the up-regulation of gut microbial fermentation metabolites like vanillic and syringic acid are some of the most important findings reported in the reviewed literature. Our results confirm the intact passage of certain wine compounds, such as tartaric acid and other wine acids, to the human organism. In an era where the health effects of wine consumption are of growing interest, this review offers a holistic perspective on the metabolic underpinnings of this centuries-old tradition.
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Affiliation(s)
- Pelagia Lekka
- Food Chemistry Laboratory, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zographou, 15771 Athens, Greece;
| | - Elizabeth Fragopoulou
- School of Health Science and Education, Department of Nutrition and Dietetics, Harokopio University, 17671 Athens, Greece;
| | - Antonia Terpou
- Department of Agricultural Development, Agrofood and Management of Natural Resources, School of Agricultural Development, Nutrition & Sustainability, National and Kapodistrian University of Athens, 34400 Psachna, Greece;
| | - Marilena Dasenaki
- Food Chemistry Laboratory, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zographou, 15771 Athens, Greece;
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Yu C, Zheng HH, Zhang YZ, Du CT, Xie GH. Identification of canine mammary tumor-associated metabolites using untargeted metabolomics. Theriogenology 2023; 211:84-96. [PMID: 37603937 DOI: 10.1016/j.theriogenology.2023.08.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 08/15/2023] [Accepted: 08/15/2023] [Indexed: 08/23/2023]
Abstract
The canine mammary tumor is the most common tumor type in female dogs and seriously threatens their life. Currently, no effective treatments are available for this condition. Hence, it is essential to identify biomarkers that positively influence the early diagnosis and treatment and prognosis of this disease. To provide a basis for early diagnosis of canine breast tumors, in this study, 23 dogs with mammary tumors were identified via histopathological examination combined with ancillary diagnoses via blood examinations and diagnostic imaging. The canine mammary tumor and tumor-adjacent healthy tissues were collected, and their metabolites were identified utilizing a UHPLC-qTOF-MS-based untargeted metabolomics approach. The metabolic results revealed a total of 979 ion features in the positive polarity mode and 371 ion features in the negative polarity mode in the tissues of two groups; among them, 536 differential metabolites (385 in the positive and 151 in the negative polarity mode) were analyzed by PCA and PLS-DA. Subsequently, the enrichment pathways purine metabolism, alpha-linolenic acid metabolism, vitamin B6 metabolism, and fatty acid biosynthesis were analyzed using Metaboanalyst 4.0, which suggested that these pathways were valuable diagnostic and therapeutic targets. Moreover, the receiver operating characteristic curves further confirmed 13Z,16Z-docosadienoic acid, 23-nordeoxycholic acid, and (±)12(13)-DiHOME as expected candidate biomarkers of canine mammary tumors. In conclusion, the discovery of tumor biomarkers based on untargeted metabolomics is informative for pathological mechanism studies and facilitates the early diagnosis of canine mammary tumors.
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Affiliation(s)
- Chao Yu
- College of Veterinary Medicine, Jilin University, Changchun, 130062, China; State Key Laboratory for Zoonotic Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, 130062, Changchun, China
| | - Hui-Hua Zheng
- College of Veterinary Medicine, Jilin University, Changchun, 130062, China; College of Animal Science and Technology and College of Veterinary Medicine of Zhejiang A&F University, 666 Wusu Street, Lin'an District, Hangzhou, Zhejiang, 311300, China
| | - Yu-Zhu Zhang
- College of Veterinary Medicine, Jilin University, Changchun, 130062, China; State Key Laboratory for Zoonotic Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, 130062, Changchun, China
| | - Chong-Tao Du
- College of Veterinary Medicine, Jilin University, Changchun, 130062, China; State Key Laboratory for Zoonotic Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, 130062, Changchun, China.
| | - Guang-Hong Xie
- College of Veterinary Medicine, Jilin University, Changchun, 130062, China; State Key Laboratory for Zoonotic Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, 130062, Changchun, China.
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Zhan Y, Wang H, Wu Z, Zeng Z. Study on the Common Molecular Mechanism of Metabolic Acidosis and Myocardial Damage Complicated by Neonatal Pneumonia. Metabolites 2023; 13:1118. [PMID: 37999214 PMCID: PMC10673214 DOI: 10.3390/metabo13111118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 10/09/2023] [Accepted: 10/11/2023] [Indexed: 11/25/2023] Open
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 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.
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Affiliation(s)
- Yifei Zhan
- College of Environmental and Chemical Engineering, Dalian University, Dalian 116622, China;
| | - Huaiyan Wang
- Department of Neonatology, Changzhou Medical Center, Changzhou Maternity and Child Health Care Hospital, Nanjing Medical University, Changzhou 213000, China;
| | - Zeying Wu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China
- School of Chemical Engineering and Material Sciences, Changzhou Institute of Technology, Changzhou 213032, China
| | - Zhongda Zeng
- College of Environmental and Chemical Engineering, Dalian University, Dalian 116622, China;
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Kajtazi A, Russo G, Wicht K, Eghbali H, Lynen F. Facilitating structural elucidation of small environmental solutes in RPLC-HRMS by retention index prediction. CHEMOSPHERE 2023; 337:139361. [PMID: 37392796 DOI: 10.1016/j.chemosphere.2023.139361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 06/06/2023] [Accepted: 06/26/2023] [Indexed: 07/03/2023]
Abstract
Implementing effective environmental management strategies requires a comprehensive understanding of the chemical composition of environmental pollutants, particularly in complex mixtures. Utilizing innovative analytical techniques, such as high-resolution mass spectrometry and predictive retention index models, can provide valuable insights into the molecular structures of environmental contaminants. Liquid Chromatography-High-Resolution Mass Spectrometry is a powerful tool for the identification of isomeric structures in complex samples. However, there are some limitations that can prevent accurate isomeric structure identification, particularly in cases where the isomers have similar mass and fragmentation patterns. Liquid chromatographic retention, determined by the size, shape, and polarity of the analyte and its interactions with the stationary phase, contains valuable 3D structural information that is vastly underutilized. Therefore, a predictive retention index model is developed which is transferrable to LC-HRMS systems and can assist in the structural elucidation of unknowns. The approach is currently restricted to carbon, hydrogen, and oxygen-based molecules <500 g mol-1. The methodology facilitates the acceptance of accurate structural formulas and the exclusion of erroneous hypothetical structural representations by leveraging retention time estimations, thereby providing a permissible tolerance range for a given elemental composition and experimental retention time. This approach serves as a proof of concept for the development of a Quantitative Structure-Retention Relationship model using a generic gradient LC approach. The use of a widely used reversed-phase (U)HPLC column and a relatively large set of training (101) and test compounds (14) demonstrates the feasibility and potential applicability of this approach for predicting the retention behaviour of compounds in complex mixtures. By providing a standard operating procedure, this approach can be easily replicated and applied to various analytical challenges, further supporting its potential for broader implementation.
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Affiliation(s)
- Ardiana Kajtazi
- Separation Science Group, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281 S4bis, B-9000 Ghent, Belgium
| | - Giacomo Russo
- School of Applied Sciences, Sighthill Campus, Edinburgh Napier University, 9 Sighthill Ct, EH11 4BN, Edinburgh, United Kingdom
| | - Kristina Wicht
- Separation Science Group, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281 S4bis, B-9000 Ghent, Belgium
| | - Hamed Eghbali
- Packaging and Specialty Plastics R&D, Dow Benelux B.V., Terneuzen, 4530 AA, the Netherlands
| | - Frédéric Lynen
- Separation Science Group, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281 S4bis, B-9000 Ghent, Belgium.
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Chen H, Zhou H, Liang Y, Huang Z, Yang S, Wang X, She Z, Wei Z, Zhang Q. UHPLC-HRMS-based serum untargeted lipidomics: Phosphatidylcholines and sphingomyelins are the main disturbed lipid markers to distinguish colorectal advanced adenoma from cancer. J Pharm Biomed Anal 2023; 234:115582. [PMID: 37473505 DOI: 10.1016/j.jpba.2023.115582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 07/02/2023] [Accepted: 07/12/2023] [Indexed: 07/22/2023]
Abstract
Colorectal advanced adenoma (CAA) is a key precancerous lesion of colorectal cancer (CRC), and early diagnosis can lessen CRC morbidity and mortality. Although abnormal lipid metabolism is associated with the development of CRC, there are no studies on the biomarkers and mechanism of lipid metabolism linked to CAA carcinogenesis. Hence, we performed a lipidomics study of serum samples from 46 CAA, and 50 CRC patients by the ultra high-performance liquid chromatography tandem high resolution mass spectrometry (UHPLC-HRMS) in both electrospray ionization (ESI) modes. Differential lipids were selected by univariate and multivariate statistics analysis, and their diagnostic performance was evaluated using a receiver operating characteristic curve (ROC) analysis. Combining P < 0.05 and variable importance in projection (VIP) > 1, 59 differential lipids were obtained totally. Ten of them showed good discriminant ability for CAA and CRC (AUC > 0.900). Especially, the lipid panel consisting of PC 44:5, PC 35:6e, and SM d40:3 showed the highest selection frequency and outperformed (AUC = 0.952). Additionally, phosphatidylcholine (PC) and sphingomyelin (SM) were the main differential and high-performance lipids. In short, this is the first study to explore the biomarkers and mechanism for CAA-CRC sequence with large-scale serum lipidomics. The findings should provide valuable reference and new clues for the development of diagnostic and therapeutic strategies of CRC.
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Affiliation(s)
- Hongwei Chen
- Medical College, Guangxi University, Nanning, Guangxi 530004, PR China
| | - Hailin Zhou
- Medical College, Guangxi University, Nanning, Guangxi 530004, PR China
| | - Yunxiao Liang
- Department of Gastroenterology, People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, Guangxi 530021, PR China
| | - Zongsheng Huang
- Department of Gastroenterology, People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, Guangxi 530021, PR China
| | - Shanyi Yang
- Medical College, Guangxi University, Nanning, Guangxi 530004, PR China
| | - Xuancheng Wang
- Medical College, Guangxi University, Nanning, Guangxi 530004, PR China
| | - Zhiyong She
- Medical College, Guangxi University, Nanning, Guangxi 530004, PR China
| | - Zhijuan Wei
- Medical College, Guangxi University, Nanning, Guangxi 530004, PR China
| | - Qisong Zhang
- Medical College, Guangxi University, Nanning, Guangxi 530004, PR China; Hubei Provincial Key Laboratory of Occurrence and Intervention of Rheumatic Diseases, Hubei Minzu University, Enshi, Hubei 44500, PR China; Center for Instrumental Analysis, Guangxi University, Nanning, Guangxi 530004, PR China.
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40
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Hao JD, Chen YY, Wang YZ, An N, Bai PR, Zhu QF, Feng YQ. Novel Peak Shift Correction Method Based on the Retention Index for Peak Alignment in Untargeted Metabolomics. Anal Chem 2023; 95:13330-13337. [PMID: 37609864 DOI: 10.1021/acs.analchem.3c02583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Peak alignment is a crucial step in liquid chromatography-mass spectrometry (LC-MS)-based large-scale untargeted metabolomics workflows, as it enables the integration of metabolite peaks across multiple samples, which is essential for accurate data interpretation. Slight differences or fluctuations in chromatographic separation conditions, however, can cause the chromatographic retention time (RT) shift between consecutive analyses, ultimately affecting the accuracy of peak alignment between samples. Here, we introduce a novel RT shift correction method based on the retention index (RI) and apply it to peak alignment. We synthesized a series of N-acyl glycine (C2-C23) homologues via the amidation reaction between glycine with normal saturated fatty acids (C2-C23) as calibrants able to respond proficiently in both mass spectrometric positive- and negative-ion modes. Using these calibrants, we established an N-acyl glycine RI system. This RI system is capable of covering a broad chromatographic space and addressing chromatographic RT shift caused by variations in flow rate, gradient elution, instrument systems, and LC separation columns. Moreover, based on the RI system, we developed a peak shift correction model to enhance peak alignment accuracy. Applying the model resulted in a significant improvement in the accuracy of peak alignment from 15.5 to 80.9% across long-term data spanning a period of 157 days. To facilitate practical application, we developed a Python-based program, which is freely available at https://github.com/WHU-Fenglab/RI-based-CPSC.
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Affiliation(s)
- Jun-Di Hao
- Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Yao-Yu Chen
- Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Yan-Zhen Wang
- Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Na An
- Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Pei-Rong Bai
- Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Quan-Fei Zhu
- School of Public Health, Wuhan University, Wuhan 430071, China
| | - Yu-Qi Feng
- Department of Chemistry, Wuhan University, Wuhan 430072, China
- Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan 430071, China
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41
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Luo Y, Huang Y, Deng L, Li Z, Li C. Metabolomic Profiling of Female Mink Serum during Early to Mid-Pregnancy to Reveal Metabolite Changes. Genes (Basel) 2023; 14:1759. [PMID: 37761899 PMCID: PMC10531253 DOI: 10.3390/genes14091759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 08/29/2023] [Accepted: 08/29/2023] [Indexed: 09/29/2023] Open
Abstract
Mink embryos enter a period of diapause after the embryo develops into the blastocyst, and its reactivation is mainly caused by an increase in polyamine. The specific process of embryo diapause regulation and reactivation remains largely unexamined. This study aimed to identify changes in metabolites in the early pregnancy of mink by comparing and analyzing in serum metabolites up to twenty-nine days after mating. Blood samples were taken on the first day of mating, once a week until the fifth week. Metabolomic profiles of the serum samples taken during this period were analyzed by ultra-performance liquid chromatography/mass spectrometry. Multivariate statistical analyses identified differential metabolite expression at different time points in both positive and negative ion modes. The levels of dopamine, tyramine, L-phenylalanine, L-tyrosine, tyrosine, L-kynurenine, L-lysine, L-arginine, D-ornithine, and leucine changed significantly. These metabolites may be associated with the process of embryo diapause and subsequent reactivation.
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Affiliation(s)
| | | | | | | | - Chunjin Li
- College of Animal Science, Jilin University, Changchun 130062, China; (Y.L.); (Y.H.); (L.D.); (Z.L.)
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42
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Jin Y, Chi J, LoMonaco K, Boon A, Gu H. Recent Review on Selected Xenobiotics and Their Impacts on Gut Microbiome and Metabolome. Trends Analyt Chem 2023; 166:117155. [PMID: 37484879 PMCID: PMC10361410 DOI: 10.1016/j.trac.2023.117155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
As it is well known, the gut is one of the primary sites in any host for xenobiotics, and the many microbial metabolites responsible for the interactions between the gut microbiome and the host. However, there is a growing concern about the negative impacts on human health induced by toxic xenobiotics. Metabolomics, broadly including lipidomics, is an emerging approach to studying thousands of metabolites in parallel. In this review, we summarized recent advancements in mass spectrometry (MS) technologies in metabolomics. In addition, we reviewed recent applications of MS-based metabolomics for the investigation of toxic effects of xenobiotics on microbial and host metabolism. It was demonstrated that metabolomics, gut microbiome profiling, and their combination have a high potential to identify metabolic and microbial markers of xenobiotic exposure and determine its mechanism. Further, there is increasing evidence supporting that reprogramming the gut microbiome could be a promising approach to the intervention of xenobiotic toxicity.
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Affiliation(s)
- Yan Jin
- Center for Translational Science, Florida International University, Port St. Lucie, FL 34987, USA
| | - Jinhua Chi
- Center for Translational Science, Florida International University, Port St. Lucie, FL 34987, USA
| | - Kaelene LoMonaco
- Center for Translational Science, Florida International University, Port St. Lucie, FL 34987, USA
| | - Alexandria Boon
- Center for Translational Science, Florida International University, Port St. Lucie, FL 34987, USA
| | - Haiwei Gu
- Center for Translational Science, Florida International University, Port St. Lucie, FL 34987, USA
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43
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Kartowikromo KY, Olajide OE, Hamid AM. Collision cross section measurement and prediction methods in omics. JOURNAL OF MASS SPECTROMETRY : JMS 2023; 58:e4973. [PMID: 37620034 PMCID: PMC10530098 DOI: 10.1002/jms.4973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/26/2023] [Accepted: 07/20/2023] [Indexed: 08/26/2023]
Abstract
Omics studies such as metabolomics, lipidomics, and proteomics have become important for understanding the mechanisms in living organisms. However, the compounds detected are structurally different and contain isomers, with each structure or isomer leading to a different result in terms of the role they play in the cell or tissue in the organism. Therefore, it is important to detect, characterize, and elucidate the structures of these compounds. Liquid chromatography and mass spectrometry have been utilized for decades in the structure elucidation of key compounds. While prediction models of parameters (such as retention time and fragmentation pattern) have also been developed for these separation techniques, they have some limitations. Moreover, ion mobility has become one of the most promising techniques to give a fingerprint to these compounds by determining their collision cross section (CCS) values, which reflect their shape and size. Obtaining accurate CCS enables its use as a filter for potential analyte structures. These CCS values can be measured experimentally using calibrant-independent and calibrant-dependent approaches. Identification of compounds based on experimental CCS values in untargeted analysis typically requires CCS references from standards, which are currently limited and, if available, would require a large amount of time for experimental measurements. Therefore, researchers use theoretical tools to predict CCS values for untargeted and targeted analysis. In this review, an overview of the different methods for the experimental and theoretical estimation of CCS values is given where theoretical prediction tools include computational and machine modeling type approaches. Moreover, the limitations of the current experimental and theoretical approaches and their potential mitigation methods were discussed.
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Affiliation(s)
| | - Orobola E Olajide
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama, USA
| | - Ahmed M Hamid
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama, USA
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Zhang Y, Liao J, Le W, Wu G, Zhang W. Improving the Data Quality of Untargeted Metabolomics through a Targeted Data-Dependent Acquisition Based on an Inclusion List of Differential and Preidentified Ions. Anal Chem 2023; 95:12964-12973. [PMID: 37594469 DOI: 10.1021/acs.analchem.3c02888] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/19/2023]
Abstract
Metabolomics based on high-resolution mass spectrometry has become a powerful technique in biomedical research. The development of various analytical tools and online libraries has promoted the identification of biomarkers. However, how to make mass spectrometry collect more data information is an important but underestimated research topic. Herein, we combined full-scan and data-dependent acquisition (DDA) modes to develop a new targeted DDA based on the inclusion list of differential and preidentified ions (dpDDA). In this workflow, the MS1 datasets for statistical analysis and metabolite preidentification were first obtained using full-scan, and then, the MS/MS datasets for metabolite identification were obtained using targeted DDA of quality control samples based on the inclusion list. Compared with the current methods (DDA, data-independent acquisition, targeted DDA with time-staggered precursor ion list, and iterative exclusion DDA), dpDDA showed better stability, higher characteristic ion coverage, higher differential metabolites' MS/MS coverage, and higher quality MS/MS spectra. Moreover, the same trend was verified in the analysis of large-scale clinical samples. More surprisingly, dpDDA can distinguish patients with different severities of coronary heart disease (CHD) based on the Canadian Cardiovascular Society angina classification, which we cannot distinguish through conventional metabolomics data collection. Finally, dpDDA was employed to differentiate CHD from healthy control, and targeted metabolomics confirmed that dpDDA could identify a more complete metabolic pathway network. At the same time, four unreported potential CHD biomarkers were identified, and the area under the receiver operating characteristic curve was greater than 0.85. These results showed that dpDDA would expand the discovery of biomarkers based on metabolomics, more comprehensively explore the key metabolites and their association with diseases, and promote the development of precision medicine.
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Affiliation(s)
- Yuhao Zhang
- School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, Jiangsu 211198, China
| | - Jingyu Liao
- School of Pharmacy, Guangdong Pharmaceutical University, Guangdong 510006, China
| | - Wanqi Le
- Institute of Interdisciplinary Medical Sciences, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Gaosong Wu
- Institute of Interdisciplinary Medical Sciences, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Weidong Zhang
- School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, Jiangsu 211198, China
- Institute of Interdisciplinary Medical Sciences, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
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45
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Koussiouris J, Looby N, Kulasingam V, Chandran V. A Solid-Phase Microextraction-Liquid Chromatography-Mass Spectrometry Method for Analyzing Serum Lipids in Psoriatic Disease. Metabolites 2023; 13:963. [PMID: 37623906 PMCID: PMC10456752 DOI: 10.3390/metabo13080963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 08/16/2023] [Accepted: 08/18/2023] [Indexed: 08/26/2023] Open
Abstract
Approximately 25% of psoriasis patients have an inflammatory arthritis termed psoriatic arthritis (PsA). There is strong interest in identifying and validating biomarkers that can accurately and reliably predict conversion from psoriasis to PsA using novel technologies such as metabolomics. Lipids, in particular, are of key interest in psoriatic disease. We sought to develop a liquid chromatography-mass spectrometry (LC-MS) method to be used in conjunction with solid-phase microextraction (SPME) for analyzing fatty acids and similar molecules. A total of 25 chromatographic methods based on published lipid studies were tested on two LC columns. As a proof of concept, serum samples from psoriatic disease patients (n = 27 psoriasis and n = 26 PsA) were processed using SPME and run on the selected LC-MS method. The method that was best for analyzing fatty acids and fatty acid-like molecules was optimized and applied to serum samples. A total of 18 tentatively annotated features classified as fatty acids and other lipid compounds were statistically significant between psoriasis and PsA groups using both multivariate and univariate approaches. The SPME-LC-MS method developed and optimized was capable of detecting fatty acids and similar lipids that may aid in differentiating psoriasis and PsA patients.
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Affiliation(s)
- John Koussiouris
- Schroeder Arthritis Institute, Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada; (J.K.); (N.L.)
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada;
| | - Nikita Looby
- Schroeder Arthritis Institute, Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada; (J.K.); (N.L.)
| | - Vathany Kulasingam
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada;
- Division of Clinical Biochemistry, Laboratory Medicine Program, University Health Network, Toronto, ON M5G 2C4, Canada
| | - Vinod Chandran
- Schroeder Arthritis Institute, Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada; (J.K.); (N.L.)
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada;
- Division of Rheumatology, Department of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON M5S 1A8, Canada
- Department of Medicine, Memorial University, St. John’s, NL A1B 3V6, Canada
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46
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Guo L, Jin H. Research progress of metabolomics in psoriasis. Chin Med J (Engl) 2023; 136:1805-1816. [PMID: 37106557 PMCID: PMC10406024 DOI: 10.1097/cm9.0000000000002504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Indexed: 04/29/2023] Open
Abstract
ABSTRACT Psoriasis is a chronic inflammatory skin disease with significant physical and psychological burdens. The interplay between the innate and adaptive immune systems is thought to contribute to the pathogenesis; however, the details of the pathogenesis remain unclear. In addition, reliable biomarkers for diagnosis, assessment of disease activity, and monitoring of therapeutic response are limited. Metabolomics is an emerging science that can be used to identify and analyze low molecular weight molecules in biological systems. During the past decade, metabolomics has been widely used in psoriasis research, and substantial progress has been made. This review summarizes and discusses studies that applied metabolomics to psoriatic disease. These studies have identified dysregulation of amino acids, carnitines, fatty acids, lipids, and carbohydrates in psoriasis. The results from these studies have advanced our understanding of: (1) the molecular mechanisms of psoriasis pathogenesis; (2) diagnosis of psoriasis and assessment of disease activity; (3) the mechanism of treatment and how to monitor treatment response; and (4) the link between psoriasis and comorbid diseases. We discuss common research strategies and progress in the application of metabolomics to psoriasis, as well as emerging trends and future directions.
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Affiliation(s)
- Lan Guo
- Department of Dermatology, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, National Clinical Research Center for Dermatologic and Immunologic Diseases, Beijing 100730, China
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Kao TJ, Lin CL, Yang WB, Li HY, Hsu TI. Dysregulated lipid metabolism in TMZ-resistant glioblastoma: pathways, proteins, metabolites and therapeutic opportunities. Lipids Health Dis 2023; 22:114. [PMID: 37537607 PMCID: PMC10398973 DOI: 10.1186/s12944-023-01881-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 07/26/2023] [Indexed: 08/05/2023] Open
Abstract
Glioblastoma (GBM) is a highly aggressive and lethal brain tumor with limited treatment options, such as the chemotherapeutic agent, temozolomide (TMZ). However, many GBM tumors develop resistance to TMZ, which is a major obstacle to effective therapy. Recently, dysregulated lipid metabolism has emerged as an important factor contributing to TMZ resistance in GBM. The dysregulation of lipid metabolism is a hallmark of cancer and alterations in lipid metabolism have been linked to multiple aspects of tumor biology, including proliferation, migration, and resistance to therapy. In this review, we aimed to summarize current knowledge on lipid metabolism in TMZ-resistant GBM, including key metabolites and proteins involved in lipid synthesis, uptake, and utilization, and recent advances in the application of metabolomics to study lipid metabolism in GBM. We also discussed the potential of lipid metabolism as a target for novel therapeutic interventions. Finally, we highlighted the challenges and opportunities associated with developing these interventions for clinical use, and the need for further research to fully understand the role of lipid metabolism in TMZ resistance in GBM. Our review suggests that targeting dysregulated lipid metabolism may be a promising approach to overcome TMZ resistance and improve outcomes in patients with GBM.
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Affiliation(s)
- Tzu-Jen Kao
- Ph.D. Program in Medical Neuroscience, College of Medical Science and Technology, Taipei Medical University and National Health Research Institutes, Taipei, 110, Taiwan
- International Master Program in Medical Neuroscience, College of Medical Science and Technology, Taipei Medical University, Taipei, 110, Taiwan
- TMU Research Center of Neuroscience, Taipei Medical University, Taipei, 110, Taiwan
| | | | - Wen-Bin Yang
- TMU Research Center of Neuroscience, Taipei Medical University, Taipei, 110, Taiwan
| | - Hao-Yi Li
- Department of Biochemistry, Ludwig-Maximilians-University, Munich, 81377, Germany
- Gene Center, Ludwig-Maximilians-University, Munich, 81377, Germany
| | - Tsung-I Hsu
- Ph.D. Program in Medical Neuroscience, College of Medical Science and Technology, Taipei Medical University and National Health Research Institutes, Taipei, 110, Taiwan.
- International Master Program in Medical Neuroscience, College of Medical Science and Technology, Taipei Medical University, Taipei, 110, Taiwan.
- TMU Research Center of Neuroscience, Taipei Medical University, Taipei, 110, Taiwan.
- TMU Research Center of Cancer Translational Medicine, Taipei, 110, Taiwan.
- Ph.D. Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical University, Taipei, 110, Taiwan.
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Chen C, Wang J, Pan D, Wang X, Xu Y, Yan J, Wang L, Yang X, Yang M, Liu G. Applications of multi-omics analysis in human diseases. MedComm (Beijing) 2023; 4:e315. [PMID: 37533767 PMCID: PMC10390758 DOI: 10.1002/mco2.315] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 05/25/2023] [Accepted: 05/31/2023] [Indexed: 08/04/2023] Open
Abstract
Multi-omics usually refers to the crossover application of multiple high-throughput screening technologies represented by genomics, transcriptomics, single-cell transcriptomics, proteomics and metabolomics, spatial transcriptomics, and so on, which play a great role in promoting the study of human diseases. Most of the current reviews focus on describing the development of multi-omics technologies, data integration, and application to a particular disease; however, few of them provide a comprehensive and systematic introduction of multi-omics. This review outlines the existing technical categories of multi-omics, cautions for experimental design, focuses on the integrated analysis methods of multi-omics, especially the approach of machine learning and deep learning in multi-omics data integration and the corresponding tools, and the application of multi-omics in medical researches (e.g., cancer, neurodegenerative diseases, aging, and drug target discovery) as well as the corresponding open-source analysis tools and databases, and finally, discusses the challenges and future directions of multi-omics integration and application in precision medicine. With the development of high-throughput technologies and data integration algorithms, as important directions of multi-omics for future disease research, single-cell multi-omics and spatial multi-omics also provided a detailed introduction. This review will provide important guidance for researchers, especially who are just entering into multi-omics medical research.
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Affiliation(s)
- Chongyang Chen
- Key Laboratory of Nuclear MedicineMinistry of HealthJiangsu Key Laboratory of Molecular Nuclear MedicineJiangsu Institute of Nuclear MedicineWuxiChina
- Co‐innovation Center of NeurodegenerationNantong UniversityNantongChina
| | - Jing Wang
- Shenzhen Key Laboratory of Modern ToxicologyShenzhen Medical Key Discipline of Health Toxicology (2020–2024)Shenzhen Center for Disease Control and PreventionShenzhenChina
| | - Donghui Pan
- Key Laboratory of Nuclear MedicineMinistry of HealthJiangsu Key Laboratory of Molecular Nuclear MedicineJiangsu Institute of Nuclear MedicineWuxiChina
| | - Xinyu Wang
- Key Laboratory of Nuclear MedicineMinistry of HealthJiangsu Key Laboratory of Molecular Nuclear MedicineJiangsu Institute of Nuclear MedicineWuxiChina
| | - Yuping Xu
- Key Laboratory of Nuclear MedicineMinistry of HealthJiangsu Key Laboratory of Molecular Nuclear MedicineJiangsu Institute of Nuclear MedicineWuxiChina
| | - Junjie Yan
- Key Laboratory of Nuclear MedicineMinistry of HealthJiangsu Key Laboratory of Molecular Nuclear MedicineJiangsu Institute of Nuclear MedicineWuxiChina
| | - Lizhen Wang
- Key Laboratory of Nuclear MedicineMinistry of HealthJiangsu Key Laboratory of Molecular Nuclear MedicineJiangsu Institute of Nuclear MedicineWuxiChina
| | - Xifei Yang
- Shenzhen Key Laboratory of Modern ToxicologyShenzhen Medical Key Discipline of Health Toxicology (2020–2024)Shenzhen Center for Disease Control and PreventionShenzhenChina
| | - Min Yang
- Key Laboratory of Nuclear MedicineMinistry of HealthJiangsu Key Laboratory of Molecular Nuclear MedicineJiangsu Institute of Nuclear MedicineWuxiChina
| | - Gong‐Ping Liu
- Co‐innovation Center of NeurodegenerationNantong UniversityNantongChina
- Department of PathophysiologySchool of Basic MedicineKey Laboratory of Ministry of Education of China and Hubei Province for Neurological DisordersTongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
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Xu L, Ge Q, Lu H, Zhuang Y, Geng X, Chen X, Liu X, Sun H, Guo Z, Sun J, Qi F, Niu X, Wang A, Sun W, He J. Cerebrospinal fluid metabolite alterations in patients with different etiologies, diagnoses, and prognoses of disorders of consciousness. Brain Behav 2023; 13:e3070. [PMID: 37421239 PMCID: PMC10454269 DOI: 10.1002/brb3.3070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 04/29/2023] [Accepted: 03/05/2023] [Indexed: 07/10/2023] Open
Abstract
INTRODUCTION Medical management of disorders of consciousness (DoC) is a growing issue imposing a major burden on families and societies. Recovery rates vary widely among patients with DoC, and recovery predictions strongly influence decisions on medical care. However, the specific mechanisms underlying different etiologies, consciousness levels, and prognoses are still unclear. METHODS We analyzed the comprehensive cerebrospinal fluid (CSF) metabolome through liquid chromatography-mass spectrometry. Metabolomic analyses were used to identify the metabolic differences between patients with different etiologies, diagnoses, and prognoses. RESULTS We found that the CSF levels of multiple acylcarnitines were lower in patients with traumatic DoC, suggesting mitochondrial function preservation in the CNS, which might contribute to the better consciousness outcomes of these patients. Metabolites related to glutamate and GABA metabolism were altered and showed a good ability to distinguish the patients in the minimally conscious state and the vegetative state. Moreover, we identified 8 phospholipids as potential biomarkers to predict the recovery of consciousness. CONCLUSIONS Our findings shed light on the differences in physiological activities underlying DoC with different etiologies and identified some potential biomarkers used for DoC diagnosis and prognosis.
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Affiliation(s)
- Long Xu
- Department of NeurosurgeryBeijing Tiantan HospitalCapital Medical UniversityBeijingChina
- Department of NeurosurgeryChina National Clinical Research Center for Neurological Diseases (NCRC‐ND)BeijingChina
| | - Qianqian Ge
- Department of NeurosurgeryBeijing Tiantan HospitalCapital Medical UniversityBeijingChina
| | - Hezhen Lu
- Department of clinical laboratoryChina‐Japan Union Hospital of Jilin UniversityChangchunChina
- Core Instrument Facility, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic MedicinePeking Union Medical CollegeBeijingChina
| | - Yutong Zhuang
- Department of NeurosurgeryBeijing Tiantan HospitalCapital Medical UniversityBeijingChina
| | - Xiaoli Geng
- Department of NeurosurgeryBeijing Tiantan HospitalCapital Medical UniversityBeijingChina
| | - Xueling Chen
- Department of NeurosurgeryBeijing Tiantan HospitalCapital Medical UniversityBeijingChina
| | - Xiaoyan Liu
- Core Instrument Facility, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic MedicinePeking Union Medical CollegeBeijingChina
| | - Haidan Sun
- Core Instrument Facility, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic MedicinePeking Union Medical CollegeBeijingChina
| | - Zhengguang Guo
- Core Instrument Facility, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic MedicinePeking Union Medical CollegeBeijingChina
| | - Jiameng Sun
- Core Instrument Facility, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic MedicinePeking Union Medical CollegeBeijingChina
| | - Feng Qi
- Core Instrument Facility, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic MedicinePeking Union Medical CollegeBeijingChina
| | - Xia Niu
- Core Instrument Facility, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic MedicinePeking Union Medical CollegeBeijingChina
| | - Aiwei Wang
- Core Instrument Facility, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic MedicinePeking Union Medical CollegeBeijingChina
| | - Wei Sun
- Core Instrument Facility, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic MedicinePeking Union Medical CollegeBeijingChina
| | - Jianghong He
- Department of NeurosurgeryBeijing Tiantan HospitalCapital Medical UniversityBeijingChina
- Department of NeurosurgeryChina National Clinical Research Center for Neurological Diseases (NCRC‐ND)BeijingChina
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Wang M, Zhang R, Zhang S, Zhou X, Song Y, Wang Q. Simultaneous quantitation of multiple myeloma related dietary metabolites in serum using HILIC-LC-MS/MS. Food Nutr Res 2023; 67:9135. [PMID: 37533448 PMCID: PMC10392861 DOI: 10.29219/fnr.v67.9135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 04/13/2023] [Accepted: 05/02/2023] [Indexed: 08/04/2023] Open
Abstract
Background Recent studies from targeted and untargeted metabolomics have consistently revealed that diet-related metabolites, including carnitine (C0), several species of acylcarnitines (AcyCNs), amino acids, ceramides, and lysophosphatidylcholines (LPCs) may serve as potential multiple myeloma (MM) biomarkers. However, most of these approaches had some intrinsic limitations, namely low reproducibility and compromising the accuracy of the results. Objective This study developed and validated a precise, efficient, and reliable liquid chromatography tandem mass spectrometric (LC-MS/MS) method for measuring these 28 metabolic risk factors in human serum. Design This method employed isopropanol to extract the metabolites from serum, gradient elution on a hydrophilic interaction liquid chromatographic column (HILIC) for chromatographic separation, and multiple reaction monitor (MRM) mode with positive electrospray ionization (ESI) for mass spectrometric detection. Results The correlation coefficients of linear response for this method were more than 0.9984. Analytical recoveries ranged from 91.3 to 106.3%, averaging 99.5%. The intra-run and total coefficients of variation were 1.1-5.9% and 2.0-9.6%, respectively. We have simultaneously determined the serological levels of C0, several subclasses of AcyCNs, amino acids, ceramides, and LPCs within 15 min for the first time. Conclusion The established LC-MS/MS method was accurate, sensitive, efficient, and could be valuable in providing insights into the association between diet patterns and MM disease and added value in further clinical research.
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Affiliation(s)
- Mo Wang
- Department of Clinical Laboratory, Beijing Chaoyang Hospital, Beijing Center for Clinical Laboratories, The Third Clinical Medical College of Capital Medical University, Beijing, P.R. China
| | - Rui Zhang
- Department of Clinical Laboratory, Beijing Chaoyang Hospital, Beijing Center for Clinical Laboratories, The Third Clinical Medical College of Capital Medical University, Beijing, P.R. China
| | - Shunli Zhang
- Department of Clinical Laboratory, Beijing Chaoyang Hospital, Beijing Center for Clinical Laboratories, The Third Clinical Medical College of Capital Medical University, Beijing, P.R. China
| | - Xiaojie Zhou
- Department of Clinical Laboratory, Beijing Chaoyang Hospital, The Third Clinical Medical College of Capital Medical University, Beijing, P.R. China
| | - Yichuan Song
- Department of Clinical Laboratory, Beijing Chaoyang Hospital, Capital Medical University, Beijing, P.R. China
| | - Qingtao Wang
- Department of Clinical Laboratory, Beijing Chaoyang Hospital, Beijing Center for Clinical Laboratories, The Third Clinical Medical College of Capital Medical University, Beijing, P.R. China
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