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Lin C, Tian Q, Guo S, Xie D, Cai Y, Wang Z, Chu H, Qiu S, Tang S, Zhang A. Metabolomics for Clinical Biomarker Discovery and Therapeutic Target Identification. Molecules 2024; 29:2198. [PMID: 38792060 PMCID: PMC11124072 DOI: 10.3390/molecules29102198] [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: 03/13/2024] [Revised: 04/10/2024] [Accepted: 04/25/2024] [Indexed: 05/26/2024] Open
Abstract
As links between genotype and phenotype, small-molecule metabolites are attractive biomarkers for disease diagnosis, prognosis, classification, drug screening and treatment, insight into understanding disease pathology and identifying potential targets. Metabolomics technology is crucial for discovering targets of small-molecule metabolites involved in disease phenotype. Mass spectrometry-based metabolomics has implemented in applications in various fields including target discovery, explanation of disease mechanisms and compound screening. It is used to analyze the physiological or pathological states of the organism by investigating the changes in endogenous small-molecule metabolites and associated metabolism from complex metabolic pathways in biological samples. The present review provides a critical update of high-throughput functional metabolomics techniques and diverse applications, and recommends the use of mass spectrometry-based metabolomics for discovering small-molecule metabolite signatures that provide valuable insights into metabolic targets. We also recommend using mass spectrometry-based metabolomics as a powerful tool for identifying and understanding metabolic patterns, metabolic targets and for efficacy evaluation of herbal medicine.
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Affiliation(s)
- Chunsheng Lin
- Graduate School and Second Affiliated Hospital, Heilongjiang University of Chinese Medicine, Harbin 150040, China; (C.L.); (S.G.); (Y.C.); (Z.W.)
| | - Qianqian Tian
- Faculty of Social Sciences, The University of Hong Kong, Hong Kong 999077, China;
| | - Sifan Guo
- Graduate School and Second Affiliated Hospital, Heilongjiang University of Chinese Medicine, Harbin 150040, China; (C.L.); (S.G.); (Y.C.); (Z.W.)
- International Advanced Functional Omics Platform, Scientific Experiment Center, International Joint Research Center on Traditional Chinese and Modern Medicine, Hainan Engineering Research Center for Biological Sample Resources of Major Diseases (First Affiliated Hospital of Hainan Medical University), Key Laboratory of Tropical Cardiovascular Diseases Research of Hainan Province, Hainan Medical University, Xueyuan Road 3, Haikou 571199, China; (D.X.); (S.Q.); (S.T.)
| | - Dandan Xie
- International Advanced Functional Omics Platform, Scientific Experiment Center, International Joint Research Center on Traditional Chinese and Modern Medicine, Hainan Engineering Research Center for Biological Sample Resources of Major Diseases (First Affiliated Hospital of Hainan Medical University), Key Laboratory of Tropical Cardiovascular Diseases Research of Hainan Province, Hainan Medical University, Xueyuan Road 3, Haikou 571199, China; (D.X.); (S.Q.); (S.T.)
| | - Ying Cai
- Graduate School and Second Affiliated Hospital, Heilongjiang University of Chinese Medicine, Harbin 150040, China; (C.L.); (S.G.); (Y.C.); (Z.W.)
- International Advanced Functional Omics Platform, Scientific Experiment Center, International Joint Research Center on Traditional Chinese and Modern Medicine, Hainan Engineering Research Center for Biological Sample Resources of Major Diseases (First Affiliated Hospital of Hainan Medical University), Key Laboratory of Tropical Cardiovascular Diseases Research of Hainan Province, Hainan Medical University, Xueyuan Road 3, Haikou 571199, China; (D.X.); (S.Q.); (S.T.)
| | - Zhibo Wang
- Graduate School and Second Affiliated Hospital, Heilongjiang University of Chinese Medicine, Harbin 150040, China; (C.L.); (S.G.); (Y.C.); (Z.W.)
- International Advanced Functional Omics Platform, Scientific Experiment Center, International Joint Research Center on Traditional Chinese and Modern Medicine, Hainan Engineering Research Center for Biological Sample Resources of Major Diseases (First Affiliated Hospital of Hainan Medical University), Key Laboratory of Tropical Cardiovascular Diseases Research of Hainan Province, Hainan Medical University, Xueyuan Road 3, Haikou 571199, China; (D.X.); (S.Q.); (S.T.)
| | - Hang Chu
- Department of Biomedical Sciences, Beijing City University, Beijing 100193, China;
| | - Shi Qiu
- International Advanced Functional Omics Platform, Scientific Experiment Center, International Joint Research Center on Traditional Chinese and Modern Medicine, Hainan Engineering Research Center for Biological Sample Resources of Major Diseases (First Affiliated Hospital of Hainan Medical University), Key Laboratory of Tropical Cardiovascular Diseases Research of Hainan Province, Hainan Medical University, Xueyuan Road 3, Haikou 571199, China; (D.X.); (S.Q.); (S.T.)
| | - Songqi Tang
- International Advanced Functional Omics Platform, Scientific Experiment Center, International Joint Research Center on Traditional Chinese and Modern Medicine, Hainan Engineering Research Center for Biological Sample Resources of Major Diseases (First Affiliated Hospital of Hainan Medical University), Key Laboratory of Tropical Cardiovascular Diseases Research of Hainan Province, Hainan Medical University, Xueyuan Road 3, Haikou 571199, China; (D.X.); (S.Q.); (S.T.)
| | - Aihua Zhang
- Graduate School and Second Affiliated Hospital, Heilongjiang University of Chinese Medicine, Harbin 150040, China; (C.L.); (S.G.); (Y.C.); (Z.W.)
- International Advanced Functional Omics Platform, Scientific Experiment Center, International Joint Research Center on Traditional Chinese and Modern Medicine, Hainan Engineering Research Center for Biological Sample Resources of Major Diseases (First Affiliated Hospital of Hainan Medical University), Key Laboratory of Tropical Cardiovascular Diseases Research of Hainan Province, Hainan Medical University, Xueyuan Road 3, Haikou 571199, China; (D.X.); (S.Q.); (S.T.)
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Yang Y, Zheng X, Lv H, Tang B, Zhong Y, Luo Q, Bi Y, Yang K, Zhong H, Chen H, Lu C. The causal relationship between serum metabolites and the risk of psoriasis: a Mendelian randomization and meta-analysis study. Front Immunol 2024; 15:1343301. [PMID: 38529280 PMCID: PMC10961426 DOI: 10.3389/fimmu.2024.1343301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 02/22/2024] [Indexed: 03/27/2024] Open
Abstract
Objective To explore the influence of serum metabolites on the risk of psoriasis. Methods In the initial stage, we applied Mendelian randomization to evaluate the association between 1,400 serum metabolites and the risk of psoriasis. Causal effects were primarily assessed through the Inverse-Variance Weighted method and Wald Ratio's odds ratios, and 95% confidence intervals. False Discovery Rate was used for multiple comparison corrections. Sensitivity analyses were conducted using Cochran's Q Test, MR-PRESSO. MR-Steiger Test was employed to check for reverse causality. In the validation stage, we sought other sources of psoriasis GWAS data to verify the initial results and used meta-analysis to combine the effect sizes to obtain robust causal relationships. In addition, we also conducted metabolic pathway enrichment analysis on known metabolites that have a causal relationship with the risk of psoriasis in both stages. Results In the initial stage, we identified 112 metabolites causally associated with psoriasis, including 32 metabolite ratios and 80 metabolites (69 known and 11 unknown). In the validation stage, 24 metabolites (16 known, 1 unknown, and 7 metabolite ratios) were confirmed to have a causal relationship with psoriasis onset. Meta-analysis results showed that the overall effect of combined metabolites was consistent with the main analysis in direction and robust in the causal relationship with psoriasis onset. Of the 16 known metabolites, most were attributed to lipid metabolism, with 5 as risk factors and 8 as protective factors for psoriasis. Peptidic metabolite Gamma-glutamylvaline levels had a negative causal relationship with psoriasis, while exogenous metabolite Catechol sulfate levels and amino acid 3-methylglutaconate levels had a positive causal relationship with the disease onset. The metabolites associated with psoriasis risk in the two stages are mainly enriched in the following metabolic pathways: Glutathione metabolism, Alpha Linolenic Acid and Linoleic Acid Metabolism, Biosynthesis of unsaturated fatty acids, Arachidonic acid metabolism, Glycerophospholipid metabolism. Conclusion Circulating metabolites may have a potential causal relationship with psoriasis risk, and targeting specific metabolites may benefit psoriasis diagnosis, disease assessment, and treatment.
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Affiliation(s)
- Yujie Yang
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xuwei Zheng
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Haiying Lv
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Bin Tang
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine (Guangdong Provincial Hospital of Chinese Medicine), Guangzhou, China
- Guangdong Provincial Key Laboratory of Clinical Research on Traditional Chinese Medicine Syndrome, Guangzhou, China
- Guangdong Provincial Clinical Medicine Research Center for Chinese Medicine Dermatology, Guangzhou, China
- Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yiyuan Zhong
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Qianqian Luo
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yang Bi
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Kexin Yang
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Haixin Zhong
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Haiming Chen
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine (Guangdong Provincial Hospital of Chinese Medicine), Guangzhou, China
- Guangdong Provincial Key Laboratory of Clinical Research on Traditional Chinese Medicine Syndrome, Guangzhou, China
- Guangdong Provincial Clinical Medicine Research Center for Chinese Medicine Dermatology, Guangzhou, China
- Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Chuanjian Lu
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine (Guangdong Provincial Hospital of Chinese Medicine), Guangzhou, China
- Guangdong Provincial Key Laboratory of Clinical Research on Traditional Chinese Medicine Syndrome, Guangzhou, China
- Guangdong Provincial Clinical Medicine Research Center for Chinese Medicine Dermatology, Guangzhou, China
- Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, Guangzhou University of Chinese Medicine, Guangzhou, China
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He K, Wang Z, Liu M, Du W, Yin T, Bai R, Duan Q, Wang Y, Lei H, Zheng Y. Exploring the Effect of Xiao-Chai-Hu Decoction on Treating Psoriasis Based on Network Pharmacology and Experiment Validation. Curr Pharm Des 2024; 30:215-229. [PMID: 38532341 DOI: 10.2174/0113816128288527240108110844] [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: 10/20/2023] [Accepted: 12/27/2023] [Indexed: 03/28/2024]
Abstract
BACKGROUND Psoriasis is a chronic, inflammatory and recurrent skin disease. Xiao-Chai-Hu Decoction (XCHD) has shown good effects against some inflammatory diseases and cancers. However, the pharmacological effect and mechanisms of XCHD on psoriasis are not yet clear. OBJECTIVE To uncover the effect and mechanisms of XCHD on psoriasis by integrating network pharmacology, molecular docking, and in vivo experiments. METHODS The active ingredients and corresponding targets of XCHD were screened through Traditional Chinese Medicine Systems Pharmacology Database and Analysis (TCMSP) and Traditional Chinese Medicine Integrated Database (TCMID). Differentially expressed genes (DEGs) of psoriasis were obtained from the gene expression omnibus (GEO) database. The XCHD-psoriasis intersection targets were obtained by intersecting XCHD targets, and DEGs were used to establish the "herb-active ingredient-target" network and Protein-Protein Interaction (PPI) Network. The hub targets were identified based on the PPI network by Cytoscape software. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis were performed next. Molecular docking was executed via AutoDockTools-1.5.6. Finally, in vivo experiments were carried out further to validate the therapeutic effects of XCHD on psoriasis. RESULTS 58 active components and 219 targets of XCHD were screened. 4 top-active components (quercetin, baicalein, wogonin and kaempferol) and 7 hub targets (IL1B, CXCL8, CCND1, FOS, MMP9, STAT1 and CCL2) were identified. GO and KEGG pathway enrichment analyses indicated that the TNF signaling pathway, IL-17 signaling pathway and several pathways were involved. Molecular docking results indicated that hub genes had a good affinity to the corresponding key compounds. In imiquimod (IMQ)-induced psoriasis mouse models, XCHD could significantly improve psoriasis-like skin lesions, downregulate KRT17 and Ki67, and inhibit inflammation cytokines and VEGF. CONCLUSION XCHD showed the therapeutic effect on psoriasis by regulating keratinocyte differentiation, and suppressing inflammation and angiogenesis, which provided a theoretical basis for further experiments and clinical research.
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Affiliation(s)
- Ke He
- Department of Dermatology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Ziyang Wang
- Department of Dermatology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Meng Liu
- Department of Dermatology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Wenqian Du
- Department of Dermatology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Tingyi Yin
- Department of Dermatology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Ruimin Bai
- Department of Dermatology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Qiqi Duan
- Department of Dermatology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Yuqian Wang
- Department of Dermatology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Hao Lei
- Department of Dermatology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Yan Zheng
- Department of Dermatology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
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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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Using a System Pharmacology Method to Search for the Potential Targets and Pathways of Yinqiaosan against COVID-19. JOURNAL OF HEALTHCARE ENGINEERING 2022; 2022:9248674. [PMID: 35340244 PMCID: PMC8941516 DOI: 10.1155/2022/9248674] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 01/04/2022] [Accepted: 02/09/2022] [Indexed: 12/12/2022]
Abstract
The first reported case of coronavirus disease 2019 (COVID-19) occurred in Wuhan, Hubei, China. Thereafter, it spread through China and worldwide in only a few months, reaching a pandemic level. It can cause severe respiratory illnesses such as pneumonia and lung failure. Since the onset of the disease, the rapid response and intervention of traditional Chinese medicine (TCM) have played a significant role in the effective control of the epidemic. Yinqiaosan (YQS) was used to treat COVID-19 pneumonia, with good curative effects. However, a systematic overview of its active compounds and the therapeutic mechanisms underlying its action has yet to be performed. The purpose of the current study is to explore the compounds and mechanism of YQS in treating COVID-19 pneumonia using system pharmacology. A system pharmacology method involving drug-likeness assessment, oral bioavailability forecasting, virtual docking, and network analysis was applied to estimate the active compounds, hub targets, and key pathways of YQS in the treatment of COVID-19 pneumonia. With this method, 117 active compounds were successfully identified in YQS, and 77 potential targets were obtained from the targets of 95 compounds and COVID-19 pneumonia. The results show that YQS may act in treating COVID-19 pneumonia and its complications (atherosclerosis and nephropathy) through Kaposi sarcoma-related herpesvirus infection and the AGE-RAGE signaling pathway in diabetic complications and pathways in cancer. We distinguished the hub molecular targets within pathways such as TNF, GAPDH, MAPK3, MAPK1, EGFR, CASP3, MAPK8, mTOR, IL-2, and MAPK14. Five of the more highly active compounds (acacetin, kaempferol, luteolin, naringenin, and quercetin) have anti-inflammatory and antioxidative properties. In summary, by introducing a systematic network pharmacology method, our research perfectly forecasts the active compounds, potential targets, and key pathways of YQS applied to COVID-19 and helps to comprehensively clarify its mechanism of action.
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