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Fu X, Luo ZX, Yin HH, Liu YN, Du XG, Cheng W, Liu JY. Metabolomics study reveals blood biomarkers for early diagnosis of chronic kidney disease and IgA nephropathy: A retrospective cross-sectional study. Clin Chim Acta 2024; 555:117815. [PMID: 38309556 DOI: 10.1016/j.cca.2024.117815] [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: 12/08/2023] [Revised: 01/10/2024] [Accepted: 01/29/2024] [Indexed: 02/05/2024]
Abstract
BACKGROUND AND AIMS Chronic kidney disease (CKD) causes low quality of life and alarming morbidity and mortality. The crucial to retard CKD progression is to diagnose early for timely treatment. IgA nephropathy (IgAN) is a typical CKD and the most common glomerulonephritis. Both CKD and IgAN lack accurate and sensitive blood biomarkers for early diagnosis. Here we report the potential of plasma biomarkers for early diagnosis of CKD and IgAN. MATERIALS AND METHODS Plasma levels of metabolites derived from tryptophan were quantified with an LC-MS/MS-based metabolomics for two cohorts. Based on the predictive probability of each metabolite, multivariate models including logistic regression and random forest were used to establish the early diagnostic biomarkers for CKD and IgAN. RESULTS The plasma melatonin diagnosed early CKD (stages Ⅰ-Ⅱ) with an accuracy exceeding 95%, and a panel of melatonin and tryptophan achieved a remarkable 100% accuracy in diagnosing early CKD. Furthermore, indole-3-lactic acid had an excellent ability to distinguish IgAN among CKD patients. Based on the CKD screening and IgAN diagnosis primarily contributed by melatonin and indole-3-lactic acid, early IgAN could be diagnosed with an accuracy of over 85%. CONCLUSIONS This study provides promising plasma biomarkers for early diagnosis of CKD and IgAN.
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Affiliation(s)
- Xian Fu
- CNTTI of the Institute of Life Sciences & Anesthesia Department of the Second Affiliated Hospital, Chongqing Medical University, Chongqing 400016, China; Basic Medicine Research and Innovation Center for Novel Target and Therapeutic Intervention, Ministry of Education, Chongqing 400016, China; College of Pharmacy, Chongqing Medical University, Chongqing 400016, China
| | - Zhi-Xiao Luo
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Hou-Hua Yin
- CNTTI of the Institute of Life Sciences & Anesthesia Department of the Second Affiliated Hospital, Chongqing Medical University, Chongqing 400016, China; Basic Medicine Research and Innovation Center for Novel Target and Therapeutic Intervention, Ministry of Education, Chongqing 400016, China
| | - Ya-Nan Liu
- CNTTI of the Institute of Life Sciences & Anesthesia Department of the Second Affiliated Hospital, Chongqing Medical University, Chongqing 400016, China; Basic Medicine Research and Innovation Center for Novel Target and Therapeutic Intervention, Ministry of Education, Chongqing 400016, China
| | - Xiao-Gang Du
- Department of Nephrology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China.
| | - Wei Cheng
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China.
| | - Jun-Yan Liu
- CNTTI of the Institute of Life Sciences & Anesthesia Department of the Second Affiliated Hospital, Chongqing Medical University, Chongqing 400016, China; Basic Medicine Research and Innovation Center for Novel Target and Therapeutic Intervention, Ministry of Education, Chongqing 400016, China; College of Pharmacy, Chongqing Medical University, Chongqing 400016, China.
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Wang L, Yu X, Li H, He D, Zeng S, Xiang Z. Cell and rat serum, urine and tissue metabolomics analysis elucidates the key pathway changes associated with chronic nephropathy and reveals the mechanism of action of rhein. Chin Med 2023; 18:158. [PMID: 38041193 PMCID: PMC10691122 DOI: 10.1186/s13020-023-00862-1] [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: 08/22/2023] [Accepted: 11/21/2023] [Indexed: 12/03/2023] Open
Abstract
BACKGROUND Rhein can significantly delay the progression of chronic nephropathy. However, its mechanism of action has not been adequately elaborated, which hinders its extensive clinical application. In this work, the effects of rhein on models of TGF-β-induced NRK-49F cellular fibrosis and rat renal ischemia-reperfusion fibrosis were evaluated using metabolomics and western blotting. METHODS The metabolic profiles of NRK-49F cells and rat urine, serum, and kidney tissues in the control, model, and rhein groups were investigated using UPLC-QTOF-MS. The levels of p-P65, p-IKK, p-AKT, p-P38, p-JNK and AP-1 in NRK-49F cells were measured using western blotting and immunofluorescence methods. Molecular docking and network pharmacology methods were employed to explore the relationship between the potential targets of rhein and key proteins in the NF-κB and MAPK signaling pathways. RESULTS Various potential metabolites, including sphingolipids, ceramides, phosphatidylcholine, and lysophosphatidylcholine,14-hydroxy-E4-neuroprostane E, and 5-HPETE, were present in the cell, tissue, urine, and serum samples; however, few metabolites matches exactly among the four type of biological samples. These differential metabolites can effectively differentiated between the control, model, and rhein groups. Pathway enrichment analysis of differential metabolites unveiled that sphingolipid metabolism, arachidonic acid metabolism, and glycerophospholipid metabolism were closely related to nephropathy. Phosphorylation levels of AKT, IKK, P65 and AP-1 in NRK-49F cells was reduced by rhein treatment. Network pharmacology and molecular docking showed that the potential targets of rhein might regulated the expression of MAPK and AKT in the NF-κB and MAPK signaling pathways. CONCLUSION In brief, rhein might delays the progression of chronic nephropathy via the metabolic pathways, NF-κB and MAPKs signaling pathways, which provides the foundation for its development and clinical application.
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Affiliation(s)
- Li Wang
- Department of Pharmaceutical Analysis and Drug Metabolism, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, People's Republic of China
- Medical School, Hangzhou City University, Hangzhou, 310015, China
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, 310015, China
| | - Xixi Yu
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, 325035, China
| | - Hongju Li
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Dahong He
- Medical School, Hangzhou City University, Hangzhou, 310015, China
| | - Su Zeng
- Department of Pharmaceutical Analysis and Drug Metabolism, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, People's Republic of China.
| | - Zheng Xiang
- Medical School, Hangzhou City University, Hangzhou, 310015, China.
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, 310015, China.
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Deng BQ, Li MY, Fu X, Luo Y, Qiao Q, Liu JY. Targeted Metabolomics Study of Human Plasma Revealed Activation of the Cytochrome P450 Epoxygenase/Epoxide Hydrolase Axis in Patients with IgA Nephropathy. J Proteome Res 2022; 21:2969-2978. [PMID: 36301320 DOI: 10.1021/acs.jproteome.2c00471] [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: 01/19/2023]
Abstract
IgA nephropathy (IgAN) is the most common primary glomerulonephritis and a leading cause of chronic kidney disease. The pathogenic mechanism of IgAN remains largely unknown and thus a specific therapeutic target is lacking. Here, we reported that the cytochrome P450 (CYP) epoxygenase/epoxide hydrolase (EH) axis was activated in the patients and is likely a therapeutic target for IgAN. Specifically, quantitative profiling of the plasma from IgAN patients and healthy controls revealed significant changes in plasma levels of CYP/EH-mediated lipid epoxides and diols. Subsequently, CYP2C8, CYP2C18, CYP2J2, EPHX1, and EPHX2 were found to be significantly increased in whole blood cells at mRNA levels from the IgAN patients when compared with those of healthy controls. Immunohistochemical analysis showed that all five CYPs and two EHs were upregulated in the kidney tissue from IgAN patients when compared with normative renal tissue, but the expression locations of the proteins were different with most of them. Treatment of HK-2 cells with IgA1 increased cell viability, compressed cell apoptosis, and increased the protein levels of CYP2C9, EPHX1, and EPHX2. All the results agreed that CYPs/EHs axis is likely the prophylactic and therapeutic target for IgAN, providing IgAN patients with a new intervention strategy.
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Affiliation(s)
- Bing-Qing Deng
- Division of Nephrology, Dushu Lake Hospital Affiliated to Soochow University, Soochow 215135, China
| | - Meng-Yuan Li
- Department of Nephrology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Xian Fu
- Center for Novel Target and Therapeutic Invention, Institute of Life Sciences, Chongqing Medical University, Chongqing 400016, China
| | - Ying Luo
- Department of Clinical Laboratory, Changning Maternity and Infant Health Hospital, East China Normal University, Shanghai 200050, China
| | - Qing Qiao
- Division of Nephrology, Dushu Lake Hospital Affiliated to Soochow University, Soochow 215135, China
| | - Jun-Yan Liu
- Center for Novel Target and Therapeutic Invention, Institute of Life Sciences, Chongqing Medical University, Chongqing 400016, China
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Hu D, Wu M, Chen G, Deng B, Yu H, Huang J, Luo Y, Li M, Zhao D, Liu J. Multiple techniques collectively reveal the attenuation of kidney injury by trimethylamine
N
‐oxide (TMAO) production manipulation. Br J Pharmacol 2022; 179:4344-4359. [PMID: 35428974 DOI: 10.1111/bph.15856] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 01/24/2022] [Accepted: 04/07/2022] [Indexed: 11/02/2022] Open
Affiliation(s)
- Da‐Yong Hu
- Division of Nephrology and Rheumatology Shanghai Tenth People’s Hospital
- Center for Nephrology & Metabolomics Tongji University School of Medicine
| | - Ming‐Yu Wu
- Division of Nephrology and Rheumatology Shanghai Tenth People’s Hospital
- Center for Nephrology & Metabolomics Tongji University School of Medicine
| | - Guang‐Qi Chen
- Division of Nephrology and Rheumatology Shanghai Tenth People’s Hospital
- Center for Nephrology & Metabolomics Tongji University School of Medicine
| | - Bing‐Qing Deng
- Division of Nephrology and Rheumatology Shanghai Tenth People’s Hospital
- Center for Nephrology & Metabolomics Tongji University School of Medicine
| | - Hai‐Bo Yu
- Division of Nephrology and Rheumatology Shanghai Tenth People’s Hospital
- Center for Nephrology & Metabolomics Tongji University School of Medicine
| | - Jian Huang
- Division of Nephrology and Rheumatology Shanghai Tenth People’s Hospital
- Center for Nephrology & Metabolomics Tongji University School of Medicine
| | - Ying Luo
- Division of Nephrology and Rheumatology Shanghai Tenth People’s Hospital
- Center for Nephrology & Metabolomics Tongji University School of Medicine
| | - Meng‐Yuan Li
- Division of Nephrology and Rheumatology Shanghai Tenth People’s Hospital
- Center for Nephrology & Metabolomics Tongji University School of Medicine
| | - Da‐Ke Zhao
- Division of Nephrology and Rheumatology Shanghai Tenth People’s Hospital
- Center for Nephrology & Metabolomics Tongji University School of Medicine
| | - Jun‐Yan Liu
- Division of Nephrology and Rheumatology Shanghai Tenth People’s Hospital
- Center for Nephrology & Metabolomics Tongji University School of Medicine
- Center for Novel Target and Therapeutic Intervention, Institute of Life Sciences Chongqing Medical University
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5
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Yang Q, Wang Y, Zhang Y, Li F, Xia W, Zhou Y, Qiu Y, Li H, Zhu F. NOREVA: enhanced normalization and evaluation of time-course and multi-class metabolomic data. Nucleic Acids Res 2020; 48:W436-W448. [PMID: 32324219 PMCID: PMC7319444 DOI: 10.1093/nar/gkaa258] [Citation(s) in RCA: 129] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 03/21/2020] [Accepted: 04/04/2020] [Indexed: 12/23/2022] Open
Abstract
Biological processes (like microbial growth & physiological response) are usually dynamic and require the monitoring of metabolic variation at different time-points. Moreover, there is clear shift from case-control (N=2) study to multi-class (N>2) problem in current metabolomics, which is crucial for revealing the mechanisms underlying certain physiological process, disease metastasis, etc. These time-course and multi-class metabolomics have attracted great attention, and data normalization is essential for removing unwanted biological/experimental variations in these studies. However, no tool (including NOREVA 1.0 focusing only on case-control studies) is available for effectively assessing the performance of normalization method on time-course/multi-class metabolomic data. Thus, NOREVA was updated to version 2.0 by (i) realizing normalization and evaluation of both time-course and multi-class metabolomic data, (ii) integrating 144 normalization methods of a recently proposed combination strategy and (iii) identifying the well-performing methods by comprehensively assessing the largest set of normalizations (168 in total, significantly larger than those 24 in NOREVA 1.0). The significance of this update was extensively validated by case studies on benchmark datasets. All in all, NOREVA 2.0 is distinguished for its capability in identifying well-performing normalization method(s) for time-course and multi-class metabolomics, which makes it an indispensable complement to other available tools. NOREVA can be accessed at https://idrblab.org/noreva/.
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Affiliation(s)
- Qingxia Yang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Yunxia Wang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ying Zhang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Fengcheng Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Weiqi Xia
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ying Zhou
- Zhejiang Provincial Key Laboratory for Drug Clinical Research and Evaluation & The First Affiliated Hospital, Zhejiang University, Hangzhou 310000, China
| | - Yunqing Qiu
- Zhejiang Provincial Key Laboratory for Drug Clinical Research and Evaluation & The First Affiliated Hospital, Zhejiang University, Hangzhou 310000, China
| | - Honglin Li
- School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Feng Zhu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
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6
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Gollasch B, Wu G, Dogan I, Rothe M, Gollasch M, Luft FC. Effects of hemodialysis on plasma oxylipins. Physiol Rep 2020; 8:e14447. [PMID: 32562348 PMCID: PMC7305238 DOI: 10.14814/phy2.14447] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 04/04/2020] [Accepted: 04/24/2020] [Indexed: 12/17/2022] Open
Abstract
Chronic kidney disease (CKD) is an important risk factor for cardiovascular and all‐cause mortality. Survival rates among end‐stage renal disease (ESRD) hemodialysis patients are poor and most deaths are related to cardiovascular disease. Oxylipins constitute a family of oxygenated natural products, formed from fatty acid by pathways involving at least one step of dioxygen‐dependent oxidation. They are derived from polyunsaturated fatty acids (PUFAs) by cyclooxygenase (COX) enzymes, by lipoxygenases (LOX) enzymes, or by cytochrome P450 epoxygenase. Oxylipins have physiological significance and some could be of regulatory importance. The effects of decreased renal function and dialysis treatment on oxylipin metabolism are unknown. We studied 15 healthy persons and 15 CKD patients undergoing regular hemodialysis treatments and measured oxylipins (HPLC‐MS lipidomics) derived from cytochrome P450 (CYP) monooxygenase and lipoxygenase (LOX)/CYP ω/(ω‐1)‐hydroxylase pathways in circulating blood. We found that all four subclasses of CYP epoxy metabolites were increased after the dialysis treatment. Rather than resulting from altered soluble epoxide hydrolase (sEH) activity, the oxylipins were released and accumulated in the circulation. Furthermore, hemodialysis did not change the majority of LOX/CYP ω/(ω‐1)‐hydroxylase metabolites. Our data support the idea that oxylipin profiles discriminate ESRD patients from normal controls and are influenced by renal replacement therapies.
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Affiliation(s)
- Benjamin Gollasch
- Experimental and Clinical Research Center (ECRC), a joint institution between the Charité University Medicine and Max Delbrück Center (MDC) for Molecular Medicine, Berlin-Buch, Germany.,HELIOS Klinikum Berlin-Buch, Berlin, Germany
| | - Guanlin Wu
- Experimental and Clinical Research Center (ECRC), a joint institution between the Charité University Medicine and Max Delbrück Center (MDC) for Molecular Medicine, Berlin-Buch, Germany.,Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Association, Berlin, Germany
| | | | | | - Maik Gollasch
- Experimental and Clinical Research Center (ECRC), a joint institution between the Charité University Medicine and Max Delbrück Center (MDC) for Molecular Medicine, Berlin-Buch, Germany.,Department of Geriatrics, University of Greifswald, University District Hospital Wolgast, Greifswald, Germany
| | - Friedrich C Luft
- Experimental and Clinical Research Center (ECRC), a joint institution between the Charité University Medicine and Max Delbrück Center (MDC) for Molecular Medicine, Berlin-Buch, Germany
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Oxidized lipids in the metabolic profiling of neuroendocrine tumors - Analytical challenges and biological implications. J Chromatogr A 2020; 1625:461233. [PMID: 32709312 DOI: 10.1016/j.chroma.2020.461233] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/08/2020] [Accepted: 05/10/2020] [Indexed: 02/08/2023]
Abstract
Untargeted metabolomics can be a great tool for exploring new scientific areas; however, wrong metabolite annotation questions the credibility and puts the success of the entire research at risk. Therefore, an effort should be made to improve the quality and robustness of the annotation despite of the challenges, especially when final identification with standards is not possible. Through non-targeted analysis of human plasma samples, from a large cancer cohort study using RP-LC-ESI-QTOF-MS/MS, we have resolved MS/MS annotation through spectral matching, directed to hydroxyeicosatetraenoic acids (HETEs) and, MS/MS structural elucidation for newly annotated oxidized lyso-phosphatidylcholines (oxLPCs). The annotation of unknowns is supported with structural information from fragmentation spectra as well as the fragmentation mechanisms involved, necessarily including data from both polarity modes and different collision energies. In this work, we present evidences that various oxidation products show significant differences between cancer patients and control individuals and we establish a workflow to help identify such modifications. We report here the upregulation of HETEs and oxLPCs in patients with neuroendocrine tumors (NETs). To our knowledge, this is the first attempt to determine HETEs in NETs and one of very few studies where oxLPCs are annotated. The obtained results provide an important insight regarding lipid oxidation in NETs, although their physiological functions still have to be established and require further research.
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Liu JY. Inhibition of Soluble Epoxide Hydrolase for Renal Health. Front Pharmacol 2019; 9:1551. [PMID: 30687105 PMCID: PMC6335332 DOI: 10.3389/fphar.2018.01551] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Accepted: 12/19/2018] [Indexed: 12/31/2022] Open
Abstract
A soluble epoxide hydrolase (sEH) mediates the metabolism of epoxy fatty acids to form the corresponding vicinal diols, which are usually inactive or less active than the epoxide substrates. The sEH enzyme presents in many organs, including but not limited to the liver, heart, spleen, lung, and kidney. Here we summarized the changes in the expression and activity of sEH in multiple renal diseases, such as acute kidney injury (AKI), diabetic nephrology (DN), chronic kidney diseases (CKD), hypertension-mediated renal damage, and other renal dysfunctions. We also discussed the pharmacologic effects and the underlying mechanisms of sEH inhibition by using an inhibitor of sEH and/or the generic deletion of sEH on multiple renal diseases. We believe that sEH is a potential therapeutic target for renal dysfunction although the target disease needs further investigation.
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Affiliation(s)
- Jun-Yan Liu
- Center for Nephrology and Metabolomics, Tongji University School of Medicine, Shanghai, China
- Division of Nephrology, Shanghai Tenth Peoples Hospital, Tongji University School of Medicine, Shanghai, China
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