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Govender IS, Mokoena R, Stoychev S, Naicker P. Urine-HILIC: Automated Sample Preparation for Bottom-Up Urinary Proteome Profiling in Clinical Proteomics. Proteomes 2023; 11:29. [PMID: 37873871 PMCID: PMC10594433 DOI: 10.3390/proteomes11040029] [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: 07/31/2023] [Revised: 09/20/2023] [Accepted: 09/25/2023] [Indexed: 10/25/2023] Open
Abstract
Urine provides a diverse source of information related to a patient's health status and is ideal for clinical proteomics due to its ease of collection. To date, most methods for the preparation of urine samples lack the throughput required to analyze large clinical cohorts. To this end, we developed a novel workflow, urine-HILIC (uHLC), based on an on-bead protein capture, clean-up, and digestion without the need for bottleneck processing steps such as protein precipitation or centrifugation. The workflow was applied to an acute kidney injury (AKI) pilot study. Urine from clinical samples and a pooled sample was subjected to automated sample preparation in a KingFisher™ Flex magnetic handling station using the novel approach based on MagReSyn® HILIC microspheres. For benchmarking, the pooled sample was also prepared using a published protocol based on an on-membrane (OM) protein capture and digestion workflow. Peptides were analyzed by LCMS in data-independent acquisition (DIA) mode using a Dionex Ultimate 3000 UPLC coupled to a Sciex 5600 mass spectrometer. The data were searched in Spectronaut™ 17. Both workflows showed similar peptide and protein identifications in the pooled sample. The uHLC workflow was easier to set up and complete, having less hands-on time than the OM method, with fewer manual processing steps. Lower peptide and protein coefficient of variation was observed in the uHLC technical replicates. Following statistical analysis, candidate protein markers were filtered, at ≥8.35-fold change in abundance, ≥2 unique peptides and ≤1% false discovery rate, and revealed 121 significant, differentially abundant proteins, some of which have known associations with kidney injury. The pilot data derived using this novel workflow provide information on the urinary proteome of patients with AKI. Further exploration in a larger cohort using this novel high-throughput method is warranted.
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Affiliation(s)
- Ireshyn Selvan Govender
- NextGen Health, Council for Scientific and Industrial Research, Pretoria 0001, South Africa
- ReSyn Biosciences, Edenvale 1610, South Africa
| | - Rethabile Mokoena
- NextGen Health, Council for Scientific and Industrial Research, Pretoria 0001, South Africa
- School of Molecular and Cellular Biology, University of the Witwatersrand, Johannesburg 2193, South Africa
| | - Stoyan Stoychev
- NextGen Health, Council for Scientific and Industrial Research, Pretoria 0001, South Africa
- ReSyn Biosciences, Edenvale 1610, South Africa
| | - Previn Naicker
- NextGen Health, Council for Scientific and Industrial Research, Pretoria 0001, South Africa
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Cai H, Wang J, Luo Y, Wang F, He G, Zhou G, Peng X. Lindera aggregata intervents adenine-induced chronic kidney disease by mediating metabolism and TGF-β/Smad signaling pathway. Biomed Pharmacother 2020; 134:111098. [PMID: 33341058 DOI: 10.1016/j.biopha.2020.111098] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 11/30/2020] [Accepted: 12/02/2020] [Indexed: 12/28/2022] Open
Abstract
INTRODUCTION Lindera aggregata is a main Chinese herb of ancient prescriptions Suoquan pill applied for treating the chronic kidney disease (CKD). A large number of application histories of Lindera aggregata in the treatment of CKD have been recorded in Chinese traditional medical literature. The previous reports revealed that Lindera aggregata can treat CKD. METHODS Rats were randomly divided into control, model, Huangkui,Lindera aggregata ethanol extract (LEE) and Lindera aggregata water extract (LWE) groups. hematoxylin-eosin (HE) staining was used to detect the pathology of kidney. The levels of serum creatinine (Scr), serum Neutrophil gelatinase-associated lipocalin (NGAL), blood urea nitrogen (BUN), urine protein (UP), kidney index(KI) were evaluated. The UPLC - QTOF/MS were applied to probe the metabolic profile. Furthermore, Indoxyl sulfate-induced human renal tubular epithelial (HK-2) cell model was built to determine the expression levels of pathogenesis-related proteins. RESULTS The results demonstrated that LEE and LWE significantly inhibited the rebound in Scr, BUN, NGAL, UP and KI in models, except for the effect of LWE at low dose (LWE-L) and LEE at low dose (LEE-L) on KI and the effect of LWE-H at high dose (LWE-H) and LEE-L on BUN and NGAL. Moreover,Lindera aggregata extracts alleviated renal tubular dilatation, interstitial fibrosis and interstitial inflammation. By analysis, twenty-eight metabolites were related to CKD. After intervention of Lindera aggregata extracts, some metabolites approach to a normal-like level, such as Indoxyl sulfate. These metabolites are mainly involved in tryptophan, fatty acid, glycerophospholipid, tyrosine and arachidonic acid metabolic pathways. Furthermore, Lindera aggregata extracts mediate the expression of smad2, smad3, smad7 and TGF-β in Indoxyl sulfate-induced HK-2 cell. CONCLUSIONS Lindera aggregata extracts can mitigate adenine-induced CKD by modulating the metabolic profile and TGF-β/Smad signaling pathway, providing important supports for developing protective agent of Lindera aggregata for CKD.
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Affiliation(s)
- Hongdie Cai
- Zhejiang Pharmaceutical College, Ningbo 315100, PR China.
| | - Juan Wang
- Zhejiang Pharmaceutical College, Ningbo 315100, PR China.
| | - Yiyuan Luo
- Zhejiang Pharmaceutical College, Ningbo 315100, PR China.
| | - Furong Wang
- Zhejiang Pharmaceutical College, Ningbo 315100, PR China.
| | - Guoqing He
- Zhejiang Hongshiliang Group Tiantaishan Spicebush Root Co. Ltd, Taizhou 317200, PR China
| | - Gen Zhou
- Zhejiang Hongshiliang Group Tiantaishan Spicebush Root Co. Ltd, Taizhou 317200, PR China
| | - Xin Peng
- Ningbo Research Institute of Zhejiang University, No. 1, Qianhu South Road, Ningbo 315100, PR China.
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Abstract
The current unidimensional paradigm of kidney disease detection is incompatible with the complexity and heterogeneity of renal pathology. The diagnosis of kidney disease has largely focused on glomerular filtration, while assessment of kidney tubular health has notably been absent. Following insult, the kidney tubular cells undergo a cascade of cellular responses that result in the production and accumulation of low-molecular-weight proteins in the urine and systemic circulation. Modern advancements in molecular analysis and proteomics have allowed the identification and quantification of these proteins as biomarkers for assessing and characterizing kidney diseases. In this review, we highlight promising biomarkers of kidney tubular health that have strong underpinnings in the pathophysiology of kidney disease. These biomarkers have been applied to various specific clinical settings from the spectrum of acute to chronic kidney diseases, demonstrating the potential to improve patient care.
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Affiliation(s)
- William R Zhang
- Kidney Health Research Collaborative, University of California San Francisco School of Medicine, San Francisco, California 94121, USA
| | - Chirag R Parikh
- Division of Nephrology, Johns Hopkins School of Medicine, Baltimore, Maryland 21287, USA;
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Cai H, Su S, Li Y, Zeng H, Zhu Z, Guo J, Zhu Y, Guo S, Yu L, Qian D, Tang Y, Duan J. Protective effects of Salvia miltiorrhiza on adenine-induced chronic renal failure by regulating the metabolic profiling and modulating the NADPH oxidase/ROS/ERK and TGF-β/Smad signaling pathways. JOURNAL OF ETHNOPHARMACOLOGY 2018; 212:153-165. [PMID: 29032117 DOI: 10.1016/j.jep.2017.09.021] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 08/12/2017] [Accepted: 09/18/2017] [Indexed: 06/07/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Chronic renal failure (CRF) is defined as a progressive and irreversible loss of renal function and associated with inflammation and oxidative stress. Salvia miltiorrhiza (SM) is an important Chinese herb used in traditional Chinese medicine for treating cardiovascular diseases. The previous studies showed the SM exhibited significant protective effects on CRF. In this present study, the metabolic profiling changes and action mechanism of SM on CRF were explored. AIMS OF THE STUDY The aims of this study were to illustrate the metabolic profiling changes of adenine induced CRF and analyze the protective effects and action mechanisms of SM ethanol extract (SMEE) and water extract (SMWE). MATERIALS AND METHODS The animals were divided into normal group, CRF model group, Huangkui capsule-treated group, SMEE-treated group and SMWE-treated group. The UPLC-QTOFMS coupled with multivariate statistical methods were used to explore the changes of metabolic profile in plasma, urine and renal tissue from CRF rats simultaneously after treatment with SMEE and SMWE. Hematoxylin eosin (HE) staining and Masson staining were applied to observe pathological changes in renal tissue. Biochemical indicators including serum urea nitrogen (BUN), urine protein (UP) and serum creatinine (Scr) were measured according to the manufacturer's instructions of kits. Furthermore, HK-2 cell damaged model induced by ISF was established to access the protective effects and action mechanism. The dichlorodihydrofluorescein diacetate (DCFH-DA) assay was used to determine the reactive oxygen species (ROS) and Western blot was applied to analyze the expression of pathogenesis-related proteins in different groups. RESULTS The results showed that the ethanol extract (SMEE) and water extract (SMWE) of SM significantly inhibited the elevation of serum creatinine (Scr), blood urea nitrogen (BUN), urine protein (UP) and indoxyl sulfate (ISF) in adenine-induced CRF rats, especially SMEE exhibited more significant effects. Moreover, SM extracts obviously improved the symptoms of glomerular and tubular atrophy, focal calcium deposits, interstitial fibrosis, interstitial inflammation, and renal tissues. By metabolomics analysis, fifty-nine metabolites (thirteen in plasma, twenty-seven in urine and nineteen in kidney tissue) were up-regulated or down-regulated and contributed to CRF progress. After treatment of SM extracts, the altered metabolites were restored back to normal level. These potential biomarkers underpinning the metabolic pathways are including phenylalanine metabolism, pyrimidine metabolism, purine metabolism and tryptophan metabolism. Furthermore, SM extracts prevent epithelial-mesenchymal transition (EMT) of human renal tubular epithelial (HK-2) cell by inhibiting NADPH oxidase/ROS/ERK and TGF-β/Smad signaling pathways. CONCLUSIONS SMEE and SMWE can significantly alleviate adenine-induced CRF via regulation of the metabolic profiling and modulation of NADPH oxidase/ROS/ERK and TGF-β/Smad signaling pathways, which provided important supports for the development of protective agent of SM for CRF.
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Affiliation(s)
- Hongdie Cai
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, and Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, PR China; Zhejiang Pharmaceutical College, Ningbo 310053, PR China.
| | - Shulan Su
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, and Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, PR China.
| | - Yonghui Li
- Hainan Provincial Key Laboratory of R&D of Tropical Herbs, School of Pharmacy, Hainan Medical University, Haikou 571199, PR China.
| | - Huiting Zeng
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, and Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, PR China.
| | - Zhenhua Zhu
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, and Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, PR China.
| | - Jianming Guo
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, and Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, PR China.
| | - Yue Zhu
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, and Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, PR China.
| | - Sheng Guo
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, and Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, PR China.
| | - Li Yu
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, and Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, PR China.
| | - Dawei Qian
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, and Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, PR China.
| | - Yuping Tang
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, and Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, PR China.
| | - Jinao Duan
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, and Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, PR China.
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Zhao YY. Metabolomics in chronic kidney disease. Clin Chim Acta 2013; 422:59-69. [PMID: 23570820 DOI: 10.1016/j.cca.2013.03.033] [Citation(s) in RCA: 172] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Revised: 03/23/2013] [Accepted: 03/27/2013] [Indexed: 12/24/2022]
Abstract
Chronic kidney disease (CKD) represents a major challenge to public healthcare. Traditional clinical biomarkers of renal function (blood urea nitrogen and serum creatinine) are not sensitive or specific enough and only increase significantly after the presence of substantial CKD. Therefore, more sensitive biomarkers of CKD are needed. CKD-specific biomarkers at an early disease stage and early diagnosis of specific renal diseases would enable improved therapeutic treatment and reduced the personal and financial burdens. The goal of metabolomics is to identify non-targeted, global small-molecule metabolite profiles of complex samples, such as biofluids and tissues. This method offers the potential for a holistic approach to clinical medicine, as well as improvements in disease diagnoses and the understanding of pathological mechanisms. This review article presents an overview of the recent developments in the field of metabolomics, followed by an in-depth discussion of its application to the study of CKD (primary, chronic glomerulonephritis such as IgA nephropathy; secondary, chronic renal injury such as diabetic nephropathy; chronic renal failure including end-stage kidney disease with and without undergoing replacement therapies, etc), including metabolomic analytical technologies, chemometrics, and metabolomics in experimental and clinical research. We describe the current status of the identification of metabolic biomarkers in CKD. Several markers have been confirmed across multiple studies to detect CKD earlier than traditional clinical chemical and histopathological methods. The application of metabolomics in CKD studies provides researchers the opportunity to gain new insights into metabolic profiling and pathophysiological mechanisms. Particular challenges in the field are presented and placed within the context of future applications of metabolomic approaches to the studies of CKD.
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Affiliation(s)
- Ying-Yong Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, the College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, PR China.
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Sheehan D, Rainville LC, Tyther R, McDonagh B. Redox proteomics in study of kidney-associated hypertension: new insights to old diseases. Antioxid Redox Signal 2012; 17:1560-70. [PMID: 22607037 DOI: 10.1089/ars.2012.4705] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
SIGNIFICANCE The kidney helps to maintain low blood pressure in the human body, and impaired kidney function is a common attribute of aging that is often associated with high blood pressure (hypertension). Kidney-related pathologies are important contributors (either directly or indirectly) to overall human mortality. In comparison with other organs, kidney has an unusually wide range of oxidative status, ranging from the well-perfused cortex to near-anoxic medulla. RECENT ADVANCES Oxidative stress has been implicated in many kidney pathologies, especially chronic kidney disease, and there is considerable research interest in oxidative stress biomarkers for earlier prediction of disease onset. Proteomics approaches have been taken to study of human kidney tissue, serum/plasma, urine, and animal models of hypertension. CRITICAL ISSUES Redox proteomics, in which oxidative post-translational modifications can be identified in protein targets of oxidative or nitrosative stress, has not been very extensively pursued in this set of pathologies. FUTURE DIRECTIONS Proteomics studies of kidney and related tissues have relevance to chronic kidney disease, and redox proteomics, in particular, represents an under-exploited toolkit for identification of novel biomarkers in this commonly occurring pathology.
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Affiliation(s)
- David Sheehan
- Proteomics Research Group, Department of Biochemistry, University College Cork, Cork, Ireland.
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Abstract
This review provides an introduction to mass spectrometry based proteomics and discusses several proteomics approaches that are relevant in understanding the pathophysiology of fibrotic disorders and the approaches that are frequently used in biomarker discovery.
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Affiliation(s)
- Marjan Gucek
- NHLBI Proteomics Core , National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health, 10 Center Drive, Bethesda, MD 20892, USA
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Zhao YY, Liu J, Cheng XL, Bai X, Lin RC. Urinary metabonomics study on biochemical changes in an experimental model of chronic renal failure by adenine based on UPLC Q-TOF/MS. Clin Chim Acta 2011; 413:642-9. [PMID: 22227165 DOI: 10.1016/j.cca.2011.12.014] [Citation(s) in RCA: 134] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2011] [Revised: 12/16/2011] [Accepted: 12/16/2011] [Indexed: 01/28/2023]
Abstract
BACKGROUND Chronic renal failure (CRF) is a serious clinical symptom, occurring as the end result of all kinds of chronic kidney disease and its pathophysiological mechanism is not yet well understood. We investigated the metabolic profiling of urine samples from CRF model rats to find potential disease biomarkers and research pathology of CRF. METHODS An animal model of CRF was produced by adenine. Metabolic profiling of the urine was performed by using ultra performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UPLC Q-TOF/MS). Acquired data were subjected to principal component analysis (PCA) for differentiating the CRF and the normal control groups. Potential biomarkers were screened by using S-plot and were identified by the accurate mass, isotopic pattern and MS(E) fragments information obtained from UPLC Q-TOF/MS analysis. RESULTS 12 metabolites in urine were identified as potential biomarkers. Adenine-induced CRF rats were characterized by the increase of phytosphingosine, adrenosterone, tryptophan, 2,8-dihydroxyadenine, creatinine, and dihydrosphingosine together with the decrease of N-acetylleucine, 3-O-methyldopa, ethyl-N2-acetyl-L-argininate, dopamine, phenylalanine and kynurenic acid in urine. The altered metabolites demonstrated perturbations of amino acids metabolism, phospholipids metabolism and creatinine metabolism in CRF rats. CONCLUSION This work shows that metabonomics method is a valuable tool in CRF mechanism study and assists in clinical diagnosis of CRF.
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Affiliation(s)
- Ying-Yong Zhao
- Department of Traditional Chinese Medicine, the College of Life Sciences, Northwest University, Xi'an, Shaanxi, China.
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Prunotto M, Ghiggeri G, Bruschi M, Gabbiani G, Lescuyer P, Hocher B, Chaykovska L, Berrera M, Moll S. Renal fibrosis and proteomics: current knowledge and still key open questions for proteomic investigation. J Proteomics 2011; 74:1855-70. [PMID: 21642026 DOI: 10.1016/j.jprot.2011.05.031] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2011] [Revised: 04/27/2011] [Accepted: 05/22/2011] [Indexed: 12/25/2022]
Abstract
Renal tubulo-interstitial fibrosis is a non-specific process, representing the final common pathway for all kidney diseases, irrespective of their initial cause, histological injury, or etiology, leading to gradual expansion of the fibrotic mass which destroys the normal structure of the tissue and results in organ dysfunction and, ultimately, in end-stage organ failure. Proteomic studies of the fibrotic pathophysiological mechanisms have been performed in cell cultures, animal models and human tissues, addressing some of the key issues. This article will review proteomic contribution to the raising current knowledge on renal fibrosis biology and also mention seminal open questions to which proteomic techniques and proteomists could fruitfully contribute.
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Affiliation(s)
- Marco Prunotto
- RenalChild Foundation, G. Gaslini Children Hospital, Genoa, Italy.
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