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Yoodee S, Peerapen P, Rattananinsruang P, Detsangiamsak S, Sukphan S, Thongboonkerd V. Large-scale identification of calcium oxalate stone inhibitory proteins in normal human urine. Int J Biol Macromol 2024; 275:133646. [PMID: 38969041 DOI: 10.1016/j.ijbiomac.2024.133646] [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: 05/20/2024] [Revised: 06/25/2024] [Accepted: 07/02/2024] [Indexed: 07/07/2024]
Abstract
Recent evidence has shown that proteins in normal human urine can inhibit calcium oxalate (CaOx) kidney stone formation. Herein, we performed fast protein liquid chromatography (FPLC) to fractionate normal human urinary proteins using anion-exchange (DEAE) and size-exclusion (Superdex 200) materials. FPLC fractions (F1-F15) were examined by CaOx crystallization, growth, aggregation and crystal-cell adhesion assays. The fractions with potent inhibitory activities against CaOx crystals were then subjected to mass spectrometric protein identification. The data revealed that 13 of 15 fractions showed inhibitory activities in at least one crystal assay. Integrating CaOx inhibitory scores demonstrated that F6, F7 and F8 had the most potent inhibitory activities. NanoLC-ESI-Qq-TOF MS/MS identified 105, 93 and 53 proteins in F6, F7 and F8, respectively. Among them, 60 were found in at least two fractions and/or listed among known inhibitors with solid experimental evidence in the StoneMod database (https://www.stonemod.org). Interestingly, 10 of these 60 potential inhibitors have been reported with lower urinary levels in CaOx stone formers compared with healthy (non-stone) individuals, strengthening their roles as potent CaOx stone inhibitors. Our study provides the largest dataset of potential CaOx stone inhibitory proteins that will be useful for further elucidations of stone-forming mechanisms and ultimately for therapeutic/preventive applications.
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Affiliation(s)
- Sunisa Yoodee
- Medical Proteomics Unit, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Paleerath Peerapen
- Medical Proteomics Unit, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Piyaporn Rattananinsruang
- Medical Proteomics Unit, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Sasinun Detsangiamsak
- Medical Proteomics Unit, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Sirirat Sukphan
- Medical Proteomics Unit, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Visith Thongboonkerd
- Medical Proteomics Unit, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand.
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Li Y, Lu X, Yu Z, Wang H, Gao B. Meta-data analysis of kidney stone disease highlights ATP1A1 involvement in renal crystal formation. Redox Biol 2023; 61:102648. [PMID: 36871182 PMCID: PMC10009205 DOI: 10.1016/j.redox.2023.102648] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 02/11/2023] [Accepted: 02/25/2023] [Indexed: 03/02/2023] Open
Abstract
Nephrolithiasis is a complicated disease affected by various environmental and genetic factors. Crystal-cell adhesion is a critical initiation process during kidney stone formation. However, genes regulated by environmental and genetic factors in this process remain unclear. In the present study, we integrated the gene expression profile data and the whole-exome sequencing data of patients with calcium stones, and found that ATP1A1 might be a key susceptibility gene involved in calcium stone formation. The study showed that the T-allele of rs11540947 in the 5'-untranslated region of ATP1A1 was associated with a higher risk of nephrolithiasis and lower activity of a promoter of ATP1A1. Calcium oxalate crystal deposition decreased ATP1A1 expression in vitro and in vivo and was accompanied by the activation of the ATP1A1/Src/ROS/p38/JNK/NF-κB signaling pathway. However, the overexpression of ATP1A1 or treatment with pNaKtide, a specific inhibitor of the ATP1A1/Src complex, inhibited the ATP1A1/Src signal system and alleviated oxidative stress, inflammatory responses, apoptosis, crystal-cell adhesion, and stone formation. Moreover, the DNA methyltransferase inhibitor 5-aza-2'-deoxycytidine reversed ATP1A1 down-regulation induced by crystal deposition. In conclusion, this is the first study to show that ATP1A1, a gene modulated by environmental factors and genetic variations, plays an important role in renal crystal formation, suggesting that ATP1A1 may be a potential therapeutic target for treating calcium stones.
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Affiliation(s)
- Yang Li
- Department of Biochemistry and Molecular Biology, Life Science School, Liaoning University, Shenyang, 110036, China; Department of Cell biology and Genetics, Shenyang Medical College, Shenyang 110034, China
| | - Xiuli Lu
- Department of Biochemistry and Molecular Biology, Life Science School, Liaoning University, Shenyang, 110036, China
| | - Zhihao Yu
- Department of Cell biology and Genetics, Shenyang Medical College, Shenyang 110034, China
| | - Haozhen Wang
- Department of Biochemistry and Molecular Biology, Life Science School, Liaoning University, Shenyang, 110036, China
| | - Bing Gao
- Department of Cell biology and Genetics, Shenyang Medical College, Shenyang 110034, China.
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Peerapen P, Thongboonkerd V. Protein network analysis and functional enrichment via computational biotechnology unravel molecular and pathogenic mechanisms of kidney stone disease. Biomed J 2023; 46:100577. [PMID: 36642221 DOI: 10.1016/j.bj.2023.01.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 01/07/2023] [Accepted: 01/10/2023] [Indexed: 01/15/2023] Open
Abstract
Mass spectrometry-based proteomics has been extensively applied to current biomedical research. From such large-scale identification of proteins, several computational tools have been developed for determining protein-protein interactions (PPI) network and functional significance of the identified proteins and their complex. Analyses of PPI network and functional enrichment have been widely applied to various fields of biomedical research. Herein, we summarize commonly used tools for PPI network analysis and functional enrichment in kidney stone research and discuss their applications to kidney stone disease (KSD). Such computational approach has been used mainly to investigate PPI networks and functional significance of the proteins derived from urine of patients with kidney stone (stone formers), stone matrix, Randall's plaque, renal papilla, renal tubular cells, mitochondria and immune cells. The data obtained from computational biotechnology leads to experimental validation and investigations that offer new knowledge on kidney stone formation processes. Moreover, the computational approach may also lead to defining new therapeutic targets and preventive strategies for better outcome in KSD management.
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Affiliation(s)
- Paleerath Peerapen
- Medical Proteomics Unit, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Visith Thongboonkerd
- Medical Proteomics Unit, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.
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Proteomic analysis of inhibitory protein profiles in the urine of children with nephrolithiasis: implication for disease prevention. Int Urol Nephrol 2022; 54:2783-2788. [PMID: 35879498 DOI: 10.1007/s11255-022-03310-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 07/17/2022] [Indexed: 10/16/2022]
Abstract
PURPOSE In this study we aimed to screen for the presence of biomarkers that are downregulated in children with nephrolithiasis (RS) compared to healthy controls (HC) using a proteomic approach. We hypothesized that RS and HC would display unique inhibitory protein profiles that could be used for comparative pathway analysis. METHODS This is a prospective, controlled, pilot study of pooled urine from RS (N = 30, 24 females, mean age 12.95 ± 4.03 years) versus age- and gender-matched HC, using liquid chromatography-mass spectrometry. The criteria for protein selection were: (1) patient/control abundance ratio of < 0.5; and (2) ≤ 0.05 p-value for the Fisher's Exact Test. Results were confirmed by ELISA testing in individual samples. RESULTS 67 proteins were downregulated in RS group, and 17 of those were significantly different compared to controls. Of those seventeen proteins, five (two actins, annexin A5, keratin 6B, and serpin B4) were completely absent in the urine of stone patients but were found in controls. The remaining twelve proteins were significantly less abundant in the patient's urine compared to healthy controls. Protein-protein interaction modeling of significant proteins identified syndecan-1 as the key node, a protein associated with adhesion pathways. ELISA analysis by subgroups showed statistically significant difference in the urinary excretion of osteopontin (5.1 ± 3.22 ng/mg creatinine vs 14.1 ± 9.5 ng/mg creatinine, p = 0.046) between stone patients with hypocitraturia and controls. Urinary osteopontin concentration was positively correlated with urinary citrate excretion (r = 0.417, p = 0.03). CONCLUSIONS Children with RS have a different urinary inhibitory polypeptide profile compared to HC. Decreased urinary excretion of these proteins indicates their potential inhibitory role in renal stone formation, especially of the adhesion phase. Lower concentration of urinary osteopontin in children with nephrolithiasis and hypocitraturia suggests its potential involvement in the pathogenesis of this disease. Further characterization of these proteins in a larger sample is imperative.
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Peerapen P, Thongboonkerd V. Kidney stone proteomics: an update and perspectives. Expert Rev Proteomics 2021; 18:557-569. [PMID: 34320328 DOI: 10.1080/14789450.2021.1962301] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
INTRODUCTION Main problems of kidney stone disease are its increasing prevalence and high recurrence rate after calculi removal in almost all areas around the globe. Despite enormous efforts in the past, its pathogenic mechanisms remain unclear and need further elucidations. Proteomics has thus become an essential tool to unravel such sophisticated disease mechanisms at cellular, subcellular, molecular, tissue, and whole organism levels. AREAS COVERED This review provides abrief overview of kidney stone disease followed by updates on proteomics for investigating urinary stone modulators, matrix proteins, cellular responses to different types/doses of calcium oxalate (CaOx) crystals, sex hormones and other stimuli, crystal-cell interactions, crystal receptors, secretome, and extracellular vesicles (EVs), all of which lead to better understanding of the disease mechanisms. Finally, the future challenges and translation of these obtained data to the clinic are discussed. EXPERT OPINION Knowledge from urinary proteomics for exploring the important stone modulators (either inhibitors or promoters) will be helpful for early detection of asymptomatic cases for prompt prevention of symptoms, complications, and new stone formation. Moreover, these modulators may serve as the new therapeutic targets in the future for successful treatment and prevention of kidney stone disease by medications or other means of intervention.
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Affiliation(s)
- Paleerath Peerapen
- Medical Proteomics Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Visith Thongboonkerd
- Medical Proteomics Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
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Panunzio A, Tafuri A, Princiotta A, Gentile I, Mazzucato G, Trabacchin N, Antonelli A, Cerruto MA. Omics in urology: An overview on concepts, current status and future perspectives. Urologia 2021; 88:270-279. [PMID: 34169788 DOI: 10.1177/03915603211022960] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Recent technological advances in molecular biology have led to great progress in the knowledge of structure and function of cells and their main constituents. In this setting, 'omics' is standing out in order to significantly improve the understanding of etiopathogenetic mechanisms of disease and contribute to the development of new biochemical diagnostics and therapeutic tools. 'Omics' indicates the scientific branches investigating every aspect of cell's biology, including structures, functions and dynamics pathways. The main 'omics' are genomics, epigenomics, proteomics, transcriptomics, metabolomics and radiomics. Their diffusion, success and proliferation, addressed to many research fields, has led to many important acquisitions, even in Urology. Aim of this narrative review is to define the state of art of 'omics' application in Urology, describing the most recent and relevant findings, in both oncological and non-oncological diseases, focusing the attention on urinary tract infectious, interstitial cystitis, urolithiasis, prostate cancer, bladder cancer and renal cell carcinoma. In Urology the majority of 'omics' applications regard the pathogenesis and diagnosis of the investigated diseases. In future, its role should be implemented in order to develop specific predictors and tailored treatments.
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Affiliation(s)
- Andrea Panunzio
- Department of Urology, University of Verona, Azienda Ospedaliera Universitaria Integrata Verona, Verona, Italy
| | - Alessandro Tafuri
- Department of Urology, University of Verona, Azienda Ospedaliera Universitaria Integrata Verona, Verona, Italy.,Department of Neuroscience, Imaging and Clinical Science, Physiology and Physiopathology division, "G. D'Annunzio" University, Chieti, Italy
| | - Alessandro Princiotta
- Department of Urology, University of Verona, Azienda Ospedaliera Universitaria Integrata Verona, Verona, Italy
| | - Ilaria Gentile
- Department of Urology, University of Verona, Azienda Ospedaliera Universitaria Integrata Verona, Verona, Italy
| | - Giovanni Mazzucato
- Department of Urology, University of Verona, Azienda Ospedaliera Universitaria Integrata Verona, Verona, Italy
| | - Nicolò Trabacchin
- Department of Urology, University of Verona, Azienda Ospedaliera Universitaria Integrata Verona, Verona, Italy
| | - Alessandro Antonelli
- Department of Urology, University of Verona, Azienda Ospedaliera Universitaria Integrata Verona, Verona, Italy
| | - Maria Angela Cerruto
- Department of Urology, University of Verona, Azienda Ospedaliera Universitaria Integrata Verona, Verona, Italy
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iTRAQ-Based Comparative Proteomics Analysis of Urolithiasis Rats Induced by Ethylene Glycol. BIOMED RESEARCH INTERNATIONAL 2020; 2020:6137947. [PMID: 32509863 PMCID: PMC7246402 DOI: 10.1155/2020/6137947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 04/12/2020] [Accepted: 04/23/2020] [Indexed: 11/18/2022]
Abstract
Nephrolithiasis is a frequent chronic urological condition with a high prevalence and recurrence rate. Proteomics studies on urolithiasis rat models are highly important in characterizing the pathophysiology of kidney stones and identifying potential approaches for preventing and treating kidney stones. The isobaric tags for relative and absolute quantification (iTRAQ) were performed to identify differentially expressed proteins (DEPs) in the kidney between urolithiasis rats and control rats. The results showed that 127 DEPs (85 upregulated and 42 downregulated) were identified in urolithiasis and control rats. The functions of DEPs were predicted by Gene Ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, and protein-protein interaction (PPI) network analysis. The expression of four upregulated proteins (Tagln, Akr1c9, Spp1, and Fbn1) and four downregulated proteins (Hbb, Epb42, Hmgcs2, and Ca1) were validated by parallel reaction monitoring (PRM). Proteomics studies of ethylene glycol-induced urolithiasis rat models using iTRAQ and PRM helped to elucidate the molecular mechanism governing nephrolithiasis and to identify candidate proteins for the treatment of kidney stones.
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A Proteomic Network Approach across the Kidney Stone Disease Reveals Endoplasmic Reticulum Stress and Crystal-Cell Interaction in the Kidney. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2019; 2019:9307256. [PMID: 31772715 PMCID: PMC6854948 DOI: 10.1155/2019/9307256] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 08/18/2019] [Accepted: 08/27/2019] [Indexed: 12/30/2022]
Abstract
Crystal-cell interactions are a vital step toward kidney stone formation. However, its mechanisms remained unclear. Here, a protein-protein interaction (PPI) network analysis of a kidney stone revealed that the proteins were enriched in a posttranslational protein modification process in the endoplasmic reticulum (ER). The in vitro study showed that the markers of ER stress, including Bip and CHOP, were upregulated, PERK and ATF6 were activated, and XBP-1 mRNA was spliced. An ER stress-specific protein, caspase-12, was activated in the apoptotic cells induced by calcium oxalate monohydrate (COM) crystals. The treatment with tunicamycin, an ER stress inducer, promoted the crystal-cell adhesion assayed by atomic absorption, reduced cell viability assayed by MTT, and downregulated the expression of proteins involved in the crystal formations. The treatment with salubrinal, an ER stress inhibitor, reversed the above effects for both tunicamycin and COM crystals. The aforementioned main observations were supported by in vivo study. These data demonstrated that ER stress was an essentially biological process of crystal-cell interactions. Our findings suggest that blocking ER stress may become a potential approach to preventing a kidney stone.
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Nakazawa Y, Inoue S, Nakamura Y, Iida Y, Ishigaki Y, Miyazawa K. High‐salt diet promotes crystal deposition through hypertension in Dahl salt‐sensitive rat model. Int J Urol 2019; 26:839-846. [DOI: 10.1111/iju.14035] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 05/06/2019] [Indexed: 02/05/2023]
Affiliation(s)
- Yusuke Nakazawa
- Department of Urology Kanazawa Medical UniversityUchinada Japan
| | - Shinya Inoue
- Department of Urology Kanazawa Medical UniversityUchinada Japan
| | - Yuka Nakamura
- Medical Research Institute Kanazawa Medical UniversityUchinada Japan
| | - Yasuo Iida
- Department of General Education Kanazawa Medical University Uchinada Ishikawa Japan
| | - Yasuhito Ishigaki
- Medical Research Institute Kanazawa Medical UniversityUchinada Japan
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10
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Urinary proteome in inherited nephrolithiasis. Urolithiasis 2018; 47:91-98. [DOI: 10.1007/s00240-018-01104-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 12/08/2018] [Indexed: 12/18/2022]
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11
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Kolbach-Mandel AM, Mandel NS, Hoffmann BR, Kleinman JG, Wesson JA. Stone former urine proteome demonstrates a cationic shift in protein distribution compared to normal. Urolithiasis 2017; 45:337-346. [PMID: 28314883 PMCID: PMC5511579 DOI: 10.1007/s00240-017-0969-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 02/08/2017] [Indexed: 11/25/2022]
Abstract
Many urine proteins are found in calcium oxalate stones, yet decades of research have failed to define the role of urine proteins in stone formation. This urine proteomic study compares the relative amounts of abundant urine proteins between idiopathic calcium oxalate stone forming and non-stone forming (normal) cohorts to identify differences that might correlate with disease. Random mid-morning urine samples were collected following informed consent from 25 stone formers and 14 normal individuals. Proteins were isolated from urine using ultrafiltration. Urine proteomes for each sample were characterized using label-free spectral counting mass spectrometry, so that urine protein relative abundances could be compared between the two populations. A total of 407 unique proteins were identified with the 38 predominant proteins accounting for >82% of all sample spectral counts. The most highly abundant proteins were equivalent in stone formers and normals, though significant differences were observed in a few moderate abundance proteins (immunoglobulins, transferrin, and epidermal growth factor), accounting for 13 and 10% of the spectral counts, respectively. These proteins contributed to a cationic shift in protein distribution in stone formers compared to normals (22% vs. 18%, p = 0.04). Our data showing only small differences in moderate abundance proteins suggest that no single protein controls stone formation. Observed increases in immunoglobulins and transferrin suggest increased inflammatory activity in stone formers, but cannot distinguish cause from effect in stone formation. The observed cationic shift in protein distribution would diminish protein charge stabilization, which could lead to protein aggregation and increased risk for crystal aggregation.
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Affiliation(s)
- Ann M Kolbach-Mandel
- Division of Nephrology, Department of Medicine, Medical College of Wisconsin, 9200 W Wisconsin Avenue, Milwaukee, WI, 53226, USA
| | - Neil S Mandel
- Mandel International Stone and Molecular Analysis Center, Zablocki VA Medical Center, 5000 W. National Avenue, Milwaukee, WI, 53295, USA
- Division of Nephrology, Department of Medicine, Medical College of Wisconsin, 9200 W Wisconsin Avenue, Milwaukee, WI, 53226, USA
| | - Brian R Hoffmann
- Department of Biomedical Engineering, Cardiovascular Center, Medical College of Wisconsin, 9200 W Wisconsin Avenue, Milwaukee, WI, 53226, USA
| | - Jack G Kleinman
- Division of Nephrology, Department of Medicine, Medical College of Wisconsin, 9200 W Wisconsin Avenue, Milwaukee, WI, 53226, USA
| | - Jeffrey A Wesson
- Nephrology Section, Consultant Care Division, Zablocki Department of Veterans Affairs Medical Center, 5000 W. National Avenue (111K), Milwaukee, WI, 53295, USA.
- Division of Nephrology, Department of Medicine, Medical College of Wisconsin, 9200 W Wisconsin Avenue, Milwaukee, WI, 53226, USA.
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12
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Abstract
The most common presentation of nephrolithiasis is idiopathic calcium stones in patients without systemic disease. Most stones are primarily composed of calcium oxalate and form on a base of interstitial apatite deposits, known as Randall's plaque. By contrast some stones are composed largely of calcium phosphate, as either hydroxyapatite or brushite (calcium monohydrogen phosphate), and are usually accompanied by deposits of calcium phosphate in the Bellini ducts. These deposits result in local tissue damage and might serve as a site of mineral overgrowth. Stone formation is driven by supersaturation of urine with calcium oxalate and brushite. The level of supersaturation is related to fluid intake as well as to the levels of urinary citrate and calcium. Risk of stone formation is increased when urine citrate excretion is <400 mg per day, and treatment with potassium citrate has been used to prevent stones. Urine calcium levels >200 mg per day also increase stone risk and often result in negative calcium balance. Reduced renal calcium reabsorption has a role in idiopathic hypercalciuria. Low sodium diets and thiazide-type diuretics lower urine calcium levels and potentially reduce the risk of stone recurrence and bone disease.
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Affiliation(s)
- Fredric L Coe
- Nephrology Section MC 5100, University of Chicago Medicine, 5841 S. Maryland Avenue, Chicago, Illinois, 60637 USA
| | - Elaine M Worcester
- Nephrology Section MC 5100, University of Chicago Medicine, 5841 S. Maryland Avenue, Chicago, Illinois, 60637 USA
| | - Andrew P Evan
- Department of Anatomy and Cell Biology, Indiana University School of Medicine, 635 Barnhill Drive, MS 5055, Indianapolis, IN 46220, Indiana, USA
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13
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Brooks ER, Hoppe B, Milliner DS, Salido E, Rim J, Krevitt LM, Olson JB, Price HE, Vural G, Langman CB. Assessment of Urine Proteomics in Type 1 Primary Hyperoxaluria. Am J Nephrol 2016; 43:293-303. [PMID: 27161247 PMCID: PMC4904731 DOI: 10.1159/000445448] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 03/12/2016] [Indexed: 12/20/2022]
Abstract
BACKGROUND Primary hyperoxaluria type 1 (PH1) and idiopathic hypercalciuria (IHC) are stone-forming diseases that may result in the formation of calcium (Ca) oxalate (Ox) stones, nephrocalcinosis, and progressive chronic kidney disease (CKD). Poorer clinical outcome in PH1 is segregated by the highest urine (Ur)-Ox (UrOx), while IHC outcomes are not predictable by UrCa. We hypothesized that differences would be found in selected Ur-protein (PRO) patterns in PH1 and IHC, compared to healthy intra-familial sibling controls (C) of PH1 patients. We also hypothesized that the PRO patterns associated with higher UrOx levels would reflect injury, inflammation, biomineralization, and abnormal tissue repair processes in PH1. METHODS Twenty four-hour Ur samples were obtained from 3 cohorts: PH1 (n = 47); IHC (n = 35) and C (n = 13) and were analyzed using targeted platform-based multi-analyte profile immunoassays and for UrOx and UrCa by biochemical measurements. RESULTS Known stone matrix constituents, osteopontin, calbindin, and vitronectin were lowest in PH1 (C > IHC > PH1; p < 0.05). Ur-interleukin-10; chromogranin A; epidermal growth factor (EGF); insulin-like growth factor-1 (IGF-1), and macrophage inflammatory PRO-1α (MIP-1α) were higher in PH1 > C (p = 0.03 to p < 0.05). Fetuin A; IGF-1, MIP-1α, and vascular cell adhesion molecule-1 were highest in PH1 > IHC (p < 0.001 to p = 0.005). CONCLUSION PH1 Ur-PROs reflected overt inflammation, chemotaxis, oxidative stress, growth factors (including EGF), and pro-angiogenic and calcification regulation/inhibition compared to the C and IHC cohorts. Many of the up- and downregulated PH1-PROs found in this study are also found in CKD, acute kidney injury, stone formers, and/or stone matrices. Further data analyses may provide evidence for PH1 unique PROs or demonstrate a poorer clinical outcome.
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Affiliation(s)
- Ellen R Brooks
- Feinberg School of Medicine, Northwestern University, Department of Pediatrics, Chicago, Ill., USA
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14
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Nie S, McDermott SP, Deol Y, Tan Z, Wicha MS, Lubman DM. A quantitative proteomics analysis of MCF7 breast cancer stem and progenitor cell populations. Proteomics 2015; 15:3772-83. [PMID: 26332018 DOI: 10.1002/pmic.201500002] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Revised: 07/21/2015] [Accepted: 08/26/2015] [Indexed: 12/11/2022]
Abstract
Accumulating evidence has demonstrated that breast cancers are initiated and develop from a small population of stem-like cells termed cancer stem cells (CSCs). These cells are hypothesized to mediate tumor metastasis and contribute to therapeutic resistance. However, the molecular regulatory networks responsible for maintaining CSCs in an undifferentiated state have yet to be elucidated. In this study, we used CSC markers to isolate pure breast CSCs fractions (ALDH+ and CD44+CD24- cell populations) and the mature luminal cells (CD49f-EpCAM+) from the MCF7 cell line. Proteomic analysis was performed on these samples and a total of 3304 proteins were identified. A label-free quantitative method was applied to analyze differentially expressed proteins. Using the criteria of greater than twofold changes and p value <0.05, 305, 322 and 98 proteins were identified as significantly different in three pairwise comparisons of ALDH+ versus CD44+CD24-, ALDH+ versus CD49f-EpCAM+ and CD44+CD24- versus CD49f-EpCAM+, respectively. Pathway analysis of differentially expressed proteins by Ingenuity Pathway Analysis (IPA) revealed potential molecular regulatory networks that may regulate CSCs. Selected differential proteins were validated by Western blot assay and immunohistochemical staining. The use of proteomics analysis may increase our understanding of the underlying molecular mechanisms of breast CSCs. This may be of importance in the future development of anti-CSC therapeutics.
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Affiliation(s)
- Song Nie
- Department of Surgery, University of Michigan, Ann Arbor, MI, USA
| | - Sean P McDermott
- Department of Internal Medicine, Division of Hematology/Oncology, University of Michigan, Ann Arbor, MI, USA.,Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Yadwinder Deol
- Department of Internal Medicine, Division of Hematology/Oncology, University of Michigan, Ann Arbor, MI, USA.,Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Zhijing Tan
- Department of Surgery, University of Michigan, Ann Arbor, MI, USA
| | - Max S Wicha
- Department of Internal Medicine, Division of Hematology/Oncology, University of Michigan, Ann Arbor, MI, USA.,Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - David M Lubman
- Department of Surgery, University of Michigan, Ann Arbor, MI, USA
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15
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Kovacevic L, Lu H, Goldfarb DS, Lakshmanan Y, Caruso JA. Urine proteomic analysis in cystinuric children with renal stones. J Pediatr Urol 2015; 11:217.e1-6. [PMID: 26076823 PMCID: PMC4540695 DOI: 10.1016/j.jpurol.2015.04.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 04/25/2015] [Indexed: 11/16/2022]
Abstract
INTRODUCTION The gene mutations responsible for cystinuria do not fully explain kidney stone activity, suggesting that specific proteins may serve as promoters of cystine precipitation, aggregation or epithelial adherence. In this study we assessed (1) the differences in the urinary proteins between children with cystinuria and kidney stones (CYS) and healthy controls (HC), with particular attention to the fibrosis-related proteins, and (2) the presence of diagnostic biomarkers for CYS. MATERIAL AND METHODS We conducted a pilot study comparing individual urinary proteomes of 2 newly diagnosed children with CYS and 2 age- and gender-matched HC, using liquid chromatography-mass spectrometry. Relative protein abundance was estimated using spectral counting. Proteins of interest in both CYS and HC were selected using the following criteria: i) ≥5 spectral counts; ii) ≥2-fold difference in spectral counts; and iii) ≤0.05 p-value for the Fisher's Exact Test. DISCUSSION This study demonstrates a different urinary polypeptide profile in two children with CYS compared to two HC. Of the 623 proteins identified by proteomic analysis, 180 exhibited at least a 2-fold increased relative abundance in CYS compared to HC. Of these, 39 were involved in response to stress, 26 in response to wounding, 21 in inflammatory response, 18 in immune response, and 4 in cellular response to oxidative stress. 133 proteins were found only in children with CYS, 33 of which met the selection criteria. Of these 33 unique proteins, six are known to be associated with fibrosis pathways (Table). The major limitation of this study is the small number of samples that were analyzed. Validation using highly specific methods such as ELISA is needed. CONCLUSION We provide proteomic evidence of oxidative injury, inflammation, wound healing and fibrosis in two children with CYS. We speculate that oxidative stress and inflammation may cause remodeling via actin and vimentin pathways, leading to fibrosis. Additionally, we identified ITIH and MMP-9 as potential diagnostic biomarkers and novel therapeutic targets in CYS. These proteins merit further investigation.
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Affiliation(s)
- Larisa Kovacevic
- Department of Pediatric Urology, Children's Hospital of Michigan, Detroit, MI, USA.
| | - Hong Lu
- Department of Pediatric Urology, Children's Hospital of Michigan, Detroit, MI, USA
| | - David S Goldfarb
- Nephrology Division, NYU Langone Medical Center, New York, NY, USA
| | - Yegappan Lakshmanan
- Department of Pediatric Urology, Children's Hospital of Michigan, Detroit, MI, USA
| | - Joseph A Caruso
- Proteomic Facility, Wayne State University, Detroit, MI, USA
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Abstract
The urinary proteome is the focus of many studies due to the ease of urine collection and the relative proteome stability. Systems biology allows the combination of multiple omics studies, forming a link between proteomics, metabolomics, genomics and transcriptomics. In-depth data interpretation is achieved by bioinformatics analysis of -omics data sets. It is expected that the contribution of systems biology to the study of the urinary proteome will offer novel insights. The main focus of this review is on technical aspects of proteomics studies, available tools for systems biology analysis and the application of urinary proteomics in clinical studies and systems biology.
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Lacroix C, Caubet C, Gonzalez-de-Peredo A, Breuil B, Bouyssié D, Stella A, Garrigues L, Le Gall C, Raevel A, Massoubre A, Klein J, Decramer S, Sabourdy F, Bandin F, Burlet-Schiltz O, Monsarrat B, Schanstra JP, Bascands JL. Label-free quantitative urinary proteomics identifies the arginase pathway as a new player in congenital obstructive nephropathy. Mol Cell Proteomics 2014; 13:3421-34. [PMID: 25205225 DOI: 10.1074/mcp.m114.040121] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Obstructive nephropathy is a frequently encountered situation in newborns. In previous studies, the urinary peptidome has been analyzed for the identification of clinically useful biomarkers of obstructive nephropathy. However, the urinary proteome has not been explored yet and should allow additional insight into the pathophysiology of the disease. We have analyzed the urinary proteome of newborns (n = 5/group) with obstructive nephropathy using label free quantitative nanoLC-MS/MS allowing the identification and quantification of 970 urinary proteins. We next focused on proteins exclusively regulated in severe obstructive nephropathy and identified Arginase 1 as a potential candidate molecule involved in the development of obstructive nephropathy, located at the crossroad of pro- and antifibrotic pathways. The reduced urinary abundance of Arginase 1 in obstructive nephropathy was verified in independent clinical samples using both Western blot and MRM analysis. These data were confirmed in situ in kidneys obtained from a mouse obstructive nephropathy model. In addition, we also observed increased expression of Arginase 2 and increased total arginase activity in obstructed mouse kidneys. mRNA expression analysis of the related arginase pathways indicated that the pro-fibrotic arginase-related pathway is activated during obstructive nephropathy. Taken together we have identified a new actor in the development of obstructive nephropathy in newborns using quantitative urinary proteomics and shown its involvement in an in vivo model of disease. The present study demonstrates the relevance of such a quantitative urinary proteomics approach with clinical samples for a better understanding of the pathophysiology and for the discovery of potential therapeutic targets.
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Affiliation(s)
- Chrystelle Lacroix
- From the ‡Centre National de la Recherche Scientifique, Institut de Pharmacologie et de Biologie Structurale, F-31077 Toulouse, France; §Université Paul Sabatier, Toulouse, France
| | - Cécile Caubet
- §Université Paul Sabatier, Toulouse, France; ¶Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France
| | - Anne Gonzalez-de-Peredo
- From the ‡Centre National de la Recherche Scientifique, Institut de Pharmacologie et de Biologie Structurale, F-31077 Toulouse, France; §Université Paul Sabatier, Toulouse, France
| | - Benjamin Breuil
- §Université Paul Sabatier, Toulouse, France; ¶Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France
| | - David Bouyssié
- From the ‡Centre National de la Recherche Scientifique, Institut de Pharmacologie et de Biologie Structurale, F-31077 Toulouse, France; §Université Paul Sabatier, Toulouse, France
| | - Alexandre Stella
- From the ‡Centre National de la Recherche Scientifique, Institut de Pharmacologie et de Biologie Structurale, F-31077 Toulouse, France; §Université Paul Sabatier, Toulouse, France
| | - Luc Garrigues
- From the ‡Centre National de la Recherche Scientifique, Institut de Pharmacologie et de Biologie Structurale, F-31077 Toulouse, France; §Université Paul Sabatier, Toulouse, France
| | - Caroline Le Gall
- ‖Methodomics, Toulouse, France; **Institut de Mathématiques de Toulouse, UMR 5219, INSA de Toulouse, Université de Toulouse, 135 Avenue de Rangueil, F-31077 Toulouse, France
| | - Anthony Raevel
- §Université Paul Sabatier, Toulouse, France; ¶Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France
| | - Angelique Massoubre
- §Université Paul Sabatier, Toulouse, France; ¶Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France
| | - Julie Klein
- §Université Paul Sabatier, Toulouse, France; ¶Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France
| | - Stéphane Decramer
- §Université Paul Sabatier, Toulouse, France; ¶Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France; ‡‡Nephrology and Internal Medicine Department, University Children's Hospital, Toulouse, France
| | - Frédérique Sabourdy
- §§Laboratoire de Biochimie Métabolique, IFB, CHU Purpan, and INSERM UMR 1037, CRCT CHU Rangueil, Toulouse, France
| | - Flavio Bandin
- §Université Paul Sabatier, Toulouse, France; ¶Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France; ‡‡Nephrology and Internal Medicine Department, University Children's Hospital, Toulouse, France
| | - Odile Burlet-Schiltz
- From the ‡Centre National de la Recherche Scientifique, Institut de Pharmacologie et de Biologie Structurale, F-31077 Toulouse, France; §Université Paul Sabatier, Toulouse, France
| | - Bernard Monsarrat
- From the ‡Centre National de la Recherche Scientifique, Institut de Pharmacologie et de Biologie Structurale, F-31077 Toulouse, France; §Université Paul Sabatier, Toulouse, France
| | - Joost-Peter Schanstra
- §Université Paul Sabatier, Toulouse, France; ¶Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France;
| | - Jean-Loup Bascands
- §Université Paul Sabatier, Toulouse, France; ¶Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France;
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Phosphorylation stoichiometries of human eukaryotic initiation factors. Int J Mol Sci 2014; 15:11523-38. [PMID: 24979134 PMCID: PMC4139797 DOI: 10.3390/ijms150711523] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 04/11/2014] [Accepted: 04/29/2014] [Indexed: 12/26/2022] Open
Abstract
Eukaryotic translation initiation factors are the principal molecular effectors regulating the process converting nucleic acid to functional protein. Commonly referred to as eIFs (eukaryotic initiation factors), this suite of proteins is comprised of at least 25 individual subunits that function in a coordinated, regulated, manner during mRNA translation. Multiple facets of eIF regulation have yet to be elucidated; however, many of the necessary protein factors are phosphorylated. Herein, we have isolated, identified and quantified phosphosites from eIF2, eIF3, and eIF4G generated from log phase grown HeLa cell lysates. Our investigation is the first study to globally quantify eIF phosphosites and illustrates differences in abundance of phosphorylation between the residues of each factor. Thus, identification of those phosphosites that exhibit either high or low levels of phosphorylation under log phase growing conditions may aid researchers to concentrate their investigative efforts to specific phosphosites that potentially harbor important regulatory mechanisms germane to mRNA translation.
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Rodríguez-Suárez E, Siwy J, Zürbig P, Mischak H. Urine as a source for clinical proteome analysis: From discovery to clinical application. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:884-98. [DOI: 10.1016/j.bbapap.2013.06.016] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Revised: 06/10/2013] [Accepted: 06/20/2013] [Indexed: 01/03/2023]
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20
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Li L, Hu X, Xia Y, Xiao G, Zheng P, Wang C. Linkage of oxidative stress and mitochondrial dysfunctions to spontaneous culture degeneration in Aspergillus nidulans. Mol Cell Proteomics 2013; 13:449-61. [PMID: 24345786 DOI: 10.1074/mcp.m113.028480] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Filamentous fungi including mushrooms frequently and spontaneously degenerate during subsequent culture maintenance on artificial media, which shows the loss or reduction abilities of asexual sporulation, sexuality, fruiting, and production of secondary metabolites, thus leading to economic losses during mass production. To better understand the underlying mechanisms of fungal degeneration, the model fungus Aspergillus nidulans was employed in this study for comprehensive analyses. First, linkage of oxidative stress to culture degeneration was evident in A. nidulans. Taken together with the verifications of cell biology and biochemical data, a comparative mitochondrial proteome analysis revealed that, unlike the healthy wild type, a spontaneous fluffy sector culture of A. nidulans demonstrated the characteristics of mitochondrial dysfunctions. Relative to the wild type, the features of cytochrome c release, calcium overload and up-regulation of apoptosis inducing factors evident in sector mitochondria suggested a linkage of fungal degeneration to cell apoptosis. However, the sector culture could still be maintained for generations without the signs of growth arrest. Up-regulation of the heat shock protein chaperones, anti-apoptotic factors and DNA repair proteins in the sector could account for the compromise in cell death. The results of this study not only shed new lights on the mechanisms of spontaneous degeneration of fungal cultures but will also provide alternative biomarkers to monitor fungal culture degeneration.
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Affiliation(s)
- Lin Li
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
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21
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Boonla C, Tosukhowong P, Spittau B, Schlosser A, Pimratana C, Krieglstein K. Inflammatory and fibrotic proteins proteomically identified as key protein constituents in urine and stone matrix of patients with kidney calculi. Clin Chim Acta 2013; 429:81-9. [PMID: 24333391 DOI: 10.1016/j.cca.2013.11.036] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Revised: 11/27/2013] [Accepted: 11/27/2013] [Indexed: 11/19/2022]
Abstract
To uncover whether urinary proteins are incorporated into stones, the proteomic profiles of kidney stones and urine collected from the same patients have to be explored. We employed 1D-PAGE and nanoHPLC-ESI-MS/MS to analyze the proteomes of kidney stone matrix (n=16), nephrolithiatic urine (n=14) and healthy urine (n=3). We identified 62, 66 and 22 proteins in stone matrix, nephrolithiatic urine and healthy urine, respectively. Inflammation- and fibrosis-associated proteins were frequently detected in the stone matrix and nephrolithiatic urine. Eighteen proteins were exclusively found in the stone matrix and nephrolithiatic urine, considered as candidate biomarkers for kidney stone formation. S100A8 and fibronectin, representatives of inflammation and fibrosis, respectively, were up-regulated in nephrolithiasis renal tissues. S100A8 was strongly expressed in infiltrated leukocytes. Fibronectin was over-expressed in renal tubular cells. S100A8 and fibronectin were immunologically confirmed to exist in nephrolithiatic urine and stone matrix, but in healthy urine they were undetectable. Conclusion, both kidney stones and urine obtained from the same patients greatly contained inflammatory and fibrotic proteins. S100A8 and fibronectin were up-regulated in stone-baring kidneys and nephrolithiatic urine. Therefore, inflammation and fibrosis are suggested to be involved in the formation of kidney calculi.
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Affiliation(s)
- Chanchai Boonla
- Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330 Thailand.
| | - Piyaratana Tosukhowong
- Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330 Thailand
| | - Björn Spittau
- Department of Molecular Embryology, Institute for Anatomy and Cell Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Andreas Schlosser
- Center for Biological Systems Analysis (ZBSA), Core Facility Proteomics, University of Freiburg, 79104 Freiburg, Germany
| | - Chaowat Pimratana
- Division of Urological Surgery, Khon Kaen Hospital, Khon Kaen 40000 Thailand
| | - Kerstin Krieglstein
- Department of Molecular Embryology, Institute for Anatomy and Cell Biology, University of Freiburg, 79104 Freiburg, Germany.
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22
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Howles SA, Edwards MH, Cooper C, Thakker RV. Kidney stones: a fetal origins hypothesis. J Bone Miner Res 2013; 28:2535-9. [PMID: 23703881 PMCID: PMC3792843 DOI: 10.1002/jbmr.1993] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Revised: 04/24/2013] [Accepted: 05/09/2013] [Indexed: 11/07/2022]
Abstract
Kidney stones are common, with a multifactorial etiology involving dietary, environmental, and genetic factors. In addition, patients with nephrolithiasis are at greater risk of hypertension, diabetes mellitus, metabolic syndrome, and osteoporosis, although the basis for this is not fully understood. All of these renal stone-associated conditions have also been linked with adverse early-life events, including low-birth weight, and it has been suggested that this developmental effect is due to excess exposure to maternal glucocorticoids in utero. This is proposed to result in long-term increased hypothalamic-pituitary-axis activation; there are mechanisms through which this effect could also promote urinary lithogenic potential. We therefore hypothesize that the association between renal stone disease and hypertension, diabetes mellitus, metabolic syndrome, and osteoporosis may be related by a common pathway of programming in early life, which, if validated, would implicate the developmental origins hypothesis in the etiology of nephrolithiasis.
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Affiliation(s)
- Sarah A. Howles
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
- Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Mark H. Edwards
- MRC Lifecourse Epidemiology Unit, University of Southampton, University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Cyrus Cooper
- MRC Lifecourse Epidemiology Unit, University of Southampton, University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, United Kingdom
| | - Rajesh V. Thakker
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
- Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
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23
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McKee CM, Xu D, Kessler BM, Muschel RJ. Proteomic analysis reveals a proteolytic feedback loop in murine seminal fluid. Prostate 2013; 73:1427-40. [PMID: 23765702 DOI: 10.1002/pros.22690] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 04/30/2013] [Indexed: 12/20/2022]
Abstract
BACKGROUND Matrix metalloproteinase 9 (MMP9) has been implicated in extracellular matrix (ECM) remodelling, angiogenesis and inflammation. However, the targets for proteolysis that lead to these physiological consequences are often undefined as is the regulation of MMP9 itself. Therefore, identification of both the potential direct and indirect targets of MMP9 is critical for further understanding the effects of its proteolytic cascades. METHODS To study these cascades on a wider scale, transgenic mouse "knock-out" models and ultra-high performance liquid chromatography mass spectroscopy (UPLC-MS(E) ) were used to elucidate the MMP9 targets, inhibitors, and interactors found in mouse seminal vesicle fluid (SVF). RESULTS Proteomics analysis of SVF from wild type, mmp9-/- or pn1-/- mice detected differences in serine protease inhibitors (serpins), reproductive proteins, developmental regulators, and cancer proto-oncogenes, including Renin 1/2. Protease nexin 1 (PN1), an ECM-based inhibitor of urokinase, was elevated in the SVF of mmp9-/- mice. We observed that MMP9-mediated N-terminal cleavage of PN1 reduces this serpin's functional activity. Our data also suggest a feedback loop in which inhibition of PN1 is a critical step in permitting greater activity of MMP9. CONCLUSION This study extends the degradome of MMP9 and examines components relevant to seminal fluid physiology. PN1 is proposed to be a novel inhibitor of MMP9 activity and a block to collagen cleavage, a frequent antecedent to cancer cell invasion. The interaction of MMP9 with PN1 and other serpins may lead to a better understanding of seminal vesicle function and possible impacts on fertility, as well as provide novel therapeutic targets.
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Affiliation(s)
- Chad M McKee
- Department of Oncology, Gray Institute of Radiation Oncology and Biology, University of Oxford, Oxford, UK
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24
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Fye HKS, Wright-Drakesmith C, Kramer HB, Camey S, da Costa AN, Jeng A, Bah A, Kirk GD, Sharif MIF, Ladep NG, Okeke E, Hainaut P, Taylor-Robinson SD, Kessler BM, Mendy ME. Protein profiling in hepatocellular carcinoma by label-free quantitative proteomics in two west African populations. PLoS One 2013; 8:e68381. [PMID: 23935864 PMCID: PMC3728326 DOI: 10.1371/journal.pone.0068381] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2012] [Accepted: 05/28/2013] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Hepatocellular Carcinoma is the third most common cause of cancer related death worldwide, often diagnosed by measuring serum AFP; a poor performance stand-alone biomarker. With the aim of improving on this, our study focuses on plasma proteins identified by Mass Spectrometry in order to investigate and validate differences seen in the respective proteomes of controls and subjects with LC and HCC. METHODS Mass Spectrometry analysis using liquid chromatography electro spray ionization quadrupole time-of-flight was conducted on 339 subjects using a pooled expression profiling approach. ELISA assays were performed on four significantly differentially expressed proteins to validate their expression profiles in subjects from the Gambia and a pilot group from Nigeria. Results from this were collated for statistical multiplexing using logistic regression analysis. RESULTS Twenty-six proteins were identified as differentially expressed between the three subject groups. Direct measurements of four; hemopexin, alpha-1-antitrypsin, apolipoprotein A1 and complement component 3 confirmed their change in abundance in LC and HCC versus control patients. These trends were independently replicated in the pilot validation subjects from Nigeria. The statistical multiplexing of these proteins demonstrated performance comparable to or greater than ALT in identifying liver cirrhosis or carcinogenesis. This exercise also proposed preliminary cut offs with achievable sensitivity, specificity and AUC statistics greater than reported AFP averages. CONCLUSIONS The validated changes of expression in these proteins have the potential for development into high-performance tests usable in the diagnosis and or monitoring of HCC and LC patients. The identification of sustained expression trends strengthens the suggestion of these four proteins as worthy candidates for further investigation in the context of liver disease. The statistical combinations also provide a novel inroad of analyses able to propose definitive cut-offs and combinations for evaluation of performance.
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Affiliation(s)
- Haddy K. S. Fye
- Nuffield Department of Medicine, Henry Wellcome Building for Molecular Physiology - University of Oxford, Oxford, Oxfordshire, United Kingdom
- Department of Disease Control and Elimination, MRC Unit (UK) The Gambia Laboratories, Fajara, Banjul, The Gambia
| | - Cynthia Wright-Drakesmith
- Nuffield Department of Medicine, Henry Wellcome Building for Molecular Physiology - University of Oxford, Oxford, Oxfordshire, United Kingdom
| | - Holger B. Kramer
- Nuffield Department of Medicine, Henry Wellcome Building for Molecular Physiology - University of Oxford, Oxford, Oxfordshire, United Kingdom
| | - Suzi Camey
- Laboratory Services and Bio-bank Group, International Agency for Research on Cancer, Lyon, France
- Departamento de Estatistica, Instituto de Matematica, Universidade Federal do Rio Grande do Sul, Rio Grande, Brazil
| | - Andre Nogueira da Costa
- Laboratory Services and Bio-bank Group, International Agency for Research on Cancer, Lyon, France
| | - Adam Jeng
- Department of Disease Control and Elimination, MRC Unit (UK) The Gambia Laboratories, Fajara, Banjul, The Gambia
| | - Alasana Bah
- Department of Disease Control and Elimination, MRC Unit (UK) The Gambia Laboratories, Fajara, Banjul, The Gambia
| | - Gregory D. Kirk
- Department of Epidemiology - Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Mohamed I. F. Sharif
- Liver Unit - Division of Diabetes Endocrinology and Metabolism, Department of Medicine, Imperial College London, London, United Kingdom
| | - Nimzing G. Ladep
- Liver Unit - Division of Diabetes Endocrinology and Metabolism, Department of Medicine, Imperial College London, London, United Kingdom
| | - Edith Okeke
- Jos University Teaching Hospital, Jos, Plateau State, Nigeria
| | - Pierre Hainaut
- Laboratory Services and Bio-bank Group, International Agency for Research on Cancer, Lyon, France
- The International Prevention Research Institute, Lyon, France
| | - Simon D. Taylor-Robinson
- Liver Unit - Division of Diabetes Endocrinology and Metabolism, Department of Medicine, Imperial College London, London, United Kingdom
| | - Benedikt M. Kessler
- Nuffield Department of Medicine, Henry Wellcome Building for Molecular Physiology - University of Oxford, Oxford, Oxfordshire, United Kingdom
| | - Maimuna E. Mendy
- Laboratory Services and Bio-bank Group, International Agency for Research on Cancer, Lyon, France
- Department of Disease Control and Elimination, MRC Unit (UK) The Gambia Laboratories, Fajara, Banjul, The Gambia
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Hao J, Li W, Dan J, Ye X, Wang F, Zeng X, Wang L, Wang H, Cheng Y, Liu L, Shui W. Reprogramming- and pluripotency-associated membrane proteins in mouse stem cells revealed by label-free quantitative proteomics. J Proteomics 2013; 86:70-84. [DOI: 10.1016/j.jprot.2013.04.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Revised: 03/10/2013] [Accepted: 04/07/2013] [Indexed: 12/15/2022]
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Groessl M, Luksch H, Rösen-Wolff A, Shevchenko A, Gentzel M. Profiling of the human monocytic cell secretome by quantitative label-free mass spectrometry identifies stimulus-specific cytokines and proinflammatory proteins. Proteomics 2013; 12:2833-42. [PMID: 22837156 DOI: 10.1002/pmic.201200108] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The immune response to pathogens or injury relies on the concerted release of cytokines and proteins with biological activity important for host protection, host defense, and wound healing. Consequently, the secretome of immune cells provides a promising resource for discovery of specific molecular markers and targets for pharmacological intervention. Here, we employ label-free MS for unbiased, quantitative profiling of the human monocytic cell secretome under different proinflammatory stimuli. The quantitative secretome profiles reveal the highly stimulus-dependent cellular response and differential, specific secretion of more than 200 proteins, including important proinflammatory proteins and cytokines.
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Affiliation(s)
- M Groessl
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
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Rodríguez-Suárez E, Whetton AD. The application of quantification techniques in proteomics for biomedical research. MASS SPECTROMETRY REVIEWS 2013; 32:1-26. [PMID: 22847841 DOI: 10.1002/mas.21347] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2011] [Revised: 02/09/2012] [Accepted: 02/10/2012] [Indexed: 06/01/2023]
Abstract
The systematic analysis of biological processes requires an understanding of the quantitative expression patterns of proteins, their interacting partners and their subcellular localization. This information was formerly difficult to accrue as the relative quantification of proteins relied on antibody-based methods and other approaches with low throughput. The advent of soft ionization techniques in mass spectrometry plus advances in separation technologies has aligned protein systems biology with messenger RNA, DNA, and microarray technologies to provide data on systems as opposed to singular protein entities. Another aspect of quantitative proteomics that increases its importance for the coming few years is the significant technical developments underway both for high pressure liquid chromatography and mass spectrum devices. Hence, robustness, reproducibility and mass accuracy are still improving with every new generation of instruments. Nonetheless, the methods employed require validation and comparison to design fit for purpose experiments in advanced protein analyses. This review considers the newly developed systematic protein investigation methods and their value from the standpoint that relative or absolute protein quantification is required de rigueur in biomedical research.
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Jia W, Andaya A, Leary JA. Novel mass spectrometric method for phosphorylation quantification using cerium oxide nanoparticles and tandem mass tags. Anal Chem 2012; 84:2466-73. [PMID: 22304650 DOI: 10.1021/ac203248s] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The stoichiometry of protein phosphorylation significantly impacts protein function. The development of quantitative techniques in mass spectrometry has generated the ability to systematically monitor the regulation levels of various proteins. This study reports an integrated methodology using cerium oxide nanoparticles and isobaric tandem mass tag (TMT) labeling to assess absolute stoichiometries of protein phosphorylation. This protocol was designed to directly measure the dephosphorylation levels for a known phosphorylation site, therefore allowing for quantification of phosphosites. Both the accuracy and precision of the method were verified using standard peptides and protein tryptic digests. This novel method was then applied to quantify phosphorylations on eukaryotic initiation factor 3H (eIF3H), a protein integral to overall eukaryotic protein translation initiation. To date, this is the first report of assessment of protein phosphorylation quantification on eIF3.
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Affiliation(s)
- Weitao Jia
- Department of Molecular and Cellular Biology, University of California, Davis, One Shields Avenue, Davis, California 95616, USA
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Sarwal MM, Sigdel TK, Salomon DR. Functional proteogenomics—Embracing complexity. Semin Immunol 2011; 23:235-51. [DOI: 10.1016/j.smim.2011.08.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2011] [Accepted: 08/05/2011] [Indexed: 01/30/2023]
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