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Hong SY, Xia QD, Yang YY, Li C, Zhang JQ, Xu JZ, Qin BL, Xun Y, Wang SG. The role of microbiome: a novel insight into urolithiasis. Crit Rev Microbiol 2023; 49:177-196. [PMID: 35776498 DOI: 10.1080/1040841x.2022.2045899] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Urolithiasis, referred to as the formation of stones in the urinary tract, is a common disease with growing prevalence and high recurrence rate worldwide. Although researchers have endeavoured to explore the mechanism of urinary stone formation for novel effective therapeutic and preventative measures, the exact aetiology and pathogenesis remain unclear. Propelled by sequencing technologies and culturomics, great advances have been made in understanding the pivotal contribution of the human microbiome to urolithiasis. Indeed, there are diverse and abundant microbes interacting with the host in the urinary tract, overturning the dogma that urinary system, and urine are sterile. The urinary microbiome of stone formers was clearly distinct from healthy individuals. Besides, dysbiosis of the intestinal microbiome appears to be involved in stone formation through the gut-kidney axis. Thus, the human microbiome has potential significant implications for the aetiology of urolithiasis, providing a novel insight into diagnostic, therapeutic, and prognostic strategies. Herein, we review and summarize the landmark microbiome studies in urolithiasis and identify therapeutic implications, challenges, and future perspectives in this rapidly evolving field. To conclude, a new front has opened with the evidence for a microbial role in stone formation, offering potential applications in the prevention, and treatment of urolithiasis.
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Affiliation(s)
- Sen-Yuan Hong
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, PR China
| | - Qi-Dong Xia
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, PR China
| | - Yuan-Yuan Yang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, PR China
| | - Cong Li
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, PR China
| | - Jia-Qiao Zhang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, PR China
| | - Jin-Zhou Xu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, PR China
| | - Bao-Long Qin
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, PR China
| | - Yang Xun
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, PR China
| | - Shao-Gang Wang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, PR China
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2
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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: 0] [Impact Index Per Article: 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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3
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Gao H, Lin J, Xiong F, Yu Z, Pan S, Huang Y. Urinary Microbial and Metabolomic Profiles in Kidney Stone Disease. Front Cell Infect Microbiol 2022; 12:953392. [PMID: 36132987 PMCID: PMC9484321 DOI: 10.3389/fcimb.2022.953392] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 08/15/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundKidney stones or nephrolithiasis is a chronic metabolic disease characterized by renal colic and hematuria. Currently, a pathogenetic mechanism resulting in kidney stone formation remains elusive. We performed a multi-omic study investigating urinary microbial compositions and metabolic alterations during nephrolithiasis.MethodUrine samples from healthy and individuals with nephrolithiasis were collected for 16S rRNA gene sequencing and liquid chromatography-mass spectroscopy. Microbiome and metabolome profiles were analyzed individually and combined to construct interactome networks by bioinformatic analysis.ResultsDistinct urinary microbiome profiles were determined in nephrolithiasis patients compared with controls. Thirty-nine differentially abundant taxa between controls and nephrolithiasis patients were identified, and Streptococcus showed the most significant enrichment in nephrolithiasis patients. We also observed significantly different microbial compositions between female and male nephrolithiasis patients. The metabolomic analysis identified 112 metabolites that were differentially expressed. Two significantly enriched metabolic pathways, including biosynthesis of unsaturated fatty acids and tryptophan metabolism, were also identified in nephrolithiasis patients. Four potentially diagnostic metabolites were also identified, including trans-3-hydroxycotinine, pyroglutamic acid, O-desmethylnaproxen, and FAHFA (16:0/18:2), and could function as biomarkers for the early diagnosis of nephrolithiasis. We also identified three metabolites that contributed to kidney stone size. Finally, our integrative analysis of the urinary tract microbiome and metabolome identified distinctly different network characteristics between the two groups.ConclusionsOur study has characterized important profiles and correlations among urinary tract microbiomes and metabolomes in nephrolithiasis patients for the first time. These results shed new light on the pathogenesis of nephrolithiasis and could provide early clinical biomarkers for diagnosing the disease.
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Affiliation(s)
- Hong Gao
- Shenzhen Hospital, University of Chinese Academy of Sciences, Shenzhen, China
| | - Jiaqiong Lin
- Affiliated Dongguan Maternal and Child Healthcare Hospital, Southern Medical University, Dongguan, China
| | - Fu Xiong
- Department of Medical Genetics/Experimental Education/Administration Center, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
- Department of Fetal Medicine and Prenatal Diagnosis, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Zuhu Yu
- Shenzhen Hospital, University of Chinese Academy of Sciences, Shenzhen, China
| | - Shilei Pan
- Zhujiang Hospital, Southern Medical University, Guangzhou, China
- *Correspondence: Yuxin Huang, ; Shilei Pan,
| | - Yuxin Huang
- Zhujiang Hospital, Southern Medical University, Guangzhou, China
- *Correspondence: Yuxin Huang, ; Shilei Pan,
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4
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Kanlaya R, Thongboonkerd V. Persistent Escherichia coli infection in renal tubular cells enhances calcium oxalate crystal-cell adhesion by inducing ezrin translocation to apical membranes via Rho/ROCK pathway. Cell Mol Life Sci 2022; 79:381. [PMID: 35751006 PMCID: PMC11072855 DOI: 10.1007/s00018-022-04414-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 05/28/2022] [Accepted: 06/06/2022] [Indexed: 01/18/2023]
Abstract
Recent evidence has suggested that recurrent urinary tract infection (UTI) can cause not only infection stones but also metabolic stones (e.g., those containing calcium oxalate monohydrate or COM). However, precise mechanisms underlying UTI-induced metabolic stones remained unknown. In this study, Escherichia coli, the most common bacterium found in recurrent UTI was used to establish the in vitro model for persistent infection of renal epithelial cells. The promoting effects of persistent E. coli infection on kidney stone formation were validated by COM crystal-cell adhesion assay, followed by immunofluorescence study for changes in surface expression of the known COM crystal receptors. Among the five receptors examined, only ezrin had significantly increased level on the surface of persistently infected cells without change in its total level. Such translocation of ezrin to apical membranes was confirmed by Western blotting of apical membrane and cytosolic fractions and confocal microscopic examination. Additionally, persistent infection increased phosphorylation (Thr567) of ezrin. However, all of these changes induced by persistent E. coli infection were significantly inhibited by small-interfering RNA (siRNA) specific for ezrin or a Rho-associated kinase (ROCK)-specific inhibitor (Y-27632). In summary, this study provides a piece of evidence demonstrating that persistent infection by E. coli, one of the non-urease-producing bacteria, may contribute to COM metabolic stone formation by translocation of ezrin to apical membranes, thereby promoting COM crystal-cell adhesion. Such ezrin translocation was mediated via Rho/ROCK signaling pathway. These findings may, at least in part, explain the pathogenic mechanisms underlying recurrent UTI-induced metabolic kidney stone disease.
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Affiliation(s)
- Rattiyaporn Kanlaya
- Medical Proteomics Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, 6th Floor - SiMR Building, 2 Wanglang Road, Bangkoknoi, Bangkok, 10700, Thailand
| | - Visith Thongboonkerd
- Medical Proteomics Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, 6th Floor - SiMR Building, 2 Wanglang Road, Bangkoknoi, Bangkok, 10700, Thailand.
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5
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Deng Q, Wang Z, Wang J, Zhang J, Zhang Y, Liang H. 16S rRNA gene sequencing reveals altered composition of gut microbiota in postoperative individuals with renal stones. Lett Appl Microbiol 2022; 75:271-280. [PMID: 35306682 PMCID: PMC9544399 DOI: 10.1111/lam.13701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/14/2022] [Accepted: 03/15/2022] [Indexed: 11/28/2022]
Abstract
Renal stones are a common urological disease with high prevalence and recurrence rates. Characterizing gut microbiome profiles of first‐onset renal calculi patients, both before and after surgery, may provide valuable insights and identify potential biomarkers for the disease. In this study, we explored the associations between the gut microbiome and renal stone formation using 16S ribosomal RNA (rRNA) gene sequencing. In brief, 20 patients were recruited, and information on health and eating habits within the previous 1–3 months was collected upon admission. A total of 493 operational taxonomic units (OTUs) were detected in 40 specimens, with an average of 67,888 ± 827 reads per sample. The results of OTU‐based partial least squares discriminant analysis (PLS‐DA) analysis showed differences between RS1 (fecal specimen before surgery) and RS2 (one month later after surgery) groups, with a significantly higher level of OTU7 in the RS2 group. Taxonomy‑based comparisons of the gut microbiome showed differences in the flora composition, with the prevalence of Enterobacteriales, Enterobacteriaceae, Gammaproteobacteria and Escherichia being higher in the RS2 group and the prevalence of Pseudomonadaceae, Pseudomonadales and Pseudomonas being higher in the RS1 group. Correlation analysis showed that an increased prevalence of Enterobacteriaceae, Gammaproteobacteria and Escherichia associated with a decreased level of urea, and a decreased creatinine level was correlated with an increased prevalence of Escherichia. These data strongly suggest that the gut microbiome plays an important role in kidney stone formation, and these findings may provide new insights for the prevention, diagnosis, and treatment of renal stones.
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Affiliation(s)
- Qiong Deng
- Department of Urology Affiliated Longhua People’s Hospital Southern Medical University 518109 Guangdong
- School of Basic Medical Sciences Southern Medical University 510515 Guangdong
| | - Zhu Wang
- Department of Urology Affiliated Longhua People’s Hospital Southern Medical University 518109 Guangdong
| | - Jieyan Wang
- Department of Urology Affiliated Longhua People’s Hospital Southern Medical University 518109 Guangdong
| | - Jianwen Zhang
- Department of Urology Affiliated Longhua People’s Hospital Southern Medical University 518109 Guangdong
| | - Ying Zhang
- Department of Urology Affiliated Longhua People’s Hospital Southern Medical University 518109 Guangdong
| | - Hui Liang
- Department of Urology Affiliated Longhua People’s Hospital Southern Medical University 518109 Guangdong
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6
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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: 11] [Impact Index Per Article: 3.7] [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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7
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Zhong F, Wu W, Chen D, Lai Y, Tiselius HG, Jiang C, Huang J, Duan X, Choong S, Liang Y, Zeng G, Lei M, Wu W. The characteristic and relationship of Escherichia coli isolated from urine and stones in patients with calcium oxalate stones. Urolithiasis 2021; 49:407-414. [PMID: 33454825 DOI: 10.1007/s00240-021-01243-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 01/03/2021] [Indexed: 12/15/2022]
Abstract
Previous clinical studies have shown that Escherichia coli (E. coli) predominated in urine and stone culture from calcium oxalate (CaOx) stone disease. The characteristic and relationship between E. coli isolated from urine cultures (EUC) and stone cultures (ESC) are compared. 83 E. coli (33 EUC and 50 ESC, respectively) from 66 CaOx stone patients were recruited in the study. E. coli in urine and stones from those patients were assessed by antimicrobial susceptibility test, genotyping and phylogenetic grouping. Furthermore, whole genome sequencing and comparative genomic analysis in paired ESC and EUC isolated strains from eight patients were carried out. The E. coli strains from ESC and EUC were not only multidrug resistant (MDR), but also had the similar pattern of resistant genes. The dominant phylogenetic group was B2, which was found in 54.0% of the ESC samples and 69.7% of the EUC samples, respectively. The virulence genes of E. coli, which isolated from stones and urine in the same patients, were highly homologous and largely consistent. Meanwhile, these E. coli strains were located in the same clade originated from a common ancestor. ESC and EUC isolated from patients with CaOx stones had a high prevalence of phylogenetic groups B2. Bacterial strains isolated from urine and stones in the same patient had consistent antimicrobial susceptibility profiles, genotyping, phylogenetic groups, virulence and resistance genes, also with high sequence co-linearity and close relationships.
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Affiliation(s)
- Fangling Zhong
- Department of Urology, Minimally Invasive Surgery Center, Guangdong Key Laboratory of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510230, China
| | - Weizhou Wu
- Department of Urology, Minimally Invasive Surgery Center, Guangdong Key Laboratory of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510230, China
| | - Dong Chen
- Department of Urology, Minimally Invasive Surgery Center, Guangdong Key Laboratory of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510230, China
| | - Yongchang Lai
- Department of Urology, Minimally Invasive Surgery Center, Guangdong Key Laboratory of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510230, China
| | - Hans-Göran Tiselius
- Division of Urology, Department of Science, Intervention and Technology, Karolinska Institute, Stockholm, Sweden
| | - Chonghe Jiang
- Department of Urology, The People's Hospital of Qingyuan City, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan, China
| | - Jinkun Huang
- Department of Urology, Minimally Invasive Surgery Center, Guangdong Key Laboratory of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510230, China
| | - Xiaolu Duan
- Department of Urology, Minimally Invasive Surgery Center, Guangdong Key Laboratory of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510230, China
| | - Simon Choong
- Department of Urology, University College London Hospital, London, UK
| | - Yeping Liang
- Department of Urology, Minimally Invasive Surgery Center, Guangdong Key Laboratory of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510230, China
| | - Guohua Zeng
- Department of Urology, Minimally Invasive Surgery Center, Guangdong Key Laboratory of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510230, China
| | - Ming Lei
- Department of Urology, Minimally Invasive Surgery Center, Guangdong Key Laboratory of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510230, China.
| | - Wenqi Wu
- Department of Urology, Minimally Invasive Surgery Center, Guangdong Key Laboratory of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510230, China.
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8
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Sutthimethakorn S, Thongboonkerd V. Effects of high-dose uric acid on cellular proteome, intracellular ATP, tissue repairing capability and calcium oxalate crystal-binding capability of renal tubular cells: Implications to hyperuricosuria-induced kidney stone disease. Chem Biol Interact 2020; 331:109270. [PMID: 32991862 DOI: 10.1016/j.cbi.2020.109270] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 08/09/2020] [Accepted: 09/25/2020] [Indexed: 12/12/2022]
Abstract
Hyperuricosuria is associated with kidney stone disease, especially uric acid (UA) and calcium oxalate (CaOx) types. Nevertheless, detailed mechanisms of hyperuricosuria-induced kidney stone formation remained unclear. This study examined changes in cellular proteome and function of renal tubular cells after treatment with high-dose UA for 48-h. Quantitative proteomics using 2-DE followed by nanoLC-ESI-ETD MS/MS tandem mass spectrometry revealed significant changes in levels of 22 proteins in the UA-treated cells. These proteomic data could be confirmed by Western blotting. Functional assays revealed an increase in intracellular ATP level and enhancement of tissue repairing capability in the UA-treated cells. Interestingly, levels of HSP70 and HSP90 (the known receptors for CaOx crystals) were increased in apical membranes of the UA-treated cells. CaOx crystal-cell adhesion assay revealed significant increase in CaOx-binding capability of the UA-treated cells, whereas neutralization of the surface HSP70 and/or HSP90 using their specific monoclonal antibodies caused significant reduction in such binding capability. These findings highlighted changes in renal tubular cells in response to high-dose UA that may, at least in part, explain the pathogenic mechanisms of hyperuricosuria-induced mixed kidney stone disease.
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Affiliation(s)
- Suchitra Sutthimethakorn
- Medical Proteomics Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand; Graduate Program in Molecular Medicine, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Visith Thongboonkerd
- Medical Proteomics Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand; Center for Research in Complex Systems Science, Mahidol University, Bangkok, Thailand.
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9
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Al KF, Denstedt JD, Daisley BA, Bjazevic J, Welk BK, Pautler SE, Gloor GB, Reid G, Razvi H, Burton JP. Ureteral Stent Microbiota Is Associated with Patient Comorbidities but Not Antibiotic Exposure. Cell Rep Med 2020; 1:100094. [PMID: 33205072 PMCID: PMC7659606 DOI: 10.1016/j.xcrm.2020.100094] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 05/29/2020] [Accepted: 08/21/2020] [Indexed: 12/13/2022]
Abstract
Ureteral stents are commonly used to prevent urinary obstruction but can become colonized by bacteria and encrusted, leading to clinical complications. Despite recent discovery and characterization of the healthy urinary microbiota, stent-associated bacteria and their impact on encrustation are largely underexplored. We profile the microbiota of patients with typical short-term stents, as well as over 30 atypical cases (all with paired mid-stream urine) from 241 patients. Indwelling time, age, and various patient comorbidities correlate with alterations to the stent microbiota composition, whereas antibiotic exposure, urinary tract infection (UTI), and stent placement method do not. The stent microbiota most likely originates from adhesion of resident urinary microbes but subsequently diverges to a distinct, reproducible population, thereby negating the urine as a biomarker for stent encrustation or microbiota. Urological practice should reconsider standalone prophylactic antibiotics in favor of tailored therapies based on patient comorbidities in efforts to minimize bacterial burden, encrustation, and complications of ureteral stents.
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Affiliation(s)
- Kait F. Al
- Centre for Human Microbiome and Probiotic Research, Lawson Health Research Institute, London, ON, Canada
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON, Canada
| | - John D. Denstedt
- Division of Urology, Department of Surgery, The University of Western Ontario, London, ON, Canada
| | - Brendan A. Daisley
- Centre for Human Microbiome and Probiotic Research, Lawson Health Research Institute, London, ON, Canada
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON, Canada
| | - Jennifer Bjazevic
- Division of Urology, Department of Surgery, The University of Western Ontario, London, ON, Canada
| | - Blayne K. Welk
- Division of Urology, Department of Surgery, The University of Western Ontario, London, ON, Canada
| | - Stephen E. Pautler
- Division of Urology, Department of Surgery, The University of Western Ontario, London, ON, Canada
| | - Gregory B. Gloor
- Department of Biochemistry, The University of Western Ontario, London, ON, Canada
| | - Gregor Reid
- Centre for Human Microbiome and Probiotic Research, Lawson Health Research Institute, London, ON, Canada
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON, Canada
- Division of Urology, Department of Surgery, The University of Western Ontario, London, ON, Canada
| | - Hassan Razvi
- Division of Urology, Department of Surgery, The University of Western Ontario, London, ON, Canada
| | - Jeremy P. Burton
- Centre for Human Microbiome and Probiotic Research, Lawson Health Research Institute, London, ON, Canada
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON, Canada
- Division of Urology, Department of Surgery, The University of Western Ontario, London, ON, Canada
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10
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Aluksanasuwan S, Plumworasawat S, Malaitad T, Chaiyarit S, Thongboonkerd V. High glucose induces phosphorylation and oxidation of mitochondrial proteins in renal tubular cells: A proteomics approach. Sci Rep 2020; 10:5843. [PMID: 32246012 PMCID: PMC7125224 DOI: 10.1038/s41598-020-62665-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 03/18/2020] [Indexed: 12/11/2022] Open
Abstract
Mitochondrial dysfunction has been thought to play roles in the pathogenesis of diabetic nephropathy (DN). However, precise mechanisms underlying mitochondrial dysfunction in DN remained unclear. Herein, mitochondria were isolated from renal tubular cells after exposure to normal glucose (5.5 mM glucose), high glucose (25 mM glucose), or osmotic control (5.5 mM glucose + 19.5 mM mannitol) for 96 h. Comparative proteomic analysis revealed six differentially expressed proteins among groups that were subsequently identified by tandem mass spectrometry (nanoLC-ESI-ETD MS/MS) and confirmed by Western blotting. Several various types of post-translational modifications (PTMs) were identified in all of these identified proteins. Interestingly, phosphorylation and oxidation were most abundant in mitochondrial proteins whose levels were exclusively increased in high glucose condition. The high glucose-induced increases in phosphorylation and oxidation of mitochondrial proteins were successfully confirmed by various assays including MS/MS analyses. Moreover, high glucose also increased levels of phosphorylated ezrin, intracellular ATP and ROS, all of which could be abolished by a p38 MAPK inhibitor (SB239063), implicating a role of p38 MAPK-mediated phosphorylation in high glucose-induced mitochondrial dysfunction. These data indicate that phosphorylation and oxidation of mitochondrial proteins are, at least in part, involved in mitochondrial dysfunction in renal tubular cells during DN.
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Affiliation(s)
- Siripat Aluksanasuwan
- Medical Proteomics Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Sirikanya Plumworasawat
- Medical Proteomics Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Thanyalak Malaitad
- Medical Proteomics Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Sakdithep Chaiyarit
- Medical Proteomics Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Visith Thongboonkerd
- Medical Proteomics Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand.
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11
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Highly effective methods for expression/purification of recombinant human HSP90 and its four distinct (N-LR-M-C) domains. Anal Biochem 2020; 590:113518. [DOI: 10.1016/j.ab.2019.113518] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 11/26/2019] [Accepted: 11/27/2019] [Indexed: 02/06/2023]
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12
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Kanlaya R, Naruepantawart O, Thongboonkerd V. Flagellum Is Responsible for Promoting Effects of Viable Escherichia coli on Calcium Oxalate Crystallization, Crystal Growth, and Crystal Aggregation. Front Microbiol 2019; 10:2507. [PMID: 31749785 PMCID: PMC6848068 DOI: 10.3389/fmicb.2019.02507] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 10/17/2019] [Indexed: 12/30/2022] Open
Abstract
Urease-producing bacteria (especially Proteus mirabilis) can cause infection kidney stone. However, recent studies have shown that intact viable non-urease-producing bacteria such as Escherichia coli might also promote calcium oxalate (CaOx) kidney stone formation but with unclear mechanism. We thus hypothesized that some relevant bacterial components might be responsible for such promoting effects of the intact viable E. coli. Flagella, capsule, lipopolysaccharide (LPS), and outer membrane vesicles (OMVs) were isolated/purified and their stone modulatory activities were evaluated using CaOx crystallization, crystal growth, and crystal aggregation assays. Among these, flagella had the most potent promoting effects on CaOx crystallization, crystal growth, and crystal aggregation. Validation was performed by deflagellation demonstrating that the deflagellated intact viable E. coli had markedly reduced CaOx crystal modulatory activities in all aspects (comparable to those of the negative controls). Similarly, neutralization of the isolated/purified flagella using a specific anti-flagellin antibody, not an isotype control, could abolish the promoting effects of flagella. These findings provide direct evidence indicating that flagellum is responsible for the promoting effects of the viable E. coli on CaOx crystallization, crystal growth and aggregation.
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Affiliation(s)
- Rattiyaporn Kanlaya
- Medical Proteomics Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Orapan Naruepantawart
- Medical Proteomics Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Immunology Graduate Program, Department of Immunology, 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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13
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Johnson G, Stark N, Wolfe AJ, Putonti C. Complete Genome Sequence of a Pseudomonas aeruginosa Isolate from a Kidney Stone. Microbiol Resour Announc 2019; 8:e01073-19. [PMID: 31537684 PMCID: PMC6753288 DOI: 10.1128/mra.01073-19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 09/01/2019] [Indexed: 11/20/2022] Open
Abstract
Recently, we isolated a temperate bacteriophage, Pseudomonas phage Dobby, from a calcium oxalate kidney stone. Here, we present the complete genome of the bacterial host harboring this phage, Pseudomonas aeruginosa UMB2738. From the analysis of the genome sequence, five additional prophage sequences were identified.
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Affiliation(s)
- Genevieve Johnson
- Bioinformatics Program, Loyola University Chicago, Chicago, Illinois, USA
| | - Nicole Stark
- Department of Biology, Loyola University Chicago, Chicago, Illinois, USA
| | - Alan J Wolfe
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, USA
| | - Catherine Putonti
- Bioinformatics Program, Loyola University Chicago, Chicago, Illinois, USA
- Department of Biology, Loyola University Chicago, Chicago, Illinois, USA
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, USA
- Department of Computer Science, Loyola University Chicago, Chicago, Illinois, USA
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14
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Peerapen P, Thongboonkerd V. Protective Cellular Mechanism of Estrogen Against Kidney Stone Formation: A Proteomics Approach and Functional Validation. Proteomics 2019; 19:e1900095. [DOI: 10.1002/pmic.201900095] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 08/02/2019] [Indexed: 12/15/2022]
Affiliation(s)
- Paleerath Peerapen
- Medical Proteomics UnitOffice for Research and DevelopmentFaculty of Medicine Siriraj HospitalMahidol University Bangkok 10700 Thailand
| | - Visith Thongboonkerd
- Medical Proteomics UnitOffice for Research and DevelopmentFaculty of Medicine Siriraj HospitalMahidol University Bangkok 10700 Thailand
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15
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Johnson G, Wolfe AJ, Putonti C. Characterization of the ϕCTX-like Pseudomonas aeruginosa phage Dobby isolated from the kidney stone microbiota. Access Microbiol 2019; 1. [PMID: 32864566 PMCID: PMC7454045 DOI: 10.1099/acmi.0.000002] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Bacteriophages (phages) are vital members of the human microbiota. They are abundant even within low biomass niches of the human body, including the lower urinary tract. While several prior studies have cultured bacteria from kidney stones, this is the first study to explore phages within the kidney stone microbiota. Here we report Dobby, a temperate phage isolated from a strain of Pseudomonas aeruginosa cultured from a kidney stone. Dobby is capable of lysing clinical P. aeruginosa strains within our collection from the urinary tract. Sequencing was performed producing a 37,152 bp genome that closely resembles the temperate P. aeruginosa phage ϕCTX, a member of the P2 phage group. Dobby does not, however, encode for the cytotoxin CTX. Dobby's genome was queried against publicly available bacterial sequences identifying 44 other ϕCTX-like prophages. These prophages are integrated within the genomes of P. aeruginosa strains from a variety of environments, including strains isolated from urine samples and other niches of the human body. Phylogenetic analysis suggests that the temperate ϕCTX phage species is widespread. With the isolation of Dobby, we now have evidence that phages are members of the kidney stone microbiota. Further investigation, however, is needed to determine their abundance and diversity within these communities.
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Affiliation(s)
| | - Alan J Wolfe
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL USA
| | - Catherine Putonti
- Bioinformatics Program, Loyola University Chicago, Chicago, IL USA.,Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL USA.,Department of Biology, Loyola University Chicago, Chicago, IL USA.,Department of Computer Science, Loyola University Chicago, Chicago, IL USA
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16
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Singhto N, Kanlaya R, Nilnumkhum A, Thongboonkerd V. Roles of Macrophage Exosomes in Immune Response to Calcium Oxalate Monohydrate Crystals. Front Immunol 2018. [PMID: 29535716 PMCID: PMC5835051 DOI: 10.3389/fimmu.2018.00316] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
In kidney stone disease, macrophages secrete various mediators via classical secretory pathway and cause renal interstitial inflammation. However, whether their extracellular vesicles, particularly exosomes, are involved in kidney stone pathogenesis remained unknown. This study investigated alterations in exosomal proteome of U937-derived macrophages (by phorbol-12-myristate-13-acetate activation) after exposure to calcium oxalate monohydrate (COM) crystals for 16-h using 2-DE-based proteomics approach. Six significantly altered proteins in COM-treated exosomes were successfully identified by nanoscale liquid chromatography–electrospray ionization–electron transfer dissociation tandem mass spectrometry as proteins involved mainly in immune processes, including T-cell activation and homeostasis, Fcγ receptor-mediated phagocytosis, interferon-γ (IFN-γ) regulation, and cell migration/movement. The decreased heat shock protein 90-beta (HSP90β) and increased vimentin were confirmed by Western blotting. ELISA showed that the COM-treated macrophages produced greater level of interleukin-1β (IL-1β), one of the markers for inflammasome activation. Functional studies demonstrated that COM-treated exosomes enhanced monocyte and T-cell migration, monocyte activation and macrophage phagocytic activity, but on the other hand, reduced T-cell activation. In addition, COM-treated exosomes enhanced production of proinflammatory cytokine IL-8 by monocytes that could be restored to its basal level by small-interfering RNA targeting on vimentin (si-Vimentin). Moreover, si-Vimentin could also abolish effects of COM-treated exosomes on monocyte and T-cell migration as well as macrophage phagocytic activity. These findings provided some implications to the immune response during kidney stone pathogenesis via exosomal pathway of macrophages after exposure to COM crystals.
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Affiliation(s)
- Nilubon Singhto
- Medical Proteomics Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.,Immunology Graduate Program, Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Rattiyaporn Kanlaya
- Medical Proteomics Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.,Center for Research in Complex Systems Science, Mahidol University, Bangkok, Thailand
| | - Angkhana Nilnumkhum
- Medical Proteomics Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.,Center for Research in Complex Systems Science, Mahidol University, Bangkok, Thailand
| | - Visith Thongboonkerd
- Medical Proteomics Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.,Center for Research in Complex Systems Science, Mahidol University, Bangkok, Thailand
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17
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McCutcheon SR, Chiu KL, Lewis DD, Tan C. CRISPR-Cas Expands Dynamic Range of Gene Expression From T7RNAP Promoters. Biotechnol J 2017; 13:e1700167. [DOI: 10.1002/biot.201700167] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 11/02/2017] [Indexed: 01/06/2023]
Affiliation(s)
- Sean R. McCutcheon
- Department of Biomedical Engineering; University of California; Davis CA 95616 USA
| | - Kwan Lun Chiu
- Department of Biomedical Engineering; University of California; Davis CA 95616 USA
| | - Daniel D. Lewis
- Department of Biomedical Engineering; University of California; Davis CA 95616 USA
- Integrative Genetics and Genomics; University of California; Davis CA 95616 USA
| | - Cheemeng Tan
- Department of Biomedical Engineering; University of California; Davis CA 95616 USA
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18
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Amimanan P, Tavichakorntrakool R, Fong-Ngern K, Sribenjalux P, Lulitanond A, Prasongwatana V, Wongkham C, Boonsiri P, Umka Welbat J, Thongboonkerd V. Elongation factor Tu on Escherichia coli isolated from urine of kidney stone patients promotes calcium oxalate crystal growth and aggregation. Sci Rep 2017; 7:2953. [PMID: 28592876 PMCID: PMC5462744 DOI: 10.1038/s41598-017-03213-x] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 04/25/2017] [Indexed: 12/23/2022] Open
Abstract
Escherichia coli is the most common bacterium isolated from urine and stone matrix of calcium oxalate (CaOx) stone formers. Whether it has pathogenic role(s) in kidney stone formation or is only entrapped inside the stone remains unclear. We thus evaluated differences between E. coli isolated from urine of patients with kidney stone (EUK) and that from patients with urinary tract infection (UTI) without stone (EUU). From 100 stone formers and 200 UTI patients, only four pairs of EUK/EUU isolates had identical antimicrobial susceptibility patterns. Proteomic analysis revealed nine common differentially expressed proteins. Among these, the greater level of elongation factor Tu (EF-Tu) in EUK was validated by Western blotting. Outer membrane vesicles (OMVs) derived from EUK had greater promoting activities on CaOx crystallization, crystal growth and aggregation as compared to those derived from EUU. Neutralizing the OMVs of EUK with monoclonal anti-EF-Tu antibody, not with an isotype antibody, significantly reduced all these OMVs-induced promoting effects. Moreover, immunofluorescence staining of EF-Tu on bacterial cell surface confirmed the greater expression of surface EF-Tu on EUK (vs. EUU). Our data indicate that surface EF-Tu and OMVs play significant roles in promoting activities of E. coli on CaOx crystallization, crystal growth and aggregation.
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Affiliation(s)
- Piyawan Amimanan
- Faculty of Graduate School, Khon Kaen University, Khon Kaen, Thailand.,Centre for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
| | - Ratree Tavichakorntrakool
- Centre for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand. .,Department of Clinical Microbiology, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand.
| | - Kedsarin Fong-Ngern
- Medical Proteomics Unit, Office for Research and Development, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Pipat Sribenjalux
- Centre for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand.,Department of Clinical Microbiology, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
| | - Aroonlug Lulitanond
- Centre for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand.,Department of Clinical Microbiology, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
| | - Vitoon Prasongwatana
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Chaisiri Wongkham
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Patcharee Boonsiri
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Jariya Umka Welbat
- Department of Anatomy, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Visith Thongboonkerd
- Medical Proteomics Unit, Office for Research and Development, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand. .,Center for Research in Complex Systems Science, Mahidol University, Bangkok, Thailand.
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19
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Tosukhowong P, Kulpradit P, Chaiyarit S, Ungjareonwattana W, Kalpongnukul N, Ratchanon S, Thongboonkerd V. Lime powder treatment reduces urinary excretion of total protein and transferrin but increases uromodulin excretion in patients with urolithiasis. Urolithiasis 2017; 46:257-264. [DOI: 10.1007/s00240-017-0986-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 05/25/2017] [Indexed: 01/12/2023]
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